Effects of solution polarity and viscosity on peptide deamidation

Abstract: Deamidation kinetics were measured for a model hexapeptide (l ‐Val‐l ‐Tyr‐l ‐Pro‐l ‐Asn‐Gly‐l ‐Ala, 0.02 mg/mL) in aqueous solutions containing glycerol (0–50% w/w) and poly(vinyl pyrrolidone) (PVP, 0–20% w/w) at 37 °C and pH 10 to determine the effects of solution polarity and viscosity on reactivity. The observed pseudo‐first order deamidation rate constants, k_obs, decreased markedly when the viscosity increased from 0.7 to 13 cp, but showed no significant change at viscosities > 13 cp. Values of k_obs also increased with increasing dielectric constant and decreasing refractive index. Molecular dynamics simulations indicated that the free energy associated with Asn side‐chain motion is insensitive to changes in dielectric constant, suggesting that the observed dielectric constant dependence is instead related primarily to the height of the transition state energy barrier. An empirical model was proposed to describe the effects of the viscosity, refractive index and dielectric constant on k_obs. Analysis of the regression coefficients suggested that both permanent and induced dipoles of the medium affect the deamidation rate constant, but that solution viscosity is relatively unimportant in the range studied.     

Effect of 'pH' on the rate of asparagine deamidation in polymeric formulations: 'pH'-rate profile

The rate of Asn deamidation of a model hexapeptide (L-Val-L-Tyr-L-Pro-L-Asn-Gly-L-Ala) was measured as a function of effective pH ('pH') in glassy and rubbery polymeric solids containing poly(vinyl pyrrolidone) (PVP) and in solution controls at 70 degrees C. The reaction exhibited pseudo-first-order kinetics in all samples over a wide 'pH' range (0.5 < 'pH' < 12); the formation of similar products suggests that the reaction mechanism is unaffected by matrix type. Rates of deamidation were comparable for the polymeric and solution samples in the acidic range ('pH' < 4). Solution-state rates were faster than those in polymeric solids at neutral 'pH' (6 < 'pH' < 8), increasing to a > 10,000-fold difference in the basic range ('pH' > 8). Specific base catalysis was observed in solution and in the polymeric solids under neutral conditions (6 < 'pH' < 8). In solution, the reaction exhibited general base catalysis for 'pH' > 8, whereas the reaction was 'pH'-independent in the polymeric solids in this range. The 'pH'-rate profile and supporting buffer catalysis data are consistent with a change in the rate-determining step in the basic range from 'pH'-dependent attack of the deprotonated backbone amide nitrogen on the Asn side chain in solution to 'pH'-independent ammonia expulsion in the polymeric solids. The results suggest that polymer matrix incorporation not only affects the magnitude of the deamidation rate constant but also the 'pH' dependency of the reaction and the rate-determining step in the basic 'pH' range.     

Reactivity toward deamidation of asparagine residues in β‐turn structures

Mimetics of β‐turn structures in proteins have been used to calibrate the relative reactivities toward deamidation of asparagine residues in the two central positions of a β‐turn and in a random coil. N‐Acetyl‐Asn‐Gly‐6‐aminocaproic acid, an acyclic analog of a β‐turn mimic undergoes deamidation of the asparaginyl residue through a succinimide intermediate to generate N‐acetyl‐Asp‐N‐Gly‐6‐aminocaproic acid (6‐aminocaproic acid, hereafter Aca) and N‐acetyl‐l ‐iso‐aspartyl (isoAsp)‐Gly‐Aca (pH 8.8, 37 °C) ≈ 3‐fold faster than does the cyclic β‐turn mimic cyclo‐[L‐Asn‐Gly‐Aca] with asparagine at position 2 of the β‐turn. The latter compound, in turn, undergoes deamidation ≈ 30‐fold faster than its positional isomer cyclo‐[Gly‐Asn‐Aca] with asparagine at position 3 of the β‐turn. Both cyclic peptides assume predominantly β‐turn structures in solution, as demonstrated by NMR and circular dichroism characterization. The open‐chain compound and its isomer N‐acetyl‐Gly‐Asn‐Aca assume predominantly random coil structures. The latter isomer undergoes deamidation 2‐fold slower than the former. Thus the order of reactivity toward deamidation is: asparagine in a random coil ≈ 3× asparagine in position 2 of a β‐turn ≈ 30× asparagine in position 3 of a β‐turn.     

Chemical Pathways of Peptide Degradation. III. Effect of Primary Sequence on the Pathways of Deamidation of Asparaginyl Residues in Hexapeptides

Deamidation of Asn residues can occur either by direct hydrolysis of the Asn residue or via a cyclic imide intermediate. The effects of primary sequence on the pathways of deamidation of Asn residues were studied using Val-Tyr-X-Asn-Y-Ala hexapeptides with substitution on the C-terminal side (Y) and on the N-terminal side (X) of the Asn residue. In acidic media the peptides deamidate by direct hydrolysis of the Asn residue to yield only Asp peptides, whereas under neutral or alkaline conditions, the peptides deamidate by formation of the cyclic imide intermediates which hydrolyze to yield both isoAsp and Asp peptides. At neutral to alkaline pH's the rate of deamidation was significantly affected by the size of the amino acid on the C-terminal side of the Asn residue. The amino acid on the C-terminal side of the Asn residue has no effect on the rate of deamidation at acidic pH. Changes in the structure of the amino acid on the N-terminal side of the Asn residue had no significant effect on the rate of deamidation at all the pH's studied. For peptides that underwent deamidation slowly, a reaction involving the attack of the Asn side chain on the peptide carbonyl carbon resulting in peptide bond cleavage was also observed.     

Effects of acidic N + 1 residues on asparagine deamidation rates in solution and in the solid state

The deamidation kinetics of four model peptides (AcGQNGG, AcGQNDG, AcGQNEG, and AcGQNQG) were studied in solution (70 degrees C, pH 5-10) and in lyophilized solids [70 degrees C, 50% relative humidity, "effective pH" ('pH') 5-10] containing polyvinyl pyrrolidone. AcGQNGG, AcGQNEG, and AcGQNQG degraded exclusively through Asn deamidation, whereas AcGQNDG also displayed Asp isomerization, and Asp-Gly peptide bond cleavage. The pH/'pH'-rate profiles were consistent with a shift in the rate-determining step of Asn deamidation from carbonyl addition to expulsion of ammonia with increasing pH. In solution, AcGQNGG deamidated up to 38-fold faster than the other peptides, indicating the importance of steric effects of the N + 1 residue. AcGQNGG and AcGQNQG had up to 60 times slower rates of deamidation in the solid state than in solution. In contrast, the deamidation rates of AcGQNEG and AcGQNDG in the solid state were similar to those in solution. N + 1 Glu or Asp residue may enhance local hydration, so that the deamidation of Asn in the solid formulations actually proceeds in a solution-like environment.     

Formulation considerations for proteins susceptible to asparagine deamidation and aspartate isomerization

The asparagine (Asn) deamidation and aspartate (Asp) isomerization reactions are nonenzymatic intra-molecular reactions occurring in peptides and proteins that are a source of major stability concern in the formulation of these biomolecules. The mechanisms for the deamidation and isomerization reactions are similar since they both proceed through an intra-molecular cyclic imide (Asu) intermediate. The formation of the Asu intermediate, which involves the attack by nitrogen of the peptide backbone on the carbonyl carbon of the Asn or the Asp side chain, is the rate-limiting step in both the deamidation and the isomerization reactions at physiological pH. In this article, the influence of factors such as formulation conditions, protein primary sequence, and protein structure on the reactivity of Asn and Asp residues in proteins are reviewed. The importance of formulation conditions such as pH and solvent dielectric in influencing deamidation and isomerization reaction rates is addressed. Formulation strategies that could improve the stability of proteins to deamidation and isomerization reactions are described. The review is intended to provide information to formulation scientists, based on protein sequence and structure, to predict potential degradative sites on a protein molecule and to enable formulation scientists to set appropriate formulation conditions to minimize reactivity of Asn and Asp residues in protein therapeutics.     

Controlling deamidation rates in a model peptide: effects of temperature, peptide concentration, and additives.

The rate of deamidation of the Asn residue in Val-Tyr-Pro-Asn-Gly-Ala (VYPNGA), a model peptide, was determined at pH 9 (400 mM Tris buffer) as a function of temperature and peptide concentration. Over the temperature range 5-65 degrees C, deamidation followed Arrhenius behavior, with an apparent activation energy of 13.3 kcal/mol. Furthermore, increasing the peptide concentration slows the rate of deamidation. Self-stabilization with respect to deamidation has not been reported previously. The rate of deamidation was also determined in the presence of sucrose and poloxamer 407 (Pluronic F127). In both cases, the rate of deamidation was retarded by up to 40% at 35 degrees C. In aqueous solutions containing poloxamer 407, the degree of stabilization is independent of formation of a reversible thermosetting gel. With sucrose, maximum reduction in the deamidation rate was attained with as little as 5% (w/v). Addition of sucrose results in a greater conformational preference for a type II beta-turn structure, which presumably is less prone to intramolecular cyclization and subsequent deamidation.     

Identification and quantitation of tetrapeptide deamidation products by mass spectrometry.

A method to quantify asparagine (Asn), aspartate (Asp) and isoaspartate (isoAsp) residues in small peptides by fast atom bombardment mass spectrometry (FAB-MS) was developed. Discrimination of isoAsp from Asp residues was accomplished by selective derivatization of isoAsp residues in acetic anhydride, D2O and pyridine. Deuteration occurred at any carbon adjacent to a free alpha-carboxyl group, through a transient oxazalone intermediate, allowing the isoAsp side chain and the C-terminus to incorporate deuterium. Thus, isoAsp-containing peptides incorporate one more deuterium than peptides with Asp and two more than Asn peptides. FAB CID-MS spectra of the Asn tetrapeptide, Thr-Asn-Ser-Tyr, were used to confirm the position of deuteration to the C-terminal residue. FAB and FAB CID-MS spectra demonstrated that the 1 amu shift in mass was not caused by derivatization induced deamidation of the Asn residue. FAB-MS spectra of deuterated peptide standards and mixtures containing deamidation products were obtained over the molecular ion region and deconvoluted using non-deuterated control spectra. Deuterium incorporation values for the Asn, Asp and iosAsp containing peptide standards were 80% mono-deuterated peptide, 95% mono-deuterated peptide and 63% di-deuterated peptide, respectively. IsoAsp to Asp ratios in an unknown mixture were obtained by a least-squares minimization of the difference between the unknown deuterated mixture and the isotopic envelopes from the deuterated standards. The mixture was found to contain 85% isoAsp peptide by FAB-MS, which agreed well with 81% isoAsp peptide when assayed by reversed-phase LC.     

The effects of a histidine residue on the C-terminal side of an asparaginyl residue on the rate of deamidation using model pentapeptides

The effects of a histidine (His) residue located on the C-terminal side of an asparaginyl (Asn) residue on the rate of deamidation were studied using Gly-Gln-Asn-X-His pentapeptides. The rates of deamidation of the pentapeptides were determined at 37 degrees C (I = 0.5) as function of pH, buffer species, and buffer concentration. A capillary electrophoresis stability-indicating assay was developed to monitor simultaneously the disappearance of the starting peptides and the appearance of the degradation products. The rates of degradation of the peptides were pH dependent, increasing with pH, and followed apparent first-order kinetics. At pH values <6.5, Gly-Gln-Asn-His-His degraded faster than Gly-Gln-Asn-Gly-His, suggesting that the N+1 His residue is catalyzing the deamidation of the Asn residue. The His side chain at these pH values could function as a general acid catalyst, stabilizing the oxyanionic transition state of the cyclic imide intermediate formation. In contrast, at pH values >6.5, Gly-Gln-Asn-Gly-His deamidates more rapidly than Gly-Gln-Asn-His-His. The bulk of the side chain of the N+1 His residue versus the N+1 Gly residue apparently inhibits the flexibility of the peptide around the reaction site and, consequently, reduces the rate of the reaction. The significance of this steric hindrance effect of the N+1 His residue on the rate of deamidation was examined further. It was observed that at pH >6.0, Gly-Gln-Asn-His-His undergoes deamidation faster than Gly-Gln-Asn-Val-His. This observation indicated that, at the higher pH values, the N+1 His residue is also acting as a catalyst. Thus, at basic pH, the N+1 His residue influences the rate of deamidation via two opposing effects; that is, general base catalysis and steric interference. The pentapeptide Gly-Gln-Asn-His-His, in addition to undergoing the deamidation reaction, also undergoes bond cleavage at the Asn-His peptide bond. The enhanced rate of Asn-His peptide bond cleavage can be attributed to the general base behavior of the His residue, leading to increased nucleophilicity of the Asn side-chain amide group. Finally, we have shown that the His residue that is two amino acids removed from the Asn, the N+2 position, has little or no effect on the rate of deamidation.     

Chemical stability of peptides in polymers. 2. Discriminating between solvent and plasticizing effects of water on peptide deamidation in poly(vinylpyrrolidone).

The mechanistic role of water in the deamidation of a model asparagine-containing hexapeptide (Val-Tyr-Pro-Asn-Gly-Ala) in lyophilized formulations containing poly(vinylpyrrolidone) (PVP) and glycerol was investigated. Glycerol was used as a plasticizer to vary formulation glass transition temperature (T(g)) without significantly changing water content or activity. Increases in moisture and glycerol contents increased the rate of peptide deamidation. This increase was strongly correlated with T(g) at constant water content and activity, suggesting that increased matrix mobility facilitates deamidation. In rubbery systems (T > T(g)), deamidation rates appeared to be independent of water content and activity in formulations with similar T(g)s. However, in glassy formulations with similar T(g)s, deamidation increased with water content, suggesting a solvent/medium effect of water on reactivity in this regime. An increase in water content also affected the degradation product distribution; less of the cyclic imide intermediate and more of the hydrolytic products, isoAsp- and Asp-hexapeptides, were observed as water content increased. Thus, residual water appears to facilitate deamidation in these solid PVP formulations both by enhancing molecular mobility and by solvent/medium effects, and also participates as a chemical reactant in the subsequent breakdown of the cyclic imide.     

Effects of single d‐amino acid substitutions on disruption of β‐sheet structure and hydrophobicity in cyclic 14‐residue antimicrobial peptide analogs related to gramicidin S

Abstract: Gramicidin S (GS) is a 10‐residue cyclic β‐sheet peptide with lytic activity against the membranes of both microbial and human cells, i.e. it possesses little to no biologic specificity for either cell type. Structure–activity studies of de novo‐designed 14‐residue cyclic peptides based on GS have previously shown that higher specificity against microbial membranes, i.e. a high therapeutic index (TI), can be achieved by the replacement of a single l ‐amino acid with its corresponding d ‐enantiomer [Kondejewski, L.H. et al. (1999) J. Biol. Chem. 274 , 13181]. The diastereomer with a d ‐Lys substituted at position 4 caused the greatest improvement in specificity vs. other l to d substitutions within the cyclic 14‐residue peptide GS14, through a combination of decreased peptide amphipathicity and disrupted β‐sheet structure in aqueous conditions [McInnes, C. et al. (2000) J. Biol. Chem. 275 , 14287]. Based on this information, we have created a series of peptide diastereomers substituted only at position 4 by a d ‐ or l ‐amino acid (Leu, Phe, Tyr, Asn, Lys, and achiral Gly). The amino acids chosen in this study represent a range of hydrophobicities/hydrophilicities as a subset of the 20 naturally occurring amino acids. While the d ‐ and l ‐substitutions of Leu, Phe, and Tyr all resulted in strong hemolytic activity, the substitutions of hydrophilic d ‐amino acids d ‐Lys and d ‐Asn in GS14 at position 4 resulted in weaker hemolytic activity than in the l ‐diastereomers, which demonstrated strong hemolysis. All of the l ‐substitutions also resulted in poor antimicrobial activity and an extremely low TI, while the antimicrobial activity of the d ‐substituted peptides tended to improve based on the hydrophilicity of the residue. d ‐Lys was the most polar and most efficacious substitution, resulting in the highest TI. Interestingly, the hydrophobic d ‐amino acid substitutions had superior antimicrobial activity vs. the l ‐enantiomers although substitution of a hydrophobic d ‐amino acid increases the nonpolar face hydrophobicity. These results further support the role of hydrophobicity of the nonpolar face as a major influence on microbial specificity, but also highlights the importance of a disrupted β‐sheet structure on antimicrobial activity.     

Dimerization of a PACAP peptide analogue in DMSO via asparagine and aspartic acid residues

To optimize the stability of a peptide development candidate for the treatment of type II diabetes, formulation studies were initiated in organic solvents and compared to results obtained in aqueous solutions. Stability was assessed by reversed phase liquid chromatography (RPLC) and electrospray ionization mass spectrometry (ESI-MS). Previous studies had shown deamidation and hydrolysis to be the primary mechanisms of degradation in aqueous formulations. Surprisingly, the use of an organic solvent did not decrease the rate of degradation and, as presented here, produced degradation products including dimers. We propose here that deamidation can readily occur in polar anhydrous organic solvents such as DMSO and that the dimer forms through intermolecular nucleophilic attack of an amino acid side chain on a stabilized cyclic imide intermediate.     

Ammonia cleaves polypeptides at asparagine proline bonds

Abstract: Polypeptides that contain the sequence Asn‐Pro undergo complete cleavage at this amide bond with ammonia. One cleavage product possesses Pro as the new amino terminus and the other Asn or isoAsn as the new C‐terminus, the formation of the latter probably arising by way of a cyclic succinimide intermediate. Other Asn‐X bonds where X = Tyr, Gln, Ile, Glu, Ala, Gly, Asn or Phe did not exhibit any peptide bond cleavage, whereas when X = Leu, Thr and Ser partial cleavage was observed. Asn residues not involved in chain‐cleavage underwent deamidation to Asp as shown by MALDI‐ToF mass spectrometry (MS) analysis. The partial conversion of in‐chain Asp residues to isoAsp under the reaction conditions was inferred from RP‐HPLC and MS analysis of reaction mixtures.     

Chemical Pathways of Peptide Degradation. II. Kinetics of Deamidation of an Asparaginyl Residue in a Model Hexapeptide

Deamidation of Asn residues is a major chemical pathway of degradation of peptides and proteins. To understand better the external factors that influence deamidation, we studied the degradation of the hexapeptide Val–Tyr–Pro–Asn–Gly–Ala, a fragment of adrenocorticotropic hormone, by HPLC. The deamidation of this model peptide showed marked dependence on pH, temperature, and buffer composition. In the pH range 5 to 12, the peptide deamidated exclusively via a cyclic imide intermediate with the formation of both the Asp- and the isoAsp-hexapeptides. Buffer catalysis was also observed in the pH range of 7 to 11. However, at acidic pH's, the pathway of deamidation involved direct hydrolysis of the amide side chain of Asn residue to produce only the Asp-hexapeptide.     

Pluronic F-127 gels as a vehicle for topical formulations of indomethacin and rheological behaviour of these formulations

Topical gel formulations containing a non-steroidal anti-inflammatory drug, indomethacin (IND), were prepared using 20% w/w Lutrol PF-127 as a gel-forming agent, and 16, 20 and 24% w/w Hexylene glycol (HG) or polyethylene glycol 300 (PEG) as solvents. 1% w/w Tween 80 and 1% w/w PVP 25 were added as excipients. The effects of the amounts of solvent and excipients on the physical characteristics of IND gel such as consistency, appearance, crystallization, pH and viscosity were studied. The results indicated that 1% w/w IND is able to form a structural gel. The viscosity values were calculated from the rheograms which were determined by a Haake Rotovisco sensor at a shear rate of 10,000 l/s. Viscosities corresponding to shear rates of 1000, 3000, 6000 and 9000 l/s were also calculated. Yield points were approximated from the rheograms. Although all IND gels maintained their pseudoplastic flow behaviour, their viscosities decreased markedly with increasing shear rates. Furthermore, increasing the amount of HG or PEG gave a more viscous gel except for the 24 w/w% HG gels which turned a jelly with or without either Tween or PVP. The difference in viscosities was explained by the changes in the gel compositions. 20% of PEG-1% PVP ranked first in viscosity followed by 16% PEG-1% PVP, 16% PEG-1% Tween, 24% PEG, 20% PEG-1% Tween and 16% HG-1% PVP. The results indicate that the excipients influence the physical characteristics of the gels. The optimum concentration for gels manifesting as strength of gel was 20% PEG in combination with 1% PVP which had the highest viscosity and yield value at a low shear rate.     

Deamidation of model beta-turn cyclic peptides in the solid state

To investigate the importance of secondary structure on peptide deamidation in the solid state, two cyclic beta-turn peptides and their linear analogs were used as models of Asn residues in structured and unstructured domains, and incorporated into poly(vinyl pyrrolidone) (PVP)-based lyophilized solids. The secondary structure of the model peptides was determined in solution and the solid state using a combination of nuclear magnetic resonance (NMR) spectroscopy, circular dichroism (CD), and Fourier transform infrared (FTIR) spectroscopy. The model beta-turn cyclic peptides were found to be type II beta-turns while the linear analogs were determined to be predominantly unstructured. Quantitatively, the cyclic peptides consisted of approximately 80% beta-turn while the linear analogs contained only 30%-35% beta-turn. To characterize the solid environment, T(g), and moisture content of the solid-state formulations were determined. Accelerated stability studies were conducted in the solid state at 37 degrees C using formulations lyophilized from solutions at pH 8.8 (0.1 M borate buffer). The effect of matrix mobility on solid-state deamidation was investigated by altering the moisture content through variation of relative humidity or the addition of a plasticizer. Cyclic peptides degraded 1.2-8 times slower than the linear analogs under all of the conditions studied. The observed rate constants, however, for all of the peptides decreased dramatically (four orders of magnitude) in the glassy solids. This suggests the greater importance of matrix mobility in solid-state degradation. Molecular dynamics (MD) simulations were also performed to explore the low energy, preferred state of the peptides, and determine the structure around the beta-turn.     

A molecular dynamics simulation of reactant mobility in an amorphous formulation of a peptide in poly(vinylpyrrolidone)

The reaction pathways available for chemical decomposition in amorphous solids are determined in part by the relative mobilities of the potential reactants. In this study, molecular dynamics simulations of amorphous glasses of polyvinylpyrrolidone (PVP) containing small amounts of water, ammonia, and a small peptide, Phe-Asn-Gly, have been performed over periods of up to 100 ns to monitor the aging processes and associated structural and dynamic properties of the PVP segments and embedded solutes. Glass transition temperatures, Tg, were detected by changes in slopes of the volume-temperature profiles and the internal energy-temperature profiles for the inherent structures upon cooling at different rates. Analyses of the molecular trajectories below Tg reveal both temporal and spatial heterogeneity in polymer and solute mobility, with each molecule or part of a molecule displaying quite different relaxation behaviors for translational, rotational, and/or conformational motions. Rotations of individual polymer segments on the time scale up to 100 ns, though far from complete, are described by the Kohlrausch-Williams-Watts stretched exponential function with relaxation times tau on the order of 10-2.8 x 10(4) micros at an averaged stretching parameter beta of 0.39. The rotation rates are, on the average, faster for the side chains and for segments near the ends of the chains than for the backbones and segments near the middle of the chains. In contrast to their behavior in water, solute diffusive motions in the glassy polymer exhibit non-Einsteinian behavior over the time scale of the simulations characterized by two types of motion: (1) entrapments within relatively fluid microdomains surrounded by a matrix of relatively immobile polymer chains; and (2) jumps between microdomains with greater probability of hopping back to the solute's previous location. The average jump length and frequency are highly dependent on solute size, being much smaller for the tripeptide, Phe-Asn-Gly, than for water and ammonia. The diffusivities of water and ammonia, solutes capable of forming hydrogen bonds with the lactam residues within the polymer segments, are significantly reduced by strong electrostatic interactions. The conformational preferences of Phe-Asn-Gly were compared in the amorphous polymer and water to detect differences in the degree to which the tripeptide may be predisposed toward deamidation of the asparagine side chain in these environments. Although only minor differences are evident in peptide conformation, the conformational dynamics for the peptide embedded in the glassy polymer are characterized by a higher energy barrier between conformational states and 2.5-44-fold larger relaxation times for the dihedral angles of interest than in water. However, in the context of peptide deamidation, these differences may be of secondary importance in comparison to the more than two to three orders of magnitude reduction in the diffusivities of water, ammonia, and the tripeptide in PVP.     

Synthesis of 10‐ and 9‐membered dilactams derived from aspartic and glutamic acids

Abstract: 9‐ and 10‐membered bridged dipeptides derived from l ‐aspartic acid and l ‐ or d ‐glutamic acid were synthesized using aminoacyl incorporation reaction. Key intermediates containing internal pyroglutamyl moiety were prepared via side chain to backbone cyclization of related protected dipeptide derivatives of glutamic acid.     

Asparagine deamidation in recombinant human lymphotoxin: hindrance by three-dimensional structures

The chemical stability of recombinant human lymphotoxin (rhLT) was evaluated at pH 7, 9, and 11 and 40 degrees C using quantitative tryptic map and urea-IEF methods. Degradation products were characterized by mass spectrometry. The stability of denatured rhLT protein was also evaluated to elucidate the effects of three-dimensional structures on Asn deamidation in rhLT. Two sites that underwent Asn deamidation were identified in rhLT, Asn(19) and Asn(40)-Asn(41). At pH 11 and 40 degrees C, deamidation at Asn(19) and Asn(40)-Asn(41) had half-lives of 14 +/- 4 and 80 +/- 24 days, respectively. Upon denaturation, 31- and ninefold acceleration in the degradation rates was observed at the Asn(19) and Asn(40)-Asn(41) sites, respectively. The rate of Asn(19) degradation in denatured rhLT was comparable to that of the model peptide possessing the same primary sequence as the Asn(19)-containing region in rhLT. Analysis of the rhLT crystal structure revealed that both Asn deamidation sites were located in beta-turn structures with extensive hydrogen-bonding networks created with nearby residues in the tertiary structures. The results suggested that these tertiary and secondary structures, if held true in solution, were probably responsible for the stabilization of Asn in the native rhLT protein by reducing flexibility, thus preventing adoption of the favorable conformation required for cyclic-imide formation.     

Synthetic peptide derived from α‐fetoprotein inhibits growth of human breast cancer: investigation of the pharmacophore and synthesis optimization

Abstract: A synthetic peptide that inhibits the growth of estrogen receptor positive (ER+) human breast cancers, growing as xenografts in mice, has been reported. The cyclic 9‐mer peptide, cyclo[EMTOVNOGQ], is derived from α‐fetoprotein (AFP), a safe, naturally occurring human protein produced during pregnancy, which itself has anti‐estrogenic and anti‐breast cancer activity. To determine the pharmacophore of the peptide, a series of analogs was prepared using solid‐phase peptide synthesis. Analogs were screened in a 1‐day bioassay, which assessed their ability to inhibit the estrogen‐stimulated growth of uterus in immature mice. Deletion of glutamic acid, Glu1, abolished activity of the peptide, but glutamine (Gln) or asparagine (Asn) could be substituted for Glu1 without loss of activity. Methionine (Met2) was replaced with lysine (Lys) or tyrosine (Tyr) with retention of activity. Substitution of Lys for Met2 in the cyclic molecule resulted in a compound with activity comparable with the Met2‐containing cyclic molecule, but with a greater than twofold increase in purity and corresponding increase in yield. This Lys analog demonstrated anti‐breast cancer activity equivalent to that of the original Met‐containing peptide. Therefore, Met2 is not essential for biologic activity and substitution of Lys is synthetically advantageous. Threonine (Thr3) is a nonessential site, and can be substituted with serine (Ser), valine (Val), or alanine (Ala) without significant loss of activity. Hydroxyproline (Hyp), substituted in place of the naturally occurring prolines (Pro4, Pro7), allowed retention of activity and increased stability of the peptide during storage. Replacement of the first Pro (Pro4) with Ser maintains the activity of the peptide, but substitution of Ser for the second Pro (Pro7) abolishes the activity of the peptide. This suggests that the imino acid at residue 7 is important for conformation of the peptide, and the backbone atoms are part of the pharmacophore, but Pro4 is not essential. Valine (Val5) can be substituted only with branched‐chain amino acids (isoleucine, leucine or Thr); replacement by d ‐valine or Ala resulted in loss of biologic activity. Thus, for this site, the bulky branched side chain is essential. Asparagine (Asn6) is essential for activity. Substitution with Gln or aspartic acid (Asp), resulted in reduction of biologic activity. Removal of glycine (Gly8) resulted in a loss of activity but nonconservative substitutions can be made at this site without a loss of activity indicating that it is not part of the pharmacophore. Cyclization of the peptide is facilitated by addition of Gln9, but this residue does not occur in AFP nor is it necessary for activity. Gln9 can be replaced with Asn, resulting in a molecule with similar activity. These data indicate that the pharmacophore of the peptide includes side chains of Val5 and Asn6 and backbone atoms contributed by Thr3, Val5, Asn6, Hyp7 and Gly8. Met2 and Gln9 can be modified or replaced. Glu1 can be replaced with charged amino acids, and is not likely to be part of the binding site of the peptide. The results of this study provide information that will be helpful in the rational modification of cyclo[EMTOVNOGQ] to yield peptide analogs and peptidomimetics with advantages in synthesis, pharmacologic properties, and biologic activity.