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Shao H, Adebomi V, Bruce A, Raj M, Houk KN. Intramolecular Hydrogen Bonding Enables a Zwitterionic Mechanism for Macrocyclic Peptide Formation: Computational Mechanistic Studies of CyClick Chemistry. Angew Chem Int Ed Engl 2023; 62:e202307210. [PMID: 37475575 PMCID: PMC10592271 DOI: 10.1002/anie.202307210] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 07/19/2023] [Accepted: 07/20/2023] [Indexed: 07/22/2023]
Abstract
Macrocyclic peptides have become increasingly important in the pharmaceutical industry. We present a detailed computational investigation of the reaction mechanism of the recently developed "CyClick" chemistry to selectively form imidazolidinone cyclic peptides from linear peptide aldehydes, without using catalysts or directing groups (Angew. Chem. Int. Ed. 2019, 58, 19073-19080). We conducted computational mechanistic to investigate the effects of intramolecular hydrogen bonds (IMHBs) in promoting a kinetically facile zwitterionic mechanism in "CyClick" of pentapeptide aldehyde AFGPA. Our DFT calculations highlighted the importance of IMHB in pre-organization of the resting state, stabilization of the zwitterion intermediate, and the control of the product stereoselectivity. Furthermore, we have also identified that the low ring strain energy promotes the "CyClick" of hexapeptide aldehyde AAGPFA to form a thermodynamically more stable 15+5 imidazolidinone cyclic peptide product. In contrast, large ring strain energy suppresses "CyClick" reactivity of tetra peptide aldehyde AFPA from forming the 9+5 imidazolidinone cyclic peptide product.
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Affiliation(s)
- Huiling Shao
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095, USA
| | - Victor Adebomi
- Department of Chemistry, Emory University, Atlanta, GA, 30322, USA
| | - Angele Bruce
- Department of Chemistry, Emory University, Atlanta, GA, 30322, USA
| | - Monika Raj
- Department of Chemistry, Emory University, Atlanta, GA, 30322, USA
| | - Kendall N Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, 90095, USA
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2
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Carlini L, Chiarinelli J, Mattioli G, Castrovilli MC, Valentini V, De Stefanis A, Bauer EM, Bolognesi P, Avaldi L. Insights into the Thermally Activated Cyclization Mechanism in a Linear Phenylalanine-Alanine Dipeptide. J Phys Chem B 2022; 126:2968-2978. [PMID: 35438499 PMCID: PMC9059117 DOI: 10.1021/acs.jpcb.1c10736] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 03/31/2022] [Indexed: 11/29/2022]
Abstract
Dipeptides, the prototype peptides, exist in both linear (l-) and cyclo (c-) structures. Since the first mass spectrometry experiments, it has been observed that some l-structures may turn into the cyclo ones, likely via a temperature-induced process. In this work, combining several different experimental techniques (mass spectrometry, infrared and Raman spectroscopy, and thermogravimetric analysis) with tight-binding and ab initio simulations, we provide evidence that, in the case of l-phenylalanyl-l-alanine, an irreversible cyclization mechanism, catalyzed by water and driven by temperature, occurs in the condensed phase. This process can be considered as a very efficient strategy to improve dipeptide stability by turning the comparatively fragile linear structure into the robust and more stable cyclic one. This mechanism may have played a role in prebiotic chemistry and can be further exploited in the preparation of nanomaterials and drugs.
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Affiliation(s)
- Laura Carlini
- CNR-Istituto di Struttura
della Materia (CNR-ISM), Area della Ricerca di Roma 1, Monterotondo
Scalo 00015, Italy
| | - Jacopo Chiarinelli
- CNR-Istituto di Struttura
della Materia (CNR-ISM), Area della Ricerca di Roma 1, Monterotondo
Scalo 00015, Italy
| | - Giuseppe Mattioli
- CNR-Istituto di Struttura
della Materia (CNR-ISM), Area della Ricerca di Roma 1, Monterotondo
Scalo 00015, Italy
| | - Mattea Carmen Castrovilli
- CNR-Istituto di Struttura
della Materia (CNR-ISM), Area della Ricerca di Roma 1, Monterotondo
Scalo 00015, Italy
| | - Veronica Valentini
- CNR-Istituto di Struttura
della Materia (CNR-ISM), Area della Ricerca di Roma 1, Monterotondo
Scalo 00015, Italy
| | - Adriana De Stefanis
- CNR-Istituto di Struttura
della Materia (CNR-ISM), Area della Ricerca di Roma 1, Monterotondo
Scalo 00015, Italy
| | - Elvira Maria Bauer
- CNR-Istituto di Struttura
della Materia (CNR-ISM), Area della Ricerca di Roma 1, Monterotondo
Scalo 00015, Italy
| | - Paola Bolognesi
- CNR-Istituto di Struttura
della Materia (CNR-ISM), Area della Ricerca di Roma 1, Monterotondo
Scalo 00015, Italy
| | - Lorenzo Avaldi
- CNR-Istituto di Struttura
della Materia (CNR-ISM), Area della Ricerca di Roma 1, Monterotondo
Scalo 00015, Italy
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3
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Bojarska J, Mieczkowski A, Ziora ZM, Skwarczynski M, Toth I, Shalash AO, Parang K, El-Mowafi SA, Mohammed EHM, Elnagdy S, AlKhazindar M, Wolf WM. Cyclic Dipeptides: The Biological and Structural Landscape with Special Focus on the Anti-Cancer Proline-Based Scaffold. Biomolecules 2021; 11:1515. [PMID: 34680148 PMCID: PMC8533947 DOI: 10.3390/biom11101515] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 10/11/2021] [Accepted: 10/12/2021] [Indexed: 12/12/2022] Open
Abstract
Cyclic dipeptides, also know as diketopiperazines (DKP), the simplest cyclic forms of peptides widespread in nature, are unsurpassed in their structural and bio-functional diversity. DKPs, especially those containing proline, due to their unique features such as, inter alia, extra-rigid conformation, high resistance to enzyme degradation, increased cell permeability, and expandable ability to bind a diverse of targets with better affinity, have emerged in the last years as biologically pre-validated platforms for the drug discovery. Recent advances have revealed their enormous potential in the development of next-generation theranostics, smart delivery systems, and biomaterials. Here, we present an updated review on the biological and structural profile of these appealing biomolecules, with a particular emphasis on those with anticancer properties, since cancers are the main cause of death all over the world. Additionally, we provide a consideration on supramolecular structuring and synthons, based on the proline-based DKP privileged scaffold, for inspiration in the design of compound libraries in search of ideal ligands, innovative self-assembled nanomaterials, and bio-functional architectures.
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Affiliation(s)
- Joanna Bojarska
- Faculty of Chemistry, Institute of General & Inorganic Chemistry, Technical University of Lodz, 90-924 Lodz, Poland;
| | - Adam Mieczkowski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland;
| | - Zyta M. Ziora
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072, Australia; (Z.M.Z.); (I.T.)
| | - Mariusz Skwarczynski
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia; (M.S.); (A.O.S.)
| | - Istvan Toth
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072, Australia; (Z.M.Z.); (I.T.)
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia; (M.S.); (A.O.S.)
- School of Pharmacy, The University of Queensland, Woolloongabba, QLD 4102, Australia
| | - Ahmed O. Shalash
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia; (M.S.); (A.O.S.)
| | - Keykavous Parang
- Center for Targeted Drug Delivery, Department of Biomedical and Pharmaceutical Sciences, Harry and Diane Rinker Health Science Campus, School of Pharmacy, Chapman University, Irvine, CA 92618, USA; (K.P.); (S.A.E.-M.); (E.H.M.M.)
| | - Shaima A. El-Mowafi
- Center for Targeted Drug Delivery, Department of Biomedical and Pharmaceutical Sciences, Harry and Diane Rinker Health Science Campus, School of Pharmacy, Chapman University, Irvine, CA 92618, USA; (K.P.); (S.A.E.-M.); (E.H.M.M.)
| | - Eman H. M. Mohammed
- Center for Targeted Drug Delivery, Department of Biomedical and Pharmaceutical Sciences, Harry and Diane Rinker Health Science Campus, School of Pharmacy, Chapman University, Irvine, CA 92618, USA; (K.P.); (S.A.E.-M.); (E.H.M.M.)
| | - Sherif Elnagdy
- Botany Department, Faculty of Science, Cairo University, Giza 12613, Egypt; (S.E.); (M.A.)
| | - Maha AlKhazindar
- Botany Department, Faculty of Science, Cairo University, Giza 12613, Egypt; (S.E.); (M.A.)
| | - Wojciech M. Wolf
- Faculty of Chemistry, Institute of General & Inorganic Chemistry, Technical University of Lodz, 90-924 Lodz, Poland;
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Hao Q, He N, Wang Y, Yang X, Wang Y, Zhu Y, Qu L. Theoretical insights into phosphine‐catalyzed [4 + 2] annulation of allenoates with thiazolone‐derived alkenes. J PHYS ORG CHEM 2021. [DOI: 10.1002/poc.4215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Qiqi Hao
- Green Catalysis Center, and College of Chemistry Zhengzhou University Zhengzhou China
| | - Nan He
- Green Catalysis Center, and College of Chemistry Zhengzhou University Zhengzhou China
| | - Yi Wang
- International Education College Zhengzhou University of Light Industry Zhengzhou China
| | - Xiaoyan Yang
- Green Catalysis Center, and College of Chemistry Zhengzhou University Zhengzhou China
| | - Yonghuan Wang
- Green Catalysis Center, and College of Chemistry Zhengzhou University Zhengzhou China
| | - Yanyan Zhu
- Green Catalysis Center, and College of Chemistry Zhengzhou University Zhengzhou China
| | - Lingbo Qu
- Green Catalysis Center, and College of Chemistry Zhengzhou University Zhengzhou China
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Achour S, Hosni Z, Darghouthi S, Syme C. Assisted dipeptide bond formation: glycine as a case study. Heliyon 2021; 7:e07276. [PMID: 34195408 PMCID: PMC8225972 DOI: 10.1016/j.heliyon.2021.e07276] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 03/09/2021] [Accepted: 06/07/2021] [Indexed: 11/17/2022] Open
Abstract
Peptide bond formation is a crucial chemical process that dominates most biological mechanisms and is claimed to be a governing factor in the origin of life. Dipeptides made from glycine are studied computationally via Density Functional Theory (DFT) using two different basis sets. This reaction was investigated from both a thermodynamic and kinetic point of view. The effect of explicit assistance via the introduction of discrete solvent molecules was investigated. Water, methanol, and cyclohexane were all employed as solvent media in addition to gas to investigate their effects on the mechanism of peptide bond formation. This computational investigation revealed that methanol is slightly better than water to leverage peptide bond formation both kinetically and thermodynamically, while cyclohexane, a non-polar and non-protic solvent, is the least effective after gas as a medium of solvation. Energetic results in the gas environment are very close to those obtained in polar and protic solvents, suggesting that peptide bonds can be formed under interstellar conditions.
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Affiliation(s)
- Sofiene Achour
- University of Tunis El Manar, Research Unity of Modeling in Fundamental Sciences and Didactics, Team of Theoretical Chemistry and Reactivity, BP 254, El Manar 2, 2096, Tunisia
| | - Zied Hosni
- Sheffield Chemoinformatics Research Group, Information School, University of Sheffield, Regent Court, 211 Portobello, S1 4DP, Sheffield, UK
| | - Sarra Darghouthi
- University of Tunis El Manar, Research Unity of Modeling in Fundamental Sciences and Didactics, Team of Theoretical Chemistry and Reactivity, BP 254, El Manar 2, 2096, Tunisia
| | - Christopher Syme
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, Garscube Campus, 464 Bearsden Road, Glasgow, G61 1QH, Scotland, UK
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Sargolzaei M, Nikoofard H, Jorabchi MN. Quantum-Chemical ab initio Study of Side Chain pKa of Linear and Cyclic Lysine Dipeptides. JOURNAL OF COMPUTATIONAL BIOPHYSICS AND CHEMISTRY 2021. [DOI: 10.1142/s2737416520420028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Cyclic dipeptides show interesting biological activities such as antitumor, antiviral and so on. In biological systems, the bioavailability of drugs is determined by several parameters such as pKa values. In this study, we used DFT and thermodynamics cycle to determine pKa value of side chain of lysine in linear and cyclic dipeptides. All considered dipeptides were optimized using B3LYP and RMSD tool was used to compare the optimized structures. The calculated pKa values were compared with the available experimental data. Our results show that pKa of side chain of lysine increases for cyclic dipeptides compared to the linear ones. To justify the reason of increasing of pKa of cyclic dipeptides, we used NBO and AIM analyses. The analyses showed that a hydrogen bond in cyclic lysine dipeptides is responsible for increasing of pKa.
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Affiliation(s)
- Mohsen Sargolzaei
- Faculty of Chemistry, Shahrood University of Technology, Shahrood, Iran
| | - Hossein Nikoofard
- Faculty of Chemistry, Shahrood University of Technology, Shahrood, Iran
| | - Majid Namayandeh Jorabchi
- University of Rostock, Institute of Chemistry, Physical and Theoretical Chemistry, Albert-Einstein-Straße 21, 18059 Rostock, Germany
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7
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Yadav S, Springborg M, Singhal S, Molayem M, Goel N. Mechanistic Details and Conformational Behavior of Selective Peptide Linkage Facilitated by Au nClusters. ChemistrySelect 2020. [DOI: 10.1002/slct.202001564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Sarita Yadav
- Theoretical and Computational Chemistry Group Department of Chemistry Centre of Advanced Studies in Chemistry Panjab University Chandigarh 160014 India
| | - Michael Springborg
- Physical and Theoretical Chemistry University of Saarland Saarbrücken Germany
- School of Materials Science and Engineering Tianjin University Tianjin 300072 China
| | - Sonal Singhal
- Theoretical and Computational Chemistry Group Department of Chemistry Centre of Advanced Studies in Chemistry Panjab University Chandigarh 160014 India
| | - Mohammad Molayem
- Physical and Theoretical Chemistry University of Saarland Saarbrücken Germany
| | - Neetu Goel
- Theoretical and Computational Chemistry Group Department of Chemistry Centre of Advanced Studies in Chemistry Panjab University Chandigarh 160014 India
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8
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Sargolzaei M, Jorabchi MN. Cyclization Effect on pKa of the Side Chain of Aspartic Acid in Dipeptides: A DFT Study. LETT ORG CHEM 2020. [DOI: 10.2174/1570178616666191019124709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Cyclic dipeptides are very important compounds that have a wide range of applications in
pharmaceutical chemistry and life sciences. In the current work, the acidity of the side chain of aspartic
acid was calculated for various linear and a cyclic dipeptide. pKa values were derived using the thermodynamics
cycle and DFT/B3LYP approach. The obtained pKa values show strong acidity for cyclic
with respect to linear dipeptides. We found an intramolecular hydrogen bond in cyclic dipeptide structure,
which can be used to justify the increasing acidity of the side chain of Asp as compared to linear
structures.
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Affiliation(s)
- Mohsen Sargolzaei
- Department of Chemistry, Shahrood University of Technology, Shahrood, Iran
| | - Majid Namayandeh Jorabchi
- University of Rostock, Institute of Chemistry, Physical and Theoretical Chemistry, Albert-Einstein-Straße 21, 18059 Rostock, Germany
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9
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He N, Zhu Z, Li F, Zhu Y, Qu L, Chen H. Theoretical understanding mechanisms and stereoselectivities of [2+2] cycloaddition of ketenes with ketimines catalyzed by bifunctional N-heterocyclic carbene. Struct Chem 2020. [DOI: 10.1007/s11224-019-01389-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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10
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Otsuka Y, Arita H, Sakaji M, Yamamoto K, Kashiwagi T, Shimamura T, Ukeda H. Investigation of the formation mechanism of proline-containing cyclic dipeptide from the linear peptide. Biosci Biotechnol Biochem 2019; 83:2355-2363. [PMID: 31462170 DOI: 10.1080/09168451.2019.1659718] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Cyclic dipeptides, 2,5-diketopiperazines (DKPs), are well-known bioactive and taste compounds in food. DKPs have also been reported in various foods and particularly, Pro-containing DKPs (cyclo(-X-Pro)) are more predominant in heated and fermented foods than other type of DKPs. However, the mechanism underlying the preferential formation of Pro-containing DKPs in food remains uncertain. Herein, we attempted to elucidate the effects of reaction conditions and the mechanism of DKPs formation. The reaction conditions (heating time, heating temperature, and pH) and amino acid sequence of the linear peptides were important for the DKPs formation from linear peptides. In addition, Pro-containing DKPs were significantly formed from linear peptides with the second amino acid from the N-terminus being Pro. Based on these results, the underlying mechanism of the enrichment of Pro-containing DKPs in foods was proposed.
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Affiliation(s)
- Yuuki Otsuka
- Faculty of Agriculture and Marine Science, Kochi University, Kochi, Japan
| | - Hikaru Arita
- Faculty of Agriculture and Marine Science, Kochi University, Kochi, Japan
| | - Michio Sakaji
- Faculty of Agriculture and Marine Science, Kochi University, Kochi, Japan
| | - Kenji Yamamoto
- Research Strategy Planning Department, Suntory Holdings Ltd, Tokyo, Japan
| | - Takehiro Kashiwagi
- Faculty of Agriculture and Marine Science, Kochi University, Kochi, Japan
| | - Tomoko Shimamura
- Faculty of Agriculture and Marine Science, Kochi University, Kochi, Japan
| | - Hiroyuki Ukeda
- Center for Regional Sustainability and Innovation, Kochi University, Kochi, Japan
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Zhou ZY, Yuan J, Pan Q, Mo XM, Xie YL, Yin F, Li Z, Wong NK. Computational elucidation of the binding mechanisms of curcumin analogues as bacterial RecA inhibitors. RSC Adv 2019; 9:19869-19881. [PMID: 35519399 PMCID: PMC9065326 DOI: 10.1039/c9ra00064j] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 06/04/2019] [Indexed: 12/27/2022] Open
Abstract
Antimicrobial resistance (AMR) presents as a serious threat to global public health, which urgently demands action to develop alternative antimicrobial strategies with minimized selective pressure. The bacterial SOS response regulator RecA has emerged as a promising target in the exploration of new classes of antibiotic adjuvants, as RecA has been implicated in bacterial mutagenesis and thus AMR development through its critical roles in error-prone DNA repair. The natural product curcumin has been reported to be an effective RecA inhibitor in several Gram-negative bacteria, but details on the underlying mechanisms are wanting. In order to bridge the gap in how curcumin operates as a RecA inhibitor, we used computational approaches to model interactions between RecA protein and curcumin analogues. We first identified potential binding sites on E. coli RecA protein and classified them into four major binding pockets based on biological literature and computational findings from multiple in silico calculations. In docking analysis, curcumin-thalidomide hybrids were predicted to be superior binders of RecA compared with bis-(arylmethylidene)acetone curcumin analogues, which was further confirmed by MMGBSA calculations. Overall, this work provides mechanistic insights into bacterial RecA protein as a target for curcumin-like compounds and offers a theoretical basis for rational design and development of future antibiotic adjuvants.
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Affiliation(s)
- Zi-Yuan Zhou
- Department of Infectious Diseases, Shenzhen Third People's Hospital, The Second Hospital Affiliated to Southern University of Science and Technology Shenzhen 518112 China
- Department of Chemical Biology, School of Chemical Biology and Biotechnology, Shenzhen Graduate School of Peking University Shenzhen 518055 China
| | - Jing Yuan
- Department of Infectious Diseases, Shenzhen Third People's Hospital, The Second Hospital Affiliated to Southern University of Science and Technology Shenzhen 518112 China
| | - Qing Pan
- Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanology, Shenzhen University Shenzhen 518055 China
| | - Xiao-Mei Mo
- Department of Infectious Diseases, Shenzhen Third People's Hospital, The Second Hospital Affiliated to Southern University of Science and Technology Shenzhen 518112 China
| | - Yong-Li Xie
- Department of Infectious Diseases, Shenzhen Third People's Hospital, The Second Hospital Affiliated to Southern University of Science and Technology Shenzhen 518112 China
| | - Feng Yin
- Department of Chemical Biology, School of Chemical Biology and Biotechnology, Shenzhen Graduate School of Peking University Shenzhen 518055 China
| | - Zigang Li
- Department of Chemical Biology, School of Chemical Biology and Biotechnology, Shenzhen Graduate School of Peking University Shenzhen 518055 China
| | - Nai-Kei Wong
- Department of Infectious Diseases, Shenzhen Third People's Hospital, The Second Hospital Affiliated to Southern University of Science and Technology Shenzhen 518112 China
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12
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Freza S. Water-assisted peptide bond formation between two double amino acid molecules in the gas phase. J Mol Model 2019; 25:184. [PMID: 31175466 DOI: 10.1007/s00894-019-4081-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 05/28/2019] [Indexed: 11/27/2022]
Abstract
The gas phase mechanism of the peptide bond formation between two double amino acid (DAA) molecules described by the (NH2)2C(COOH)2 formula is investigated in the presence of a water molecule. Formations of trans and cis DAA-DAA dipeptide products along both concerted and stepwise mechanisms have been studied at the CCSD(T)/aug-cc-pVDZ//MP2/aug-cc-pVDZ level. The results indicate that the activation energy barriers estimated for the water-assisted mechanisms are significantly reduced in comparison to the corresponding uncatalyzed reactions. The trans DAA-DAA isomer is expected to dominate in the final product due to its larger stability compared to the cis DAA-DAA product.
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Affiliation(s)
- Sylwia Freza
- Laboratory of Quantum Chemistry, Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308, Gdańsk, Poland.
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13
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Belding L, Zaretsky S, Yudin AK, Dudding T. A Mechanistic Model for the Aziridine Aldehyde-Driven Macrocyclization of Peptides. J Org Chem 2018; 83:9119-9124. [PMID: 29966423 DOI: 10.1021/acs.joc.8b01198] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Aziridine aldehyde-driven macrocyclization of peptides is a powerful tool for the construction of biologically active macrocycles. While this process has been used to generate diverse collections of cyclic molecules, its mechanistic underpinnings have remained unclear. To enable progress in this area we have carried out a mechanistic study, which suggests that the cyclization owes its efficiency to a combination of electrostatic attraction between the termini of a nitrilium ion intermediate and intramolecular hydrogen bonding. Our model adequately explains the experimentally observed trends, including diastereoselectivity, and should facilitate the development of other macrocyclization reactions.
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Affiliation(s)
- Lee Belding
- Department of Chemistry , Brock University , St. Catharines , Ontario L2S 3A1 , Canada
| | - Serge Zaretsky
- Department of Chemistry , University of Toronto , Toronto , Ontario M5S 2J7 , Canada
| | - Andrei K Yudin
- Department of Chemistry , University of Toronto , Toronto , Ontario M5S 2J7 , Canada
| | - Travis Dudding
- Department of Chemistry , Brock University , St. Catharines , Ontario L2S 3A1 , Canada
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15
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Interplay of thermochemistry and Structural Chemistry, the journal (volume 27, 2016, issues 3–4) and the discipline. Struct Chem 2017. [DOI: 10.1007/s11224-017-0983-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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