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Acetic acid can catalyze succinimide formation from aspartic acid residues by a concerted bond reorganization mechanism: a computational study.

Takahashi O, Kirikoshi R, Manabe N - Int J Mol Sci (2015)

Bottom Line: The cyclization results from a bond formation between the amide nitrogen on the C-terminal side and the side-chain carboxyl carbon, which is part of an extensive bond reorganization (formation and breaking of single bonds and the interchange of single and double bonds) occurring concertedly in a cyclic structure formed by the amide NH bond, the AA molecule and the side-chain C=O group and involving a double proton transfer.The second step also involves an AA-mediated bond reorganization.Carboxylic acids other than AA are also expected to catalyze the succinimide formation by a similar mechanism.

View Article: PubMed Central - PubMed

Affiliation: Faculty of Pharmaceutical Sciences, Tohoku Pharmaceutical University, 4-4-1 Komatsushima, Aoba-ku, Sendai 981-8558, Japan. ohgi@tohoku-pharm.ac.jp.

ABSTRACT
Succinimide formation from aspartic acid (Asp) residues is a concern in the formulation of protein drugs. Based on density functional theory calculations using Ace-Asp-Nme (Ace = acetyl, Nme = NHMe) as a model compound, we propose the possibility that acetic acid (AA), which is often used in protein drug formulation for mildly acidic buffer solutions, catalyzes the succinimide formation from Asp residues by acting as a proton-transfer mediator. The proposed mechanism comprises two steps: cyclization (intramolecular addition) to form a gem-diol tetrahedral intermediate and dehydration of the intermediate. Both steps are catalyzed by an AA molecule, and the first step was predicted to be rate-determining. The cyclization results from a bond formation between the amide nitrogen on the C-terminal side and the side-chain carboxyl carbon, which is part of an extensive bond reorganization (formation and breaking of single bonds and the interchange of single and double bonds) occurring concertedly in a cyclic structure formed by the amide NH bond, the AA molecule and the side-chain C=O group and involving a double proton transfer. The second step also involves an AA-mediated bond reorganization. Carboxylic acids other than AA are also expected to catalyze the succinimide formation by a similar mechanism.

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The geometry of I•AA-1 (φ = −167°, ψ = −138°, χ1 = 117°), which is the intermediate complex directly connected to TS-1. Selected interatomic distances are shown in Å. The asterisk (*) indicates the α carbon.
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ijms-16-01613-f006: The geometry of I•AA-1 (φ = −167°, ψ = −138°, χ1 = 117°), which is the intermediate complex directly connected to TS-1. Selected interatomic distances are shown in Å. The asterisk (*) indicates the α carbon.

Mentions: Figure 2 shows the energy diagram for the two-step succinimide formation catalyzed by an AA molecule, and Figure 3, Figure 4, Figure 5, Figure 6, Figure 7, Figure 8 and Figure 9 show optimized geometries. The values of dihedral angles φ, ψ and χ1 (Figure 1) are shown in the captions to Figure 3, Figure 4, Figure 5, Figure 6, Figure 7, Figure 8 and Figure 9. R, I and P stand for the reactant (model compound), the gem-diol tetrahedral intermediate and the succinimide product, respectively. AA and W are acetic acid and water molecules, respectively. TS-1 and TS-2 are the transition states of the first and second steps (cyclization and dehydration), respectively. While geometry optimizations and zero-point energy (ZPE) calculations were performed in a vacuum, hydration free energies estimated by the SM8 (solvation model 8) continuum model [56,57] were taken into account in relative energy calculations. As may be seen from Figure 2, the effects of hydration on relative energies are small, except for complexation energies. The relative energies cited in the following are those in water, unless otherwise noted.


Acetic acid can catalyze succinimide formation from aspartic acid residues by a concerted bond reorganization mechanism: a computational study.

Takahashi O, Kirikoshi R, Manabe N - Int J Mol Sci (2015)

The geometry of I•AA-1 (φ = −167°, ψ = −138°, χ1 = 117°), which is the intermediate complex directly connected to TS-1. Selected interatomic distances are shown in Å. The asterisk (*) indicates the α carbon.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4307323&req=5

ijms-16-01613-f006: The geometry of I•AA-1 (φ = −167°, ψ = −138°, χ1 = 117°), which is the intermediate complex directly connected to TS-1. Selected interatomic distances are shown in Å. The asterisk (*) indicates the α carbon.
Mentions: Figure 2 shows the energy diagram for the two-step succinimide formation catalyzed by an AA molecule, and Figure 3, Figure 4, Figure 5, Figure 6, Figure 7, Figure 8 and Figure 9 show optimized geometries. The values of dihedral angles φ, ψ and χ1 (Figure 1) are shown in the captions to Figure 3, Figure 4, Figure 5, Figure 6, Figure 7, Figure 8 and Figure 9. R, I and P stand for the reactant (model compound), the gem-diol tetrahedral intermediate and the succinimide product, respectively. AA and W are acetic acid and water molecules, respectively. TS-1 and TS-2 are the transition states of the first and second steps (cyclization and dehydration), respectively. While geometry optimizations and zero-point energy (ZPE) calculations were performed in a vacuum, hydration free energies estimated by the SM8 (solvation model 8) continuum model [56,57] were taken into account in relative energy calculations. As may be seen from Figure 2, the effects of hydration on relative energies are small, except for complexation energies. The relative energies cited in the following are those in water, unless otherwise noted.

Bottom Line: The cyclization results from a bond formation between the amide nitrogen on the C-terminal side and the side-chain carboxyl carbon, which is part of an extensive bond reorganization (formation and breaking of single bonds and the interchange of single and double bonds) occurring concertedly in a cyclic structure formed by the amide NH bond, the AA molecule and the side-chain C=O group and involving a double proton transfer.The second step also involves an AA-mediated bond reorganization.Carboxylic acids other than AA are also expected to catalyze the succinimide formation by a similar mechanism.

View Article: PubMed Central - PubMed

Affiliation: Faculty of Pharmaceutical Sciences, Tohoku Pharmaceutical University, 4-4-1 Komatsushima, Aoba-ku, Sendai 981-8558, Japan. ohgi@tohoku-pharm.ac.jp.

ABSTRACT
Succinimide formation from aspartic acid (Asp) residues is a concern in the formulation of protein drugs. Based on density functional theory calculations using Ace-Asp-Nme (Ace = acetyl, Nme = NHMe) as a model compound, we propose the possibility that acetic acid (AA), which is often used in protein drug formulation for mildly acidic buffer solutions, catalyzes the succinimide formation from Asp residues by acting as a proton-transfer mediator. The proposed mechanism comprises two steps: cyclization (intramolecular addition) to form a gem-diol tetrahedral intermediate and dehydration of the intermediate. Both steps are catalyzed by an AA molecule, and the first step was predicted to be rate-determining. The cyclization results from a bond formation between the amide nitrogen on the C-terminal side and the side-chain carboxyl carbon, which is part of an extensive bond reorganization (formation and breaking of single bonds and the interchange of single and double bonds) occurring concertedly in a cyclic structure formed by the amide NH bond, the AA molecule and the side-chain C=O group and involving a double proton transfer. The second step also involves an AA-mediated bond reorganization. Carboxylic acids other than AA are also expected to catalyze the succinimide formation by a similar mechanism.

Show MeSH
Related in: MedlinePlus