The Catalytic Mechanism of the Marine-Derived Macrocyclase, PATGmac

Natércia F Bras, Pedro Ferreira, Ana R Calixto, Marcel Jaspars, Wael El-Sayed Mohamed Houssen Ibrahim, James H Naismith, Pedro A Fernandes, Maria J Ramos

Research output: Contribution to journalArticle

10 Citations (Scopus)
5 Downloads (Pure)

Abstract

Cyclic peptides are a class of compounds with high therapeutic potential, possessing bioactivities including anti-tumour and anti-viral (including anti-HIV). Despite their desirability, efficient design and production of these compounds has not yet been achieved. The catalytic mechanism of patellamide macrocyclization by PatG macrocyclase domain has been investigated using computational methods. We applied a quantum mechanics/molecular mechanics (QM/MM) methodology, specifically ONIOM(M06/6-311++G(2d,2p):ff94//B3LYP/6-31G(d):ff94). The mechanism proposed here begins with a proton transfer from Ser783 to His 618 and from the latter to Asp548. Nucleophilic attack of Ser783 to the substrate leads on to the formation of an acyl-enzyme covalent complex. The leaving group (AYDG) of the substrate is protonated by the substrate’s N-terminus leading to the breakage of the P1-P1’ bond. Finally, the substrate’s N-terminus attacks the P1 residue, decomposing the acyl-enzyme complex forming the macrocycle. We found that the formation and decomposition of the acyl-enzyme complex have the highest activation free energies (21.1 kcal.mol-1 and 19.8 kcal.mol-1 respectively), typical of serine proteases. Understanding the mechanism behind the macrocyclization of patellamides will be important to the application of the enzymes in the pharmaceutical and biotechnological industries.
Original languageEnglish
Pages (from-to)13089-13097
Number of pages9
JournalChemistry : a European Journal
Volume22
Issue number37
Early online date8 Jul 2016
DOIs
Publication statusPublished - 5 Sep 2016

Fingerprint

Enzymes
Substrates
Cyclic Peptides
Molecular mechanics
Proton transfer
Quantum theory
Serine Proteases
Computational methods
Bioactivity
Drug products
Free energy
Tumors
Chemical activation
Decomposition
Pharmaceutical Preparations
Industry

Keywords

  • patellamide
  • macrocyclization
  • QM/MM
  • ONIOM
  • catalytic mechanism

Cite this

The Catalytic Mechanism of the Marine-Derived Macrocyclase, PATGmac. / Bras, Natércia F; Ferreira, Pedro ; Calixto, Ana R; Jaspars, Marcel; Houssen Ibrahim, Wael El-Sayed Mohamed; Naismith, James H; Fernandes, Pedro A; Ramos, Maria J.

In: Chemistry : a European Journal, Vol. 22, No. 37, 05.09.2016, p. 13089-13097.

Research output: Contribution to journalArticle

Bras, NF, Ferreira, P, Calixto, AR, Jaspars, M, Houssen Ibrahim, WE-SM, Naismith, JH, Fernandes, PA & Ramos, MJ 2016, 'The Catalytic Mechanism of the Marine-Derived Macrocyclase, PATGmac', Chemistry : a European Journal, vol. 22, no. 37, pp. 13089-13097. https://doi.org/10.1002/chem.201601670
Bras, Natércia F ; Ferreira, Pedro ; Calixto, Ana R ; Jaspars, Marcel ; Houssen Ibrahim, Wael El-Sayed Mohamed ; Naismith, James H ; Fernandes, Pedro A ; Ramos, Maria J. / The Catalytic Mechanism of the Marine-Derived Macrocyclase, PATGmac. In: Chemistry : a European Journal. 2016 ; Vol. 22, No. 37. pp. 13089-13097.
@article{5e2c806b1f8d48818a6e86380c47a8fd,
title = "The Catalytic Mechanism of the Marine-Derived Macrocyclase, PATGmac",
abstract = "Cyclic peptides are a class of compounds with high therapeutic potential, possessing bioactivities including anti-tumour and anti-viral (including anti-HIV). Despite their desirability, efficient design and production of these compounds has not yet been achieved. The catalytic mechanism of patellamide macrocyclization by PatG macrocyclase domain has been investigated using computational methods. We applied a quantum mechanics/molecular mechanics (QM/MM) methodology, specifically ONIOM(M06/6-311++G(2d,2p):ff94//B3LYP/6-31G(d):ff94). The mechanism proposed here begins with a proton transfer from Ser783 to His 618 and from the latter to Asp548. Nucleophilic attack of Ser783 to the substrate leads on to the formation of an acyl-enzyme covalent complex. The leaving group (AYDG) of the substrate is protonated by the substrate’s N-terminus leading to the breakage of the P1-P1’ bond. Finally, the substrate’s N-terminus attacks the P1 residue, decomposing the acyl-enzyme complex forming the macrocycle. We found that the formation and decomposition of the acyl-enzyme complex have the highest activation free energies (21.1 kcal.mol-1 and 19.8 kcal.mol-1 respectively), typical of serine proteases. Understanding the mechanism behind the macrocyclization of patellamides will be important to the application of the enzymes in the pharmaceutical and biotechnological industries.",
keywords = "patellamide, macrocyclization, QM/MM, ONIOM, catalytic mechanism",
author = "Bras, {Nat{\'e}rcia F} and Pedro Ferreira and Calixto, {Ana R} and Marcel Jaspars and {Houssen Ibrahim}, {Wael El-Sayed Mohamed} and Naismith, {James H} and Fernandes, {Pedro A} and Ramos, {Maria J}",
note = "Acknowledgements This work received financial support from the European Union (FEDER funds through COMPETE) and National Funds (FCT, Funda{\cc}{\~a}o para a Ci{\^e}ncia e Tecnologia) through Projects EXCL/QEQ-COM/ 0394/2012, EXCL-II/QEQ-COM/0394/2012, and Pest-C/EQB/LA0006/2013. NFB would like to thank the Funda{\cc}{\~a}o para a Ci{\^e}ncia e a Tecnologia (FCT) for her IF starting grant (IF/01355/2014).",
year = "2016",
month = "9",
day = "5",
doi = "10.1002/chem.201601670",
language = "English",
volume = "22",
pages = "13089--13097",
journal = "Chemistry : a European Journal",
issn = "0947-6539",
publisher = "WILEY-V C H VERLAG GMBH",
number = "37",

}

TY - JOUR

T1 - The Catalytic Mechanism of the Marine-Derived Macrocyclase, PATGmac

AU - Bras, Natércia F

AU - Ferreira, Pedro

AU - Calixto, Ana R

AU - Jaspars, Marcel

AU - Houssen Ibrahim, Wael El-Sayed Mohamed

AU - Naismith, James H

AU - Fernandes, Pedro A

AU - Ramos, Maria J

N1 - Acknowledgements This work received financial support from the European Union (FEDER funds through COMPETE) and National Funds (FCT, Fundação para a Ciência e Tecnologia) through Projects EXCL/QEQ-COM/ 0394/2012, EXCL-II/QEQ-COM/0394/2012, and Pest-C/EQB/LA0006/2013. NFB would like to thank the Fundação para a Ciência e a Tecnologia (FCT) for her IF starting grant (IF/01355/2014).

PY - 2016/9/5

Y1 - 2016/9/5

N2 - Cyclic peptides are a class of compounds with high therapeutic potential, possessing bioactivities including anti-tumour and anti-viral (including anti-HIV). Despite their desirability, efficient design and production of these compounds has not yet been achieved. The catalytic mechanism of patellamide macrocyclization by PatG macrocyclase domain has been investigated using computational methods. We applied a quantum mechanics/molecular mechanics (QM/MM) methodology, specifically ONIOM(M06/6-311++G(2d,2p):ff94//B3LYP/6-31G(d):ff94). The mechanism proposed here begins with a proton transfer from Ser783 to His 618 and from the latter to Asp548. Nucleophilic attack of Ser783 to the substrate leads on to the formation of an acyl-enzyme covalent complex. The leaving group (AYDG) of the substrate is protonated by the substrate’s N-terminus leading to the breakage of the P1-P1’ bond. Finally, the substrate’s N-terminus attacks the P1 residue, decomposing the acyl-enzyme complex forming the macrocycle. We found that the formation and decomposition of the acyl-enzyme complex have the highest activation free energies (21.1 kcal.mol-1 and 19.8 kcal.mol-1 respectively), typical of serine proteases. Understanding the mechanism behind the macrocyclization of patellamides will be important to the application of the enzymes in the pharmaceutical and biotechnological industries.

AB - Cyclic peptides are a class of compounds with high therapeutic potential, possessing bioactivities including anti-tumour and anti-viral (including anti-HIV). Despite their desirability, efficient design and production of these compounds has not yet been achieved. The catalytic mechanism of patellamide macrocyclization by PatG macrocyclase domain has been investigated using computational methods. We applied a quantum mechanics/molecular mechanics (QM/MM) methodology, specifically ONIOM(M06/6-311++G(2d,2p):ff94//B3LYP/6-31G(d):ff94). The mechanism proposed here begins with a proton transfer from Ser783 to His 618 and from the latter to Asp548. Nucleophilic attack of Ser783 to the substrate leads on to the formation of an acyl-enzyme covalent complex. The leaving group (AYDG) of the substrate is protonated by the substrate’s N-terminus leading to the breakage of the P1-P1’ bond. Finally, the substrate’s N-terminus attacks the P1 residue, decomposing the acyl-enzyme complex forming the macrocycle. We found that the formation and decomposition of the acyl-enzyme complex have the highest activation free energies (21.1 kcal.mol-1 and 19.8 kcal.mol-1 respectively), typical of serine proteases. Understanding the mechanism behind the macrocyclization of patellamides will be important to the application of the enzymes in the pharmaceutical and biotechnological industries.

KW - patellamide

KW - macrocyclization

KW - QM/MM

KW - ONIOM

KW - catalytic mechanism

U2 - 10.1002/chem.201601670

DO - 10.1002/chem.201601670

M3 - Article

VL - 22

SP - 13089

EP - 13097

JO - Chemistry : a European Journal

JF - Chemistry : a European Journal

SN - 0947-6539

IS - 37

ER -