Substrate specificity of prostate-specific antigen (PSA)

Background: The serine protease prostate-specific antigen (PSA) is a useful clinical marker for prostatic malignancy. PSA is a member of the kallikrein subgroup of the (chymo)trypsin serine protease family, but differs from the prototypical member of this subgroup, tissue kallikrein, in possessing a specificity more similar to that of chymotrypsin than trypsin. We report the use of two strategies, substrate phage display and iterative optimization of natural cleavage sites, to identify labile sequences for PSA cleavage.Results: Iterative optimization and substrate phage display converged on the amino-acid sequence SS(Y/F)YIS(G/S) as preferred subsite occupancy for PSA. These sequences were cleaved by PSA with catalytic efficiencies as high as 220–3100 M⁻¹ s⁻¹, compared with values of 2–46 M⁻¹ s⁻¹ for peptides containing likely physiological target sequences of PSA from the protein semenogelin. Substrate residues that bind to secondary (non-S1) subsites have a critical role in defining labile substrates and can even cause otherwise disfavored amino acids to bind in the primary specificity (S1) pocket.Conclusions: The importance of secondary subsites in defining both the specificity and efficiency of cleavage suggests that substrate recognition by PSA is mediated by an extended binding site. Elucidation of preferred subsite occupancy allowed refinement of the structural model of PSA and should facilitate the development of more sensitive activity-based assays and the design of potent inhibitors.     

Acarbose Binding Specificity with Oral Bacterial Glucosyltransferase

ABSTRACT

Mutans streptococcus glucosyltransferases are the significant virulent factors in causing dental caries. The binding specificity of acarbose was probed with glucosyl and fructosyl sub-site binding ligands using multiple inhibition kinetics. The results indicate that acarbose and a glucosyl subsite binding ligand (1-deoxynojirimycin) are mutually or partially exclusive. On the other hand, acarbose with a fructosyl subsite ligand (fructose) might induce a conformational change leading to enhanced binding at the adjacent subsite.     

Bifunctional inhibitors of the trypsin-like activity of eukaryotic proteasomes

BACKGROUND: The 20S proteasome is a multicatalytic protease complex that exhibits trypsin-like, chymotrypsin-like and post-glutamyl-peptide hydrolytic activities associated with the active sites of the beta2, beta5 and beta1 subunits, respectively. Modulation of these activities using inhibitors is essential for a better understanding of the proteasome's mechanism of action. Although there are highly selective inhibitors of the proteasome's chymotryptic activity, inhibitors of similar specificity have not yet been identified for the other activities. RESULTS: The X-ray structure of the yeast proteasome reveals that the sidechain of Cys118 of the beta3 subunit protrudes into the S3 subsite of the beta2 active site. The location of this residue was exploited for the rational design of bidentated inhibitors containing a maleinimide moiety at the P3 position for covalent linkage to the thiol group and a carboxy-terminal aldehyde group for hemiacetal formation with the Thr1 hydroxyl group of the active site. Structure-based modelling was used to determine the optimal spacing of the maleinimide group from the P2-P1 dipeptide aldehydes and the specificity of the S1 subsite was exploited to limit the inhibitory activity to the beta2 active site. X-ray crystallographic analysis of a yeast proteasome-inhibitor adduct confirmed the expected irreversible binding of the inhibitor to the P3 subsite. CONCLUSIONS: Maleoyl-beta-alanyl-valyl-arginal is a new type of inhibitor that is highly selective for the trypsin-like activity of eukaryotic proteasomes. Despite the reactivity of the maleinimide group towards thiols, and therefore the limited use of this inhibitor for in vitro studies, it might represent an interesting new biochemical tool.     

Fluorescence-quenched solid phase combinatorial libraries in the characterization of cysteine protease substrate specificity

To map the substrate specificity of cysteine proteases, two combinatorial peptide libraries were synthesized and screened using the archetypal protease, papain. The use of PEGA resin as the solid support for library synthesis facilitated the application of an on-resin fluorescence-quenched assay. Results from the screening of library 2 indicated a preference for Pro or Val in the S3 subsite and hydrophobic residues in S2; the most prevalent residue not being Phe but Val. The S1 subsite exhibited a dual specificity for both small, nonpolar residues, Ala or Gly, as well as larger, Gln, and charged residues, Arg. Small residues predominated in the S1'-S4' subsites. Active peptides from the libraries and variations thereof were resynthesized and their kinetics of hydrolysis by papain assessed in solution phase assays. Generally, there was a good correlation between the extent of substrate cleavage on solid phase and the kcat/KM's obtained in solution phase assays. Several good substrates for papain were obtained, the best substrates being Y(NO2)PMPPLCTSMK(Abz) (kcat/KM = 2109 (mM s)-1), Y(NO2)PYAVQSPQK(Abz) (kcat/KM = 1524 (mM s)-1), and Y(NO2)PVLRQQRSK(Abz) (kcat/KM = 1450 (mM s)-1). These results were interpreted in structural terms by the use of molecular dynamics (MD). These MD calculations indicated two different modes for the binding of substrates in the narrow enzyme cleft.     

Importance of extended protease substrate recognition motifs in steering BNIP-2 cleavage by human and mouse granzymes B

Background

Previous screening of the substrate repertoires and substrate specificity profiles of granzymes resulted in long substrate lists highly likely containing bystander substrates. Here, a recently developed degradomics technology that allows distinguishing efficiently from less efficiently cleaved substrates was applied to study the degradome of mouse granzyme B (mGrB).

Results

In vitro kinetic degradome analysis resulted in the identification of 37 mGrB cleavage events, 9 of which could be assigned as efficiently targeted ones. Previously, cleavage at the IEAD₇₅ tetrapeptide motif of Bid was shown to be efficiently and exclusively targeted by human granzyme B (hGrB) and thus not by mGrB. Strikingly, and despite holding an identical P4-P1 human Bid (hBid) cleavage motif, mGrB was shown to efficiently cleave the BCL2/adenovirus E1B 19 kDa protein-interacting protein 2 or BNIP-2 at IEAD₂₈. Like Bid, BNIP-2 represents a pro-apoptotic Bcl-2 protein family member and a potential regulator of GrB induced cell death. Next, in vitro analyses demonstrated the increased efficiency of human and mouse BNIP-2 cleavage by mGrB as compared to hGrB indicative for differing Bid/BNIP-2 substrate traits beyond the P4-P1 IEAD cleavage motif influencing cleavage efficiency. Murinisation of differential primed site residues in hBNIP-2 revealed that, although all contributing, a single mutation at the P3′ position was found to significantly increase the mGrB/hGrB cleavage ratio, whereas mutating the P1′ position from I₂₉?>?T yielded a 4-fold increase in mGrB cleavage efficiency. Finally, mutagenesis analyses revealed the composite BNIP-2 precursor patterns to be the result of alternative translation initiation at near-cognate start sites within the 5′ leader sequence (5′UTR) of BNIP-2.

Conclusions

Despite their high sequence similarity, and previously explained by their distinct tetrapeptide specificities observed, the substrate repertoires of mouse and human granzymes B only partially overlap. Here, we show that the substrate sequence context beyond the P4-P1 positions can influence orthologous granzyme B cleavage efficiencies to an unmatched extent. More specifically, in BNIP-2, the identical and hGrB optimal IEAD tetrapeptide substrate motif is targeted highly efficiently by mGrB, while this tetrapeptide motif is refractory towards mGrB cleavage in Bid.

     

Potential protease inhibitors based on a functionalized cyclic sulfamide scaffold

Exploratory studies related to the design and synthesis of functionalized cyclic sulfamides (I) as potential inhibitors of proteolytic enzymes were carried out. The structural motif and three diversity sites embodied in the scaffold render it amenable to combinatorial parallel synthesis and the facile generation of lead discovery prospecting libraries. The scaffold was readily assembled starting with (DL) serine methyl ester, and a series of compounds was generated and screened against human leukocyte elastase. Modification of the P(1) recognition element, believed to be accommodated at the primary specificity site (S(1) subsite) of the enzyme, yielded compounds that inhibited the enzyme by an apparent hyperbolic partial mixed-type inhibition.     

钾(Ⅰ)(苯并－15－冠－5)新型配合物的合成及性质

在非水溶剂中合成并－１５－冠－５与碘化钾,硫氰化钾及苦味酸钾形成的三种新型固体配合物,并进行了有关物理,化学性质表征,结果表明,钾（Ⅰ）离子不仅易苯并－１５－冠－５天成常见的１：２夹心式配合物,而且还能生成稳定的１：１型固体配合物。     

Mapping of the active site of proteases in the 1960s and rational design of inhibitors/drugs in the 1990s

For several decades the specificity of proteases has been presented as an active site divided into subsites, using the nomenclature of Schechter & Berger from 1967 (S1, S2... for subsites of the active site; P1, P2... for residues of the substrate occupying the corresponding subsites). At early stages of the research (1960s) it was realized that the size of the active site was larger than expected and important interactions occur in regions remote from the catalytic site. Since the active site was found to be large it was divided into subsites, and a procedure to map it up was developed. The map provides information on the size of the active site (number of subsites), the properties of each subsite (free energy of ligand binding, nature of binding forces, etc.), and it enables rational design of new substrates and inhibitors. Already in 1968 inhibitors with binding constants ten thousand fold higher than available inhibitors, were prepared. The model of a large active site was initially met with strong opposition. Before long, however, predictions of the model (size of the active site, interactions in subsites remote from the catalytic site) were confirmed by X-ray crystallography (1970). During the 1990s proteolytic enzymes received renewed attention in biology and medicine, they became therapeutic targets, and protease inhibitors were successfully applied in the treatment of AIDS and hypertension. The model of large active site divided into subsites, proposed 38 years ago, stood the test of time. This model is still in use in basic research to evaluate enzyme activity, and in pharmaceutical research for the development of inhibitors/drugs.     

Combinatorial Peptide Library for Probing the Selectivity of the s-1 Subsite of Proteases

A combinatorial tetrapeptide library, Suc-Ala-Phe-Arg-AA₁-OR, in which R = p-formamidobenzyl ester and AA₁ = 17 of the 20 natural occurring amino acids, has been synthesized chemically and separated by a reverse phase HPLC. The library was used to study the s-1 subsite specificity of various proteases. The preferred substrate at the s-1 subsite of chymotrypsin is in the order of Trp > Tyr > Phe > Met > Leu. This agreed with the reported data that the favored substrate at the s-1 subsite for chymotrypsin-catalyzed hydrolysis is an aromatic amino acid residue. The hydrophobic amino acid residues at this subsite can be hydrolysized after a longer incubating time. This procedure of selective hydrolysis of a peptide library was used to probe the selectivity of s-1 subsites of four proteases isolated from Bacillus stearothermophilus, subtilisin Carlsberg, subtilisin BPN' and an engineered protease subtilisin 8397. The protease from Bacillus stearothermophilus favored the substrate with residue Lys, and Arg at the s-1 subsite as a trypsin-like protease. The relative reactivities of amino acid residues in the protease-catalyzed hydrolysis of the library can be used as a fingerprint to identify the protease in a protease family.     

Correlation Study on Sweetness of Amino Acid with Different Configurations and Quantum Chemical Parameters

1 INTRODUCTION Since the introduction of QSAR by Hansch and Fujita in 1964, Deutsch and Hansch have quickly used it in the study of nitrophenylamine sweet reagents. They found good correlation between their distribution coefficients in octanol/water system and sweetness degree. Subsequently, they detected that vibration of aroma-substituent compounds has so- mething to do with sweetness. Henceforth, statistic correlations between structure and sweetness ofseries compounds have been inv…     

The effect of atomic substitution on electron-phonon interactions in negatively charged B, N-substituted acenes

Electron-phonon interactions in the monoanions of B, N-substituted acenes such as B(3)N(3)F(6) (1f) and B(5)N(5)F(8) (2f) are studied, and compared with those in the monoanions of B(3)N(3)H(6) (1h) and B(5)N(5)H(8) (2h), and B(3)N(3)D(6) (1d) and B(5)N(5)D(8) (2d). The low frequency modes around 500 cm(-1) as well as the frequency modes higher than 1000 cm(-1) strongly couple to the lowest unoccupied molecular orbitals (LUMO) in 1f and 2f. The total electron-phonon coupling constants (l(LUMO)) are estimated to be 2.710 and 2.054 eV for 1f and 2f, respectively, and those are estimated to be 0.342 and 0.235 eV for 1d and 2d, respectively, while those were estimated to be 0.340 and 0.237 eV for 1h and 2h, respectively. That is, the l(LUMO) value increases much more significantly by H-F substitution than by H-D substitution in B, N-substituted acenes. The larger displacements of B and N atoms in the vibronic active modes in 1f and 2f than those in 1d and 2d due to larger atomic mass of fluorine than that of deuterium, and the phase patterns difference between the LUMO in 1f and 2f, in which the atomic orbitals between N and its neighboring F atoms form strong sigma-antibonding interactions, and that in 1d and 2d, in which the atomic orbitals between two neighboring B and N atoms form weak pi-bonding and pi-antibonding interactions, are the main reason why the l(LUMO) value increases much more significantly by H-F substitution than by H-D substitution. The reorganization energies between the neutral molecules and the corresponding monoanions are estimated to be 0.122, 0.063, 0.733, and 0.830 eV for 1h, 2h, 1f, and 2f, respectively. Therefore, the estimated reorganization energies between the neutral molecules and the corresponding monoanions for 1f and 2f are much larger than those for 1h and 2h.     

Noninvasive Early Diagnosis of Allograft Rejection by a Granzyme B Protease Responsive NIR-II Bioimaging Nanosensor

Early diagnosis of allograft rejection helps to improve the immune-related management of transplant recipients. The clinically-used core needle biopsy method is invasive and subject to sampling error. In vivo fluorescence imaging for monitoring immune-related processes has the advantages of non-invasiveness, fast feedback and high sensitivity. Herein, we report a responsive second near-infrared (NIR-II) fluorescent nanosensor (ErGZ) to detect early allograft rejection. ErGZ allows ratiometric in vivo fluorescence sensing of granzyme B, which is overexpressed in recipients’ T cells during the onset of rejection. The sensor demonstrates efficacious detection of allograft rejection with high sensitivity and specificity, which accomplishes non-invasive diagnosis of rejection in skin and deep buried islets transplant mice models 2 d and 5 d earlier than biopsy, by in vivo fluorescence imaging and urinary detection, respectively, providing a valuable approach for therapeutical management.     

Peptide microarrays for the determination of protease substrate specificity

A method is described for the preparation of substrate microarrays that allow for the rapid determination of protease substrate specificity. Peptidyl coumarin substrates, synthesized on solid support using standard techniques, are printed onto glass slides using DNA microarraying equipment. The linkage from the peptide to the slide is formed through a chemoselective reaction, resulting in an array of uniformly displayed fluorogenic substrates. The arrays can be treated with proteases to yield substrate specificity profiles. Standard instrumentation for visualization of microarrays can be used to obtain comparisons of the specificity constants for all of the prepared substrates. The utility of these arrays is demonstrated by the selective cleavage of preferred substrates with trypsin, thrombin, and granzyme B, and by assessing the extended substrate specificity of thrombin using a microarray of 361 different peptidyl coumarin substrates.     

MM-PBSA free energy analysis of endo-1,4-xylanase II (XynII)-substrate complexes: binding of the reactive sugar in a skew boat and chair conformation

The binding of xylotetraose in different conformations to the active site of endo-1,4-beta-xylanase II (XynII) from Trichoderma reesei was studied using molecular dynamics (MD) simulations and free energy analyses employing the MM-PBSA (Molecular Mechanics-Poisson-Boltzmann Surface Area) method. MD simulations of 1 ns were done for the substrate xylotetraose having the reactive sugar, which is bound in the -1 subsite of XynII in the 4C1 (chair) and 2So (skew boat) ground state conformations, and for the transition state of the XynII catalysed hydrolysis of the beta-glycosidic linkage. According to the simulations and free energy analysis, XynII binds the substrate with the -1 sugar in the 2So conformation 59.8 kJ mol(-1) tighter than the substrate with the sugar in the 4C1 conformation. The reactive 2So conformation resembles closely the reaction transition state and has the breaking glycosidic bond in a pseudo-axial orientation ready for facile bond cleavage. The transition state was calculated to be bound 77.1 kJ mol(-1) tighter than the 4C1 ground state conformation. The molecular mechanical interaction energy between the enzyme and the reactive pyranoside unit at the -1 subsite was 75.7 kJ mol(-1) more favorable for the binding of the 2So conformation than the 2C1 conformation, explaining the clearly tighter binding of the reactive structure The results of this study indicate that in the Michaelis complex XynII, a member of the family 11 xylanase, the substrate is bound in a skew boat conformation and in the catalytic reaction, the -1 sugar proceeds from the 4C1 conformation through 2So to the transition state with the -1 sugar in the 2,5B conformation.     

Vertebrate collagenase inhibitor. II. Tetrapeptidyl hydroxamic acids.

To develop a potent and specific collagenase inhibitor, a series of tetrapeptidyl hydroxamic acids were synthesized, based on the previous findings with tripeptidyl derivatives (Chem. Pharm. Bull., 38, 1007-1011, 1990). Among the series of tetrapeptidyl derivatives synthesized, R-Gly-Pro-Leu-Ala-NHOH and R-Gly-Pro-D-Leu-D-Ala-NHOH were found to be highly specific and potent inhibitors against vertebrate collagenase with an IC50 of 10(-6) M order, where R stands for Boc or acyl group. Analysis of their structure-activity relationships showed a characteristic feature of the substrate-binding site of collagenase as follows: 1) the S1 subsite forms a shallow hydrophobic pocket, although glycine residue corresponds to the subsite of the natural collagen substrate: 2) the S2 subsite constitutes a bulky pocket with less requirement for hydrophobicity: 3) the S3 subsite preferentially accommodates Pro residue: and 4) the accommodation of the P4-P1 subsites of peptidyl collagenase inhibitor to the S4-S1 subsites is required to form a tight binding of its hydroxamic acid moiety to the zinc ion at the catalytic site of the enzyme. The introduction of an enantiometric dipeptide unit, D-Leu-D-Ala, to the P2-P1 subsites demonstrated an increased binding capacity to the extended S4-S1 subsites of collagenase, thus providing proteinase-resistant inhibitor.     

Structural basis for selective inhibition of Src family kinases by PP1.

BACKGROUND: Small-molecule inhibitors that can target individual kinases are powerful tools for use in signal transduction research. It is difficult to find such compounds because of the enormous number of protein kinases and the highly conserved nature of their catalytic domains. Recently, a novel, potent, Src family selective tyrosine kinase inhibitor was reported (PP1). Here, we study the structural basis for this inhibitor's specificity for Src family kinases. RESULTS: A single residue corresponding to Ile338 (v-Src numbering; Thr338 in c-Src) in Src family tyrosine kinases largely controls PP1's ability to inhibit protein kinases. Mutation of Ile338 to a larger residue such as methionine or phenylalanine in v-Src makes this inhibitor less potent. Conversely, mutation of Ile338 to alanine or glycine increases PP1's potency. PP1 can inhibit Ser/Thr kinases if the residue corresponding to Ile338 in v-Src is mutated to glycine. We have accurately predicted several non-Src family kinases that are moderately (IC(50) approximately 1 microM) inhibited by PP1, including c-Abl and the MAP kinase p38. CONCLUSIONS: Our mutagenesis studies of the ATP-binding site in both tyrosine kinases and Ser/Thr kinases explain why PP1 is a specific inhibitor of Src family tyrosine kinases. Determination of the structural basis of inhibitor specificity will aid in the design of more potent and more selective protein kinase inhibitors. The ability to desensitize a particular kinase to PP1 inhibition of residue 338 or conversely to sensitize a kinase to PP1 inhibition by mutation should provide a useful basis for chemical genetic studies of kinase signal transduction.     

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.     

High-level ab initio versus DFT calculations on (H2O2)2 and H2O2–H2O complexes as prototypes of multiple hydrogen bond systems

The performance of B-LYP, B-P86, B3-LYP, B3-P86, and B3-PW91 density functionals to describe multiple hydrogen bond systems was studied. For this purpose we have chosen the dimers of hydrogen peroxide and the hydrogen peroxide–water complexes. The geometries and vibrational frequencies obtained with a 6-311+G(d,p) basis set were compared with those obtained at the MP2 level using the same basis set expansion. The corresponding dimerization energies were obtained using a 6-311+G(3df,2p) basis set and compared with those obtained using the G2(MP2) theory. Red shiftings of the OH donor stretching frequencies were predicted by all approaches investigated; however, in all cases, the DFT values were sizably larger than the MP2 ones. Similarly, the blue shifting of the torsion of the hydrogen peroxide subunit was larger when evaluated at the DFT level. All functionals reproduced the G2(MP2) relative stabilities of the different local minima quite well. With the exception of the B-LYP and B3-PW91 approaches, all functionals yielded binding energies which deviated from the G2(MP2) values by less than 0.5 kcal/mol, provided that G2-type basis sets were used and that the corresponding BSSE corrections were included. © 1997 John Wiley & Sons, Inc. J Comput Chem 18: 1124–1135     

Direct analysis of the major human seminal prostaglandins by thermospray high-performance liquid chromatography-mass spectrometry

Thermospray high-performance liquid chromatography-mass spectrometry (HPLC-MS) can be a powerful tool for characterizing eicosanoids in complex biological samples. The positive ion spectra obtained from primary prostaglandins such as PGE1 PGE2, 19-OHPGE1, 19-OHPGE2, PGF2 alpha, PGD2, 6-keto-PGF1 alpha and from leukotriene B4 are very simple, with base peaks corresponding to ions arising from the loss of H2O from the (M + H)+ and (M + NH4)+ ions, except for PGB2 and PGF2, where the latter two ions predominate. The application of this technique to the concurrent determination of the E1 and E2 prostaglandins and their 19-hydroxylated derivatives in human semen is described. The technique affords a moderate level of sensitivity (5-20 ng on-column) and excellent specificity so that virtually no sample manipulation is required other than dilution in acetone and centrifugation. The clear supernatant is injected directly into the HPLC-MS system. A similar analysis by either gas chromatography (GC) or GC-MS would need multi-step derivatization, thus increasing the sample manipulation required and the total analysis time.