Protease inhibitors: a panacea?

With the increasing evidence of protease involvement in several diseases, novel strategies for drug development involve the use of protease inhibitors (PIs). The local balance between protease inhibitors and proteases is an important determinant of the occurrence and progression of a particular disease. Hence, enzymes and their cognate inhibitors are finding their applications as diagnostic and prognostic markers. PIs are widely implicated for their use in host defense against infection, tissue repair and matrix production, blood coagulation, cancer, and they are, therefore, the current focus as therapeutic alternatives for major diseases such as AIDS and Alzheimer's diseases. This review is a brief summary of the varied role of protein protease inhibitors in controlling the activity of aberrant enzymes in several diseases afflicting mankind today.

Identification and characterization of functional intermediates of stem bromelain during urea and guanidine hydrochloride unfolding.

By comparing changes in enzyme activity with changes in spectral features for stem bromelain (EC.3.4.22.32) in the absence and presence of urea, Guanidine hydrochloride and ethanol; four intermediate states could be identified: two activity-enhanced state obtained in the presence of 5 M urea and 2 M GnHCl, termed X and X', respectively, and a third, similarly active state closely resembling the native protein in the presence of 8-9 M urea, termed Y. The enhanced activity of these states is due to local conformational changes accompanied by increased dynamics in the active site. Further, the enzyme does not lose its activity after substantial tertiary structure changes in 8-9 M urea (Y state), suggesting that active site containing domain is more resistant to chemical denaturation than the other structural domain. This makes stem bromelain and in general cysteine proteases an exception to the hypothesis that active site is the most labile part of enzyme.

Biochemical characterization, stability studies and N-terminal sequence of a bi-functional inhibitor from Phaseolus aureus Roxb. (Mung bean).

Herein, we report the purification and biochemical characterization of a novel bi-functional protein proteinase/amylase inhibitor from the dietary leguminous pulse Phaseolus aureus Roxb. (Vigna radiata L.) by means of acetic acid precipitation, salt fractionation, ion-exchange chromatography (DEAE-cellulose) and affinity chromatography on trypsin-sepharose column. P. aureus inhibitor is a bi-functional inhibitor since it exhibits inhibitory activity towards trypsin-like and alpha-chymotrypsin-like serine proteinases as well as against alpha-amylases. It is a helix-rich protein (Mr 13,600) containing approximately eight tyrosines, one tryptophan and two cystines. N-terminal sequence alignment reveals no homology to other proteinase inhibitors reported from Phaseolus sp. thereby confirming that it is a novel inhibitor. Inhibitory activity measurements show that the inhibitor is quite stable even at extremely high temperatures and is only slightly affected by pH changes. Circular dichroism (CD) conformational studies revealed some changes in its near- as well as far-ultraviolet spectrum at extremes of pH and temperature. Treatments with trypsin for varying time periods did not alter its proteolytic inhibitory activity but caused some reduction in its amylase inhibitory activity.

Effect of detergents and hexafluoroisopropanol on the conformation of a non-helical and a helical plant protease inhibitor.

We have earlier reported the purification of a non-helical proteinase inhibitor from Cajanus cajan and a helical proteinase/amylase inhibitor from Phaseolus aureus. The effect of detergents, viz. sodium dodecyl sulfate (SDS), sodium deoxycholate (DOC) and 3-[(3-cholamidopropy) dimethylammonio]-1-propane sulfonate (CHAPS) and hexafluoroisopropanol on the conformation of these proteinaceous inhibitors was investigated using circular dichroism spectroscopy. The present report focuses on changes in the polypeptide backbone conformation with respect to induction of helical structure. SDS causes minimal changes in the tertiary as well as secondary structure of C. cajan proteinase inhibitor. In the presence of anionic bile salt, deoxycholate, minor changes in the far-UV CD spectrum were accompanied by loss in inhibitory activity while CHAPS did not affect the inhibitor function. As judged from the changes in circular dichroic curves ([Theta](MRW) at 208 and 222 nm), the primarily disorganized polypeptide chain of C. cajan proteinase inhibitor was converted by 3,3,3,3',3',3'-hexafluoro-2-propanol (HFIP) into helical conformation. The P. aureus inhibitor showed increased helicity in the presence of SDS ([Theta](MRW) at 208 nm) as well as sodium deoxycholate and CHAPS ([Theta](MRW) at 222 nm). Fluorescence measurements show slight alterations in the emission intensities. HFIP caused a cooperative increase in alpha-helical secondary structure in the P. aureus inhibitor.

Guanidine hydrochloride denaturation of human serum albumin originates by local unfolding of some stable loops in domain III.

The effect of guanidine hydrochloride (GnHCl) on the global stability of human serum albumin (HSA) has been studied by fluorescence and circular dichroism spectroscopic measurements. The differential stability of native conformation of three HSA domains were explored by using domain-specific ligands, hemin (domain I), chloroform (domain II), bilirubin (at domain I/domain II interface) and diazepam (domain III). GnHCl induced unfolding transition curves as monitored by probes for secondary and tertiary structures were cooperative but noncoincidental. A strong ANS binding to the protein was observed around 1.8 M GnHCl, suggesting existence of intermediate states in the unfolding pathway of HSA. A gradual decrease (in the GnHCl concentration range 0.0-1.8 M) in the binding of diazepam indicates that domain III is the most labile to GnHCl denaturation. A significant increase in the binding of bilirubin up to 1.4 M GnHCl and decrease thereafter leading to complete abolishment of bilirubin binding at around 2.0 M GnHCl suggest favorable rearrangement and separation of domains I and II at 1.4 and 2.0 M GnHCl concentration, respectively. Above 1.6 M GnHCl, decrease of the binding of hemin, a ligand for domain I, chloroform, which binds in domain II and lone tryptophanyl fluorescence (Trp-214 located in domain II) indicate that at higher concentration of GnHCl domains I and II start unfolding simultaneously but the stability of domain I (7.4 Kcal/mol) is much more than domain II (4.3 Kcal/mol). A pictorial model for the unfolding of HSA domains, consistent with all these results, has been formulated, suggesting that domain III is the most labile followed by domain II while domain I is the most stable. A molten globule like state of domain III around 1.8 M GnHCl has also been identified and characterized.

Spectroscopic analysis of thermal denaturation of Cajanus cajan proteinase inhibitor at neutral and acidic pH by circular dichroism.

The conformational changes accompanying thermal denaturation under neutral, acidic and reducing conditions of Cajanus cajan proteinase inhibitor were investigated using near- and far-ultraviolet circular dichroism (CD) spectroscopy. The protein inhibitor shows a reversible N<-->D transition at neutral pH with a Tm approximately equal to 63 degrees C. The negative CD band intensities at 200 nm (far-UV) and near about 280 nm (near-UV) decrease as a result of thermal stress. The effect is more pronounced at low pH and in the presence of dithiothreitol. Only partial reversibility is observed under acidic conditions. Significant changes in the near- as well as far-ultraviolet CD spectrum are observed in the presence of dithiothreitol suggestive of the importance of disulfide linkages in maintaining the structure of C. cajan proteinase inhibitor.

Influence of salts and alcohols on the conformation of partially folded intermediate of stem bromelain at low pH.

The effect of salts and alcohols was examined on the partially folded intermediate (PFI) state of stem bromelain reported at low pH (Haq, Rasheedi, and Khan (2002) European Journal of Biochemistry 269, 47-52) by a combination of optical methods like circular dichroism, intrinsic fluorescence and ANS binding. ESI mass spectrometry was also performed to see the effect, if any, on the overall tertiary structure of the protein. Increase in ionic strength by the addition of salts resulted in folded structures somewhat different from the native enzyme. Salt-induced intermediates are characterized by increase in helical content and a significantly reduced exposure of hydrophobic clusters relative to the state at pH 2.0. The emission wavelength maximum of intrinsic fluorescence was shifted towards that of native enzyme. ESI-MS data show decreased accessibility of ionizable/protonation sites suggestive of a folded structure. On the other hand, alcohol-induced intermediates though exhibiting increased helical content are apparently largely unfolded as observed by ESI. Thermal denaturation of a representative intermediate, each from the group of salts and alcohols examined, was also performed to check their relative stabilities. While the alcohol-induced state showed a cooperative thermal transition, the salt-induced state shows non-cooperative thermal denaturation.

Protein proteinase inhibitor genes in combat against insects, pests, and pathogens: natural and engineered phytoprotection.

The continual need to increase food production necessitates the development and application of novel biotechnologies to enable the provision of improved crop varieties in a timely and cost-effective way. A milestone in this field was the introduction of Bacillus thuringiensis (Bt) entomotoxic proteins into plants. Despite the success of this technology, there is need for development of alternative strategies of phytoprotection. Biotechnology offers sustainable solutions to the problem of pests, pathogens, and plant parasitic nematodes in the form of other insecticidal protein genes. A variety of genes, besides (Bt) toxins that are now available for genetic engineering for pest resistance are genes for vegetative insecticidal proteins, proteinase inhibitors, alpha-amylase inhibitors, and plant lectins. This review presents a comprehensive summary of research efforts that focus on the potential use and advantages of using proteinase inhibitor genes to engineer insect- and pest-resistance. Crop protection by means of PI genes is an important component of Integrated Pest Management programmes.

Intermediate formation at lower urea concentration in 'B' isomer of human serum albumin: a case study using domain specific ligands.

The urea-induced unfolding of 'N' isomer (occurring at pH 7.0) and 'B' isomer (occurring at pH 9.0) of human serum albumin was studied by fluorescence and circular dichroism spectroscopic measurements. Urea-induced destabilization in different domains of both the isomers was monitored by using domain specific ligands, hemin (domain-I), chloroform, bilirubin (domain-II), and diazepam (domain-III). Urea-induced denaturation of N and B isomers of HSA showed a two-step, three-state transition with accumulation of intermediates around 4.8-5.2M and 3.0-3.4M urea concentrations, respectively. During first transition (0-4.8M urea for N isomer and 0-3.0M urea for B isomer) a continuous decrease in diazepam binding suggested major conformational changes in domain-III prior to intermediate formation. On the other hand, binding of hemin, a ligand for domain-IB and chloroform, whose binding site is located in domain-IIA remains unchanged up to 5.0M urea for N isomer and 3.0M urea for B isomer. Similarly, fluorescence intensity of Trp-214 that resides in domain-IIA remained unchanged up to the above-said urea concentrations and decreased thereafter. Absence of any decrease in hemin binding, chloroform binding, and Trp-214 fluorescence suggested the non-involvement of domain-IB and domain-IIA in intermediate formation. A significant increase in bilirubin binding prior to intermediate formation showed favorable conformational rearrangement in bilirubin binding cavity formed by loop 4 of domain-IB and loop 3 of domain-IIA. Further, a nearly complete abolishment of bilirubin binding to both isomers around 7.0M and 6.0M urea concentrations, respectively, indicated complete separation of domain-I from domain-II from each other. From these observations it can be concluded that N to B transition of human serum albumin shifted the intermediate formation towards lower urea concentration (3.0-3.4M urea for B isomer as against 4.8-5.2M urea for N isomer). Further both the intermediates were found to possess similar alpha-helical (approximately 39%) content and ligand binding properties.

Effect of pH, temperature and alcohols on the stability of glycosylated and deglycosylated stem bromelain.

The biological significance of the carbohydrate moiety of a glycoprotein has been a matter of much speculation. In the present work, we have chosen stem bromelain from Ananas comosus as a model to investigate the role of glycosylation of proteins. Stem bromelain is a thiol protease which contains a single hetero-oligosaccharide unit per molecule. Here, the deglycosylated form of the enzyme was obtained by periodate oxidation. The differences in the glycosylated and deglycosylated forms of the glycoprotein have been studied at various temperatures and pH values, using probes such as loss of enzyme activity and by the changes in fluorescence and circular dichroism spectra. Deglycosylated bromelain showed decreased enzyme activity and perturbed fluorescence and circular dichroism spectra. In addition to this, a comparative study of their activities in different organic solvents showed a marked decrease in case of deglycosylated form of the enzyme. It is thus concluded that glycosylation contributes towards the functional stability of glycoenzymes.

Guanidine hydrochloride denaturation of glycosylated and deglycosylated stem bromelain.

Glycosylation is one of the major naturally occurring covalent modifications of proteins. We have used stem bromelain, a thiol protease with a single, N-glycosylated polypeptide chain as a model to investigate the role of glycosylation of proteins. Periodate oxidation was used to obtain the deglycosylated form of the enzyme. Denaturation studies in the presence of guanidine hydrochloride (Gn*HCl) were performed using fluorescence and circular dichroism spectroscopy. The glycosylated stem bromelain was found to be stabilized by 1.9 kcal/mol as compared to the deglycosylated one. At a given concentration of denaturant, the fraction of denatured protein was higher in the case of deglycosylated stem bromelain. In short, deglycosylated bromelain showed more susceptibility towards guanidine hydrochloride denaturation, indicating the contribution of the carbohydrate part of the glycoprotein to the stability of the enzyme.

Characterization of molten globule state of fetuin at low pH.

Effect of pH over a range of 0.8-10 on bovine serum fetuin (BSF) was observed by far and near-UV circular dichroism (CD) spectroscopy, intrinsic tryptophan fluorescence and ANS fluorescence measurements. It has been reported earlier by our group that a molten globule (MG) state exists in alpha-chymotrypsinogen [Biochim. Biophys Acta 1481 (2000) 229] and stem bromelain [Eur. J. Biochem. 269 (2002) 47] at low pH. In this paper we have shown the presence of an MG form of fetuin at low pH. The far-UV CD spectra showed the regain of secondary structure at pH 1.8 as compared to the complete loss of secondary structure in presence of 6 M GnHCl. Near-UV CD spectra showed disruption of tertiary structure at pH 1.8. Tryptophan fluorescence studies indicated that there is only a slight red shift in the wavelength emission maxima (lambdamax) of fetuin at low pH as compared to a significantly red-shifted spectrum of the completely unfolded state in 6 M GnHCl, indicating that the tryptophan environment of fetuin at low pH resembles more the native form. ANS binding experiments also showed an enhancement in ANS binding with decrease in pH up to 1.8. ANS binding was absent at pH 7 and in the presence of 6 M GnHCl. Fluorescence quenching experiments were also performed with acrylamide, cesium chloride and potassium iodide. The quenching of tryptophan fluorescence by the three different quenchers indicates that low pH induces a conformational change in protein, making the tryptophan residue less accessible to solvent. This suggests that a more compact structure exists at low pH. The results, being in accordance with far-UV CD and fluorescence studies, imply the presence of MG state of fetuin at low pH. As studied by fluorescence spectroscopy, denaturation of fetuin at low pH was found to be reversible.

The acid-induced state of glucose oxidase exists as a compact folded intermediate.

A systematic investigation of the acid-induced unfolding of glucose oxidase (beta-D-glucose: oxygen 1-oxidoreductase) (GOD) from Aspergillus niger was made using steady-state tryptophan fluorescence, circular dichroism (CD), and ANS (1-anilino 8-naphthalene sulfonic acid) binding. Intrinsic tryptophan fluorescence studies showed a maximally unfolded state at pH 2.6 and the presence of a non-native intermediate in the vicinity of pH 1.4. Flavin adenine dinucleotide (FAD) fluorescence measurements indicate that the bound cofactors are released at low pH. In the pH range studied, near- and far-UV CD spectra show maximal loss of tertiary as well as secondary structure (40%) at pH 2.6 although glucose oxidase at this pH is relatively less denatured as compared to the conformation in 6M GdnHCl. Interestingly, in the vicinity of pH 1.4, glucose oxidase shows a refolded conformation (A-state) with approximately 90% of native secondary structure and native-like near-UV CD spectral features. ANS fluorescence studies, however, show maximal binding of the dye to the protein at pH 1.4, indicating a "molten-globule"-like conformation with enhanced exposure of hydrophobic surface area. Acrylamide quenching data exhibit reduced accessibility of quencher to tryptophan, suggesting a more compact conformation at low pH. Thermal stability of this state was assessed by ellipticity changes at 222 nm relative to native protein. While native glucose oxidase showed a completely reversible thermal denaturation profile, the state at pH 1.4 showed approximately 50% structural loss and the denatured state appeared to be in a different conformation exhibiting prominent beta-sheet structure (around 85 degrees C) that was not reversible. To summarize; the A-state of GOD exists as a compact folded intermediate with "molten-globule"-like characteristics, viz., native-like secondary structure but with non-native cofactor environment, enhanced hydrophobic surface area and non-cooperative thermal unfolding. That the A-state also possesses significant tertiary structure is an interesting observation made in this study.

Characterization of a proteinase inhibitor from Cajanus cajan (L.).

A protein proteinase inhibitor (PI) has been purified from pigeonpea Cajanus cajan (L.) PUSA 33 variety by acetic-acid precipitation, salt fractionation and chromatography on a DEAE-Cellulose column. The content of inhibitor was found to be 15 mg/20 g dry weight of pulse. The molecular weight of the inhibitor as determined by SDS-PAGE under reducing conditions was found to be about 14,000. It showed inhibitory activity toward proteolytic enzymes belonging to the serine protease group, namely trypsin and alpha-chymotrypsin. The inhibitory activity was stable over a wide range of pH and temperatures. Estimation of sulfhydryl groups yielded one free cysteine and at least two disulfide linkages. N-terminal sequence homology suggests that it belongs to the Kunitz inhibitor family. Structural analysis by circular dichroism shows that the inhibitor possesses a largely disordered structure.

Characterization of a partially folded intermediate of stem bromelain at low pH.

Equilibrium studies on the acid included denaturation of stem bromelain (EC 3.4.22.32) were performed by CD spectroscopy, fluorescence emission spectroscopy and binding of the hydrophobic dye, 1-anilino 8-naphthalene sulfonic acid (ANS). At pH 2.0, stem bromelain lacks a well defined tertiary structure as seen by fluorescence and near-UV CD spectra. Far-UV CD spectra show retention of some native like secondary structure at pH 2.0. The mean residue ellipticities at 208 nm plotted against pH showed a transition around pH 4.5 with loss of secondary structure leading to the formation of an acid-unfolded state. With further decrease in pH, this unfolded state regains most of its secondary structure. At pH 2.0, stem bromelain exists as a partially folded intermediate containing about 42.2% of the native state secondary structure Enhanced binding of ANS was observed in this state compared to the native folded state at neutral pH or completely unfolded state in the presence of 6 m GdnHCl indicating the exposure of hydrophobic regions on the protein molecule. Acrylamide quenching of the intrinsic tryptophan residues in the protein molecule showed that at pH 2.0 the protein is in an unfolded conformation with more tryptophan residues exposed to the solvent as compared to the native conformation at neutral pH. Interestingly, stem bromelain at pH 0.8 exhibits some characteristics of a molten globule, such as an enhanced ability to bind the fluorescent probe as well as considerable retention of secondary structure. All the above data taken together suggest the existence of a partially folded intermediate state under low pH conditions.