1
|
Dahal A, Subramanian V, Shrestha P, Liu D, Gauthier T, Jois S. Conformationally constrained cyclic grafted peptidomimetics targeting protein-protein interactions. Pept Sci (Hoboken) 2023; 115:e24328. [PMID: 38188985 PMCID: PMC10769001 DOI: 10.1002/pep2.24328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 07/03/2023] [Indexed: 01/09/2024]
Abstract
Sunflower trypsin inhibitor-1 (SFTI-1) structure is used for designing grafted peptides as a possible therapeutic agent. The grafted peptide exhibits multiple conformations in solution due to the presence of proline in the structure of the peptide. To lock the grafted peptide into a major conformation in solution, a dibenzofuran moiety (DBF) was incorporated in the peptide backbone structure, replacing the Pro-Pro sequence. NMR studies indicated a major conformation of the grafted peptide in solution. Detailed structural studies suggested that SFTI-DBF adopts a twisted beta-strand structure in solution. The surface plasmon resonance analysis showed that SFTI-DBF binds to CD58 protein. A model for the protein-SFTI-DBF complex was proposed based on docking studies. These studies suggested that SFTI-1 grafted peptide can be used to design stable peptides for therapeutic purposes by grafting organic functional groups and amino acids. However, when a similar strategy was used with another grafted peptide, the resulting peptide did not produce a single major conformation, and its biological activity was lost. Thus, conformational constraints depend on the sequence of amino acids used for SFTI-1 grafting.
Collapse
Affiliation(s)
- Achyut Dahal
- School of Basic Pharmaceutical and Toxicological Sciences, College of Pharmacy, University of Louisiana Monroe, Monroe LA 71201
| | - Vivekanandan Subramanian
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY 40536
| | - Prajesh Shrestha
- School of Basic Pharmaceutical and Toxicological Sciences, College of Pharmacy, University of Louisiana Monroe, Monroe LA 71201
- Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge 70803
| | - Dong Liu
- AgCenter Biotechnology Laboratory, LSU Agricultural Center, Baton Rouge, LA, 70803
| | - Ted Gauthier
- AgCenter Biotechnology Laboratory, LSU Agricultural Center, Baton Rouge, LA, 70803
| | - Seetharama Jois
- School of Basic Pharmaceutical and Toxicological Sciences, College of Pharmacy, University of Louisiana Monroe, Monroe LA 71201
- Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge 70803
| |
Collapse
|
2
|
Singh R, Horsten T, Prakash R, Dey S, Dehaen W. Application of the Meerwein reaction of 1,4-benzoquinone to a metal-free synthesis of benzofuropyridine analogues. Beilstein J Org Chem 2021; 17:977-982. [PMID: 33981368 PMCID: PMC8093549 DOI: 10.3762/bjoc.17.79] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 04/20/2021] [Indexed: 11/23/2022] Open
Abstract
Several new heterocyclic systems based on a hydroxybenzofuro[2,3-b]pyridine building block were prepared. This benzofuropyridine is easily available from the Meerwein reaction of benzoquinone and a heterocyclic diazonium salt, followed by reduction and cyclization. Electrophilic substitution and further condensations give polycyclic systems, including oxazolo- and chromeno-fused analogues.
Collapse
Affiliation(s)
- Rashmi Singh
- Department of Chemistry, Indian Institute of Technology (Indian School of Mines) Dhanbad, Dhanbad 826004, India.,Department of Molecular Design and Synthesis, Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001 Leuven, Belgium
| | - Tomas Horsten
- Department of Molecular Design and Synthesis, Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001 Leuven, Belgium
| | - Rashmi Prakash
- Department of Molecular Design and Synthesis, Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001 Leuven, Belgium
| | - Swapan Dey
- Department of Chemistry, Indian Institute of Technology (Indian School of Mines) Dhanbad, Dhanbad 826004, India
| | - Wim Dehaen
- Department of Molecular Design and Synthesis, Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001 Leuven, Belgium
| |
Collapse
|
3
|
Jiang P, Chen S, Xia Y, Zhang Q, Deng GJ. Access to Dibenzofurans through Dimerization/Trimerization of Cyclohexanones Followed by Dehydroaromatization. Org Lett 2020; 22:8076-8081. [DOI: 10.1021/acs.orglett.0c03023] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Pingyu Jiang
- Key Laboratory for Green Organic Synthesis and Application of Hunan Province, Key Laboratory of Environmentally Friendly Chemistry and Application of Ministry of Education, College of Chemistry, Xiangtan University, Xiangtan 411105, China
| | - Shanping Chen
- Key Laboratory for Green Organic Synthesis and Application of Hunan Province, Key Laboratory of Environmentally Friendly Chemistry and Application of Ministry of Education, College of Chemistry, Xiangtan University, Xiangtan 411105, China
| | - Yi Xia
- Key Laboratory for Green Organic Synthesis and Application of Hunan Province, Key Laboratory of Environmentally Friendly Chemistry and Application of Ministry of Education, College of Chemistry, Xiangtan University, Xiangtan 411105, China
| | - Qingqing Zhang
- Key Laboratory for Green Organic Synthesis and Application of Hunan Province, Key Laboratory of Environmentally Friendly Chemistry and Application of Ministry of Education, College of Chemistry, Xiangtan University, Xiangtan 411105, China
| | - Guo-Jun Deng
- Key Laboratory for Green Organic Synthesis and Application of Hunan Province, Key Laboratory of Environmentally Friendly Chemistry and Application of Ministry of Education, College of Chemistry, Xiangtan University, Xiangtan 411105, China
| |
Collapse
|
4
|
Dastoorani P, Khalilzadeh MA, Khaleghi F, Maghsoodlou MT, Kaminsky W, Shokuhi Rad A. Experimental and computational studies on the synthesis of diastereoselective natural-based Meldrum spiro dibenzofuran derivatives. NEW J CHEM 2019. [DOI: 10.1039/c9nj00766k] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Herein, a novel route to achieve chiral Meldrum spiro dibenzofuran derivatives was developed, which involved a 2,2-dimethyl-1,3-dioxane-4,6-dione (Meldrum's acid)-mediated Knoevenagel reaction of substituted aryl halides, followed by a Diels–Alder reaction with euparin as a natural compound.
Collapse
Affiliation(s)
| | - Mohammad A. Khalilzadeh
- Department of Chemistry
- College of Natural Resources
- North Carolina State University
- Raleigh
- USA
| | - Fatemeh Khaleghi
- The Health of Plant and Livestock Products Research Center
- Mazandaran University of Medical Sciences
- Sari
- Iran
| | | | | | - Ali Shokuhi Rad
- Department of Chemical Engineering
- Qaemshahr Branch
- Islamic Azad University
- Qaemshahr
- Iran
| |
Collapse
|
5
|
Sun J, Jiang W, Yan CG. Convenient construction of dibenzo[b,d]furanes and 2,6-diaryl-4-(2-hydroxyphenyl)pyridines via domino reaction of pyridinium ylides with 2-aryl-3-nitrochromenes. Org Chem Front 2019. [DOI: 10.1039/c9qo00079h] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The DBU promoted domino annulation reaction of 2-aryl-3-nitrochromenes with two molecular 4-(N,N-dimethylamino)-1-phenacylpyridinium bromides in DMF resulted in unprecedented 1-benzoyl-2,4-diaryldibenzo[b,d]furane derivatives in good yields.
Collapse
Affiliation(s)
- Jing Sun
- College of Chemistry & Chemical Engineering
- Yangzhou University
- Yangzhou 225002
- China
| | - Wang Jiang
- College of Chemistry & Chemical Engineering
- Yangzhou University
- Yangzhou 225002
- China
| | - Chao-Guo Yan
- College of Chemistry & Chemical Engineering
- Yangzhou University
- Yangzhou 225002
- China
| |
Collapse
|
6
|
Li J, Xu QN, Wang ZB, Li Y, Liu L. Synthesis of Dibenzofurans from Cyclic Diaryliodonium Triflates and Water via Oxygen-Iodine Exchange Approach. ACS OMEGA 2018; 3:12923-12929. [PMID: 31458015 PMCID: PMC6644658 DOI: 10.1021/acsomega.8b02345] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 09/25/2018] [Indexed: 05/13/2023]
Abstract
An efficient synthesis of a variety of dibenzofuran derivatives via Cu-catalyzed cyclization diaryliodonium salts in water is achieved. Various dibenzofuran derivatives could be obtained in good to excellent yields via this oxygen-iodine exchange approach. A concise synthesis of organic semiconducting material molecule has been achieved using this method.
Collapse
Affiliation(s)
- Jian Li
- School
of Pharmaceutical Engineering & Life Sciences and School of Petrochemical
Engineering, Changzhou University, Changzhou 213164, China
- E-mail:
| | - Qiu-Neng Xu
- School
of Pharmaceutical Engineering & Life Sciences and School of Petrochemical
Engineering, Changzhou University, Changzhou 213164, China
| | - Zheng-Bing Wang
- School
of Pharmaceutical Engineering & Life Sciences and School of Petrochemical
Engineering, Changzhou University, Changzhou 213164, China
| | - Yang Li
- School
of Pharmaceutical Engineering & Life Sciences and School of Petrochemical
Engineering, Changzhou University, Changzhou 213164, China
| | - Li Liu
- School
of Pharmaceutical Engineering & Life Sciences and School of Petrochemical
Engineering, Changzhou University, Changzhou 213164, China
| |
Collapse
|
7
|
Lahiri P, Verma H, Ravikumar A, Chatterjee J. Protein stabilization by tuning the steric restraint at the reverse turn. Chem Sci 2018; 9:4600-4609. [PMID: 29899953 PMCID: PMC5969505 DOI: 10.1039/c7sc05163h] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 04/24/2018] [Indexed: 11/23/2022] Open
Abstract
The incorporation of pseudoallylic strain by N-methylation at the solvent exposed loop in proteins leads to a stark increase in their thermodynamic stability that can be tuned by altering the amino acid composition.
Reverse turns are solvent-exposed motifs in proteins that are crucial in nucleating β-sheets and drive the protein folding. The solvent-exposed nature makes reverse turns more amenable to chemical modifications than α-helices or β-sheets towards modulating the stability of re-engineered proteins. Here, we utilize van der Waals repulsive forces in tuning the steric restraint at the reverse turn. The steric restraint induced upon N-methylation of the i+1–i+2 amide bond at the reverse turn results in well-folded and stable β-sheets in aqueous solution at room temperature. The developed superactive turn inducing motif is tolerant to a wide variety of functional groups present on coded amino acids making the designed turn fully compatible with bioactive loops in proteins. We demonstrate that the steric restraint and the functional groups at the reverse turn act in synergy to modulate the folding of re-engineered β-sheets. Introduction of the turn motifs onto a three-stranded β-sheet protein, Pin 1 WW domain, resulted in various analogs showing a cooperative two-state transition with thermal stability (TM) ranging from 62 °C to 82 °C. Despite modulating the stability of Pin 1 variants by ∼2.8 kcal mol–1 (ΔΔGf), the native fold in all the protein variants was found to be unperturbed. This structural stability is brought about by conformational preorganization at the engineered reverse turn that results in strong intramolecular hydrogen bonds along the three dimensional structure of the protein. Thus, this simple loop engineering strategy via two amino acid substitution provides us a “toolkit” to modulate the stability of β-sheet containing peptides and proteins in aqueous solution that will greatly expand the scope of de novo protein and foldamer design.
Collapse
Affiliation(s)
- Priyanka Lahiri
- Molecular Biophysics Unit , Indian Institute of Science , Bangalore 560012 , India .
| | - Hitesh Verma
- Molecular Biophysics Unit , Indian Institute of Science , Bangalore 560012 , India .
| | - Ashraya Ravikumar
- Molecular Biophysics Unit , Indian Institute of Science , Bangalore 560012 , India .
| | - Jayanta Chatterjee
- Molecular Biophysics Unit , Indian Institute of Science , Bangalore 560012 , India .
| |
Collapse
|
8
|
Ardejani MS, Powers ET, Kelly JW. Using Cooperatively Folded Peptides To Measure Interaction Energies and Conformational Propensities. Acc Chem Res 2017; 50:1875-1882. [PMID: 28723063 DOI: 10.1021/acs.accounts.7b00195] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The rates and equilibria of the folding of biopolymers are determined by the conformational preferences of the subunits that make up the sequence of the biopolymer and by the interactions that are formed in the folded state in aqueous solution. Because of the centrality of these processes to life, quantifying conformational propensities and interaction strengths is vitally important to understanding biology. In this Account, we describe our use of peptide model systems that fold cooperatively yet are small enough to be chemically synthesized to measure such quantities. The necessary measurements are made by perturbing an interaction or conformation of interest by mutation and measuring the difference between the folding free energies of the wild type (in which the interaction or conformation is undisturbed) and the mutant model peptides (in which the interaction has been eliminated or the conformational propensities modified). With the proper controls and provided that the peptide model system in question folds via a two-state process, these folding free energy differences can be accurate measures of interaction strengths or conformational propensities. This method has the advantage of having high sensitivity and high dynamic range because the energies of interest are coupled to folding free energies, which can be measured with precisions on the order of a few tenths of a kilocalorie by well-established biophysical methods, like chaotrope or thermal denaturation studies monitored by fluorescence or circular dichroism. In addition, because the model peptides can be chemically synthesized, the full arsenal of natural and unnatural amino acids can be used to tune perturbations to be as drastic or subtle as desired. This feature is particularly noteworthy because it enables the use of analytical tools developed for physical organic chemistry, especially linear free energy relationships, to decompose interaction energies into their component parts to obtain a deeper understanding of the forces that drive interactions in biopolymers. We have used this approach, primarily with the WW domain derived from the human Pin1 protein as our model system, to assess hydrogen bond strengths (especially those formed by backbone amides), the dependence of hydrogen bond strengths on the environment in which they form, β-turn propensities of both natural sequences and small molecule β-turn mimics, and the energetics of carbohydrate-protein interactions. In each case, the combination of synthetic accessibility, the ease of measuring folding energies, and the robustness of the structure of the Pin1 WW domain to mutation enabled us to obtain incisive measurements of quantities that have been challenging to measure by other methods.
Collapse
Affiliation(s)
- Maziar S. Ardejani
- Department
of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Evan T. Powers
- Department
of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Jeffery W. Kelly
- Department
of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
- Department
of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037, United States
- The
Skaggs Institute for Chemical Biology, The Scripps Research Institute, La
Jolla, California 92037, United States
| |
Collapse
|
9
|
Gokhale AS, Sable R, Walker JD, McLaughlin L, Kousoulas KG, Jois SD. Inhibition of cell adhesion and immune responses in the mouse model of collagen-induced arthritis with a peptidomimetic that blocks CD2-CD58 interface interactions. Biopolymers 2016; 104:733-42. [PMID: 26031942 DOI: 10.1002/bip.22692] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Revised: 05/15/2015] [Accepted: 05/28/2015] [Indexed: 01/04/2023]
Abstract
CD2 and CD58 are two important costimulatory molecules involved in generating the signal II required for normal immune signaling. However, this interaction can be targeted to be of benefit in cases of abnormal immune signaling seen in autoimmune diseases. Our objective in this study was to design a peptidomimetic (compound 7) based on a β-strand structure of the adhesion domain of CD2 protein to inhibit CD2-CD58 protein-protein interaction and its effect on immunomodulation in the collagen-induced arthritis (CIA) model. The ability of compound 7 to bind to CD58 protein was assessed using flow cytometry. The effect of compound 7 on modulating the immune response was evaluated in an autoimmune disease using CIA in mice. The stability of compound 7 was evaluated in mouse serum using mass spectrometry. Antibody (Ab) binding inhibition studies suggested that compound 7 binds to CD58 protein. Compound 7 was successful in modulating immune responses when administered in the CIA mouse model along with reducing anti-collagen Ab levels and decreasing the level of interferon gamma (IFN-γ) relative to control treatments. Compound 7 was found to be nonimmunogenic and stable in mouse serum up to 48 h. Results suggest that compound 7 can serve as a lead compound for immunomodulation, and could be a therapeutic agent for the autoimmune disease rheumatoid arthritis (RA).
Collapse
Affiliation(s)
- Ameya S Gokhale
- Basic Pharmaceutical Sciences, School of Pharmacy, University of Louisiana at Monroe, Monroe, LA, 71201
| | - Rushikesh Sable
- Basic Pharmaceutical Sciences, School of Pharmacy, University of Louisiana at Monroe, Monroe, LA, 71201
| | - Jason D Walker
- Pathobiological Sciences, BioMMED, School of Veterinary Medicine, Louisiana State University Baton Rouge, 70803-8434
| | - Leslie McLaughlin
- Pathobiological Sciences, BioMMED, School of Veterinary Medicine, Louisiana State University Baton Rouge, 70803-8434
| | - Konstantin G Kousoulas
- Pathobiological Sciences, BioMMED, School of Veterinary Medicine, Louisiana State University Baton Rouge, 70803-8434
| | - Seetharama D Jois
- Basic Pharmaceutical Sciences, School of Pharmacy, University of Louisiana at Monroe, Monroe, LA, 71201
| |
Collapse
|
10
|
Hong F, Chen Y, Lu B, Cheng J. One-Pot Assembly of Fused Heterocycles via
Oxidative Palladium-Catalyzed Cyclization of Arylols and Iodoarenes. Adv Synth Catal 2016. [DOI: 10.1002/adsc.201500925] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
|
11
|
Rosario-Amorin D, Ouizem S, Dickie DA, Hay BP, Podair J, Delmau LH, Paine RT. Synthesis and lanthanide coordination chemistry of CMPO-decorated dibenzothiophene and dibenzothiophene sulfone platforms. Polyhedron 2015. [DOI: 10.1016/j.poly.2015.07.066] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
12
|
Panda N, Mattan I, Nayak DK. Synthesis of Dibenzofurans via C–H Activation of o-Iodo Diaryl Ethers. J Org Chem 2015; 80:6590-7. [DOI: 10.1021/acs.joc.5b00634] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Niranjan Panda
- Department of Chemistry, National Institute of Technology Rourkela, Odisha 769008, India
| | - Irshad Mattan
- Department of Chemistry, National Institute of Technology Rourkela, Odisha 769008, India
| | - Dinesh Kumar Nayak
- Department of Chemistry, National Institute of Technology Rourkela, Odisha 769008, India
| |
Collapse
|
13
|
Tsomaia N. Peptide therapeutics: Targeting the undruggable space. Eur J Med Chem 2015; 94:459-70. [DOI: 10.1016/j.ejmech.2015.01.014] [Citation(s) in RCA: 214] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Revised: 01/07/2015] [Accepted: 01/08/2015] [Indexed: 01/04/2023]
|
14
|
Synthesis of dibenzo[b,d]furans through one-pot cascade reactions of 1-arylpenta-3,4-dien-2-ones with activated ketones. Tetrahedron Lett 2015. [DOI: 10.1016/j.tetlet.2015.01.179] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
|
15
|
Körling M, Geyer A. Stabilization of a Natural β-Hairpin by a Twist-Compatible β-Turn Mimetic. European J Org Chem 2015. [DOI: 10.1002/ejoc.201500048] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
|
16
|
Lawrence PB, Gavrilov Y, Matthews SS, Langlois MI, Shental-Bechor D, Greenblatt HM, Pandey BK, Smith MS, Paxman R, Torgerson CD, Merrell JP, Ritz CC, Prigozhin MB, Levy Y, Price JL. Criteria for Selecting PEGylation Sites on Proteins for Higher Thermodynamic and Proteolytic Stability. J Am Chem Soc 2014; 136:17547-60. [DOI: 10.1021/ja5095183] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Paul B. Lawrence
- Department
of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Yulian Gavrilov
- Department
of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Sam S. Matthews
- Department
of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Minnie I. Langlois
- Department
of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Dalit Shental-Bechor
- Department
of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Harry M. Greenblatt
- Department
of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Brijesh K. Pandey
- Department
of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Mason S. Smith
- Department
of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Ryan Paxman
- Department
of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Chad D. Torgerson
- Department
of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Jacob P. Merrell
- Department
of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Cameron C. Ritz
- Department
of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Maxim B. Prigozhin
- Department
of Chemistry, University of Illinois, Urbana, Illinois 61801, United States
| | - Yaakov Levy
- Department
of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Joshua L. Price
- Department
of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| |
Collapse
|
17
|
Reinert ZE, Horne WS. Protein backbone engineering as a strategy to advance foldamers toward the frontier of protein-like tertiary structure. Org Biomol Chem 2014; 12:8796-802. [PMID: 25285575 PMCID: PMC4211622 DOI: 10.1039/c4ob01769b] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
A variety of non-biological structural motifs have been incorporated into the backbone of natural protein sequences. In parallel work, diverse unnatural oligomers of de novo design (termed "foldamers") have been developed that fold in defined ways. In this Perspective article, we survey foundational studies on protein backbone engineering, with a focus on alterations made in the context of complex tertiary folds. We go on to summarize recent work illustrating the potential promise of these methods to provide a general framework for the construction of foldamer mimics of protein tertiary structures.
Collapse
Affiliation(s)
- Zachary E Reinert
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA.
| | | |
Collapse
|
18
|
Rosario-Amorin D, Ouizem S, Dickie DA, Paine RT, Cramer RE, Hay BP, Podair J, Delmau LH. Synthesis and Lanthanide Coordination Chemistry of Phosphine Oxide Decorated Dibenzothiophene and Dibenzothiophene Sulfone Platforms. Inorg Chem 2014; 53:5698-711. [DOI: 10.1021/ic500471w] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Daniel Rosario-Amorin
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131, United States
| | - Sabrina Ouizem
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131, United States
| | - Diane A. Dickie
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131, United States
| | - Robert T. Paine
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131, United States
| | - Roger E. Cramer
- Department
of Chemistry, University of Hawaii, Honolulu, Hawaii 96822, United States
| | - Benjamin P. Hay
- Chemical Sciences Division, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, Tennessee 37831, United States
| | - Julien Podair
- Chemical Sciences Division, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, Tennessee 37831, United States
| | - Lætitia H. Delmau
- Chemical Sciences Division, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, Tennessee 37831, United States
| |
Collapse
|
19
|
Zhao J, Zhang Q, Liu L, He Y, Li J, Li J, Zhu Q. CuI-Mediated Sequential Iodination/Cycloetherification of o-Arylphenols: Synthesis of 2- or 4-Iododibenzofurans and Mechanistic Studies. Org Lett 2012; 14:5362-5. [PMID: 23025569 DOI: 10.1021/ol302562a] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Jiaji Zhao
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 190 Kaiyuan Avenue, Guangzhou 510530, P. R. China, and Department of Chemistry, Jinan University, Huangpu Road West 601, Guangzhou 510632, P. R. China
| | - Qi Zhang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 190 Kaiyuan Avenue, Guangzhou 510530, P. R. China, and Department of Chemistry, Jinan University, Huangpu Road West 601, Guangzhou 510632, P. R. China
| | - Lanying Liu
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 190 Kaiyuan Avenue, Guangzhou 510530, P. R. China, and Department of Chemistry, Jinan University, Huangpu Road West 601, Guangzhou 510632, P. R. China
| | - Yimiao He
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 190 Kaiyuan Avenue, Guangzhou 510530, P. R. China, and Department of Chemistry, Jinan University, Huangpu Road West 601, Guangzhou 510632, P. R. China
| | - Jing Li
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 190 Kaiyuan Avenue, Guangzhou 510530, P. R. China, and Department of Chemistry, Jinan University, Huangpu Road West 601, Guangzhou 510632, P. R. China
| | - Juan Li
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 190 Kaiyuan Avenue, Guangzhou 510530, P. R. China, and Department of Chemistry, Jinan University, Huangpu Road West 601, Guangzhou 510632, P. R. China
| | - Qiang Zhu
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 190 Kaiyuan Avenue, Guangzhou 510530, P. R. China, and Department of Chemistry, Jinan University, Huangpu Road West 601, Guangzhou 510632, P. R. China
| |
Collapse
|
20
|
Yin H. Constrained peptides as miniature protein structures. ISRN BIOCHEMISTRY 2012; 2012:692190. [PMID: 25969758 PMCID: PMC4392992 DOI: 10.5402/2012/692190] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2012] [Accepted: 09/03/2012] [Indexed: 11/23/2022]
Abstract
This paper discusses the recent developments of protein engineering using both covalent and noncovalent bonds to constrain peptides, forcing them into designed protein secondary structures. These constrained peptides subsequently can be used as peptidomimetics for biological functions such as regulations of protein-protein interactions.
Collapse
Affiliation(s)
- Hang Yin
- Department of Chemistry and Biochemistry and BioFrontiers Institute, University of Colorado at Boulder, 596 University of Colorado at Boulder, Boulder, CO 80309-0596, USA
| |
Collapse
|
21
|
Lengyel GA, Horne WS. Design Strategies for the Sequence-Based Mimicry of Side-Chain Display in Protein β-Sheets by α/β-Peptides. J Am Chem Soc 2012; 134:15906-13. [DOI: 10.1021/ja306311r] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- George A. Lengyel
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - W. Seth Horne
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| |
Collapse
|
22
|
Rosario-Amorin D, Duesler EN, Paine RT, Hay BP, Delmau LH, Reilly SD, Gaunt AJ, Scott BL. Synthesis and Coordination Chemistry of Phosphine Oxide Decorated Dibenzofuran Platforms. Inorg Chem 2012; 51:6667-81. [DOI: 10.1021/ic300301d] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Daniel Rosario-Amorin
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131, United
States
| | - Eileen N. Duesler
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131, United
States
| | - Robert T. Paine
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131, United
States
| | - Benjamin P. Hay
- Chemical Sciences
Division, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, Tennessee 37831, United States
| | - Lætitia H. Delmau
- Chemical Sciences
Division, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, Tennessee 37831, United States
| | | | | | | |
Collapse
|
23
|
Reinert ZE, Musselman ED, Elcock AH, Horne WS. A PEG-Based Oligomer as a Backbone Replacement for Surface-Exposed Loops in a Protein Tertiary Structure. Chembiochem 2012; 13:1107-11. [DOI: 10.1002/cbic.201200200] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2012] [Indexed: 12/20/2022]
|
24
|
Hemgesberg M, Ohlmann DM, Schmitt Y, Wolfe MR, Müller MK, Erb B, Sun Y, Gooßen LJ, Gerhards M, Thiel WR. Simple Access to Sol-Gel Precursors Bearing Fluorescent Aromatic Core Units. European J Org Chem 2012. [DOI: 10.1002/ejoc.201200076] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
25
|
Price JL, Culyba EK, Chen W, Murray AN, Hanson SR, Wong CH, Powers ET, Kelly JW. N-glycosylation of enhanced aromatic sequons to increase glycoprotein stability. Biopolymers 2012; 98:195-211. [PMID: 22782562 PMCID: PMC3539202 DOI: 10.1002/bip.22030] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2011] [Revised: 01/17/2012] [Accepted: 01/26/2012] [Indexed: 11/12/2022]
Abstract
N-glycosylation can increase the rate of protein folding, enhance thermodynamic stability, and slow protein unfolding; however, the molecular basis for these effects is incompletely understood. Without clear engineering guidelines, attempts to use N-glycosylation as an approach for stabilizing proteins have resulted in unpredictable energetic consequences. Here, we review the recent development of three "enhanced aromatic sequons," which appear to facilitate stabilizing native-state interactions between Phe, Asn-GlcNAc and Thr when placed in an appropriate reverse turn context. It has proven to be straightforward to engineer a stabilizing enhanced aromatic sequon into glycosylation-naïve proteins that have not evolved to optimize specific protein-carbohydrate interactions. Incorporating these enhanced aromatic sequons into appropriate reverse turn types within proteins should enhance the well-known pharmacokinetic benefits of N-glycosylation-based stabilization by lowering the population of protease-susceptible unfolded and aggregation-prone misfolded states, thereby making such proteins more useful in research and pharmaceutical applications.
Collapse
Affiliation(s)
- Joshua L. Price
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602
| | - Elizabeth K. Culyba
- Department of Chemistry, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037
| | - Wentao Chen
- Department of Chemistry, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037
| | - Amber N. Murray
- Department of Chemistry, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037
| | - Sarah R. Hanson
- Department of Chemistry, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037
| | - Chi-Huey Wong
- Department of Chemistry, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037
| | - Evan T. Powers
- Department of Chemistry, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037
| | - Jeffery W. Kelly
- Department of Chemistry, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037
| |
Collapse
|
26
|
Zhao J, Wang Y, He Y, Liu L, Zhu Q. Cu-Catalyzed Oxidative C(sp2)–H Cycloetherification of o-Arylphenols for the Preparation of Dibenzofurans. Org Lett 2012; 14:1078-81. [DOI: 10.1021/ol203442a] [Citation(s) in RCA: 113] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Jiaji Zhao
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 190 Kaiyuan Avenue, Guangzhou 510530, China
| | - Yong Wang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 190 Kaiyuan Avenue, Guangzhou 510530, China
| | - Yimiao He
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 190 Kaiyuan Avenue, Guangzhou 510530, China
| | - Lanying Liu
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 190 Kaiyuan Avenue, Guangzhou 510530, China
| | - Qiang Zhu
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 190 Kaiyuan Avenue, Guangzhou 510530, China
| |
Collapse
|
27
|
Xiao B, Gong TJ, Liu ZJ, Liu JH, Luo DF, Xu J, Liu L. Synthesis of dibenzofurans via palladium-catalyzed phenol-directed C-H activation/C-O cyclization. J Am Chem Soc 2011; 133:9250-3. [PMID: 21609019 DOI: 10.1021/ja203335u] [Citation(s) in RCA: 280] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
A practical, Pd(0)/Pd(II)-catalyzed reaction was developed for phenol-directed C-H activation/C-O cyclization using air as an oxidant. The turnover-limiting step of the process was found to be C-O reductive elimination instead of C-H activation. This reaction can tolerate a variety of functional groups and is complementary to the previous methods for the synthesis of substituted dibenzofurans.
Collapse
Affiliation(s)
- Bin Xiao
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
| | | | | | | | | | | | | |
Collapse
|
28
|
Targeting Protein–Protein Interactions and Fragment-Based Drug Discovery. Top Curr Chem (Cham) 2011; 317:145-79. [DOI: 10.1007/128_2011_265] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
|
29
|
Price JL, Shental-Bechor D, Dhar A, Turner MJ, Powers ET, Gruebele M, Levy Y, Kelly JW. Context-dependent effects of asparagine glycosylation on Pin WW folding kinetics and thermodynamics. J Am Chem Soc 2010; 132:15359-67. [PMID: 20936810 PMCID: PMC2965790 DOI: 10.1021/ja106896t] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Asparagine glycosylation is one of the most common and important post-translational modifications of proteins in eukaryotic cells. N-glycosylation occurs when a triantennary glycan precursor is transferred en bloc to a nascent polypeptide (harboring the N-X-T/S sequon) as the peptide is cotranslationally translocated into the endoplasmic reticulum (ER). In addition to facilitating binding interactions with components of the ER proteostasis network, N-glycans can also have intrinsic effects on protein folding by directly altering the folding energy landscape. Previous work from our laboratories (Hanson et al. Proc. Natl. Acad. Sci. U.S.A. 2009, 109, 3131-3136; Shental-Bechor, D.; Levy, Y. Proc. Natl. Acad. Sci. U.S.A. 2008, 105, 8256-8261) suggested that the three sugar residues closest to the protein are sufficient for accelerating protein folding and stabilizing the resulting structure in vitro; even a monosaccharide can have a dramatic effect. The highly conserved nature of these three proximal sugars in N-glycans led us to speculate that introducing an N-glycosylation site into a protein that is not normally glycosylated would stabilize the protein and increase its folding rate in a manner that does not depend on the presence of specific stabilizing protein-saccharide interactions. Here, we test this hypothesis experimentally and computationally by incorporating an N-linked GlcNAc residue at various positions within the Pin WW domain, a small β-sheet-rich protein. The results show that an increased folding rate and enhanced thermodynamic stability are not general, context-independent consequences of N-glycosylation. Comparison between computational predictions and experimental observations suggests that generic glycan-based excluded volume effects are responsible for the destabilizing effect of glycosylation at highly structured positions. However, this reasoning does not adequately explain the observed destabilizing effect of glycosylation within flexible loops. Our data are consistent with the hypothesis that specific, evolved protein-glycan contacts must also play an important role in mediating the beneficial energetic effects on protein folding that glycosylation can confer.
Collapse
Affiliation(s)
- Joshua L. Price
- Departments of Chemistry and Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037
| | - Dalit Shental-Bechor
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel, 76100
| | - Apratim Dhar
- Center for Biophysics and Computational Biology and Departments of Chemistry and Physics, University of Illinois, Urbana, Illinois 61801
| | - Maurice J. Turner
- Departments of Chemistry and Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037
| | - Evan T. Powers
- Departments of Chemistry and Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037
| | - Martin Gruebele
- Center for Biophysics and Computational Biology and Departments of Chemistry and Physics, University of Illinois, Urbana, Illinois 61801
| | - Yaakov Levy
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel, 76100
| | - Jeffery W. Kelly
- Departments of Chemistry and Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037
| |
Collapse
|
30
|
Roy S, Zych AJ, Herr RJ, Cheng C, Shipps GW. Direct synthesis of Cbz-protected (2-amino)-6-(2-aminoethyl)pyridines. Tetrahedron 2010. [DOI: 10.1016/j.tet.2010.01.025] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
31
|
Wilson AJ. Inhibition of protein-protein interactions using designed molecules. Chem Soc Rev 2009; 38:3289-300. [PMID: 20449049 DOI: 10.1039/b807197g] [Citation(s) in RCA: 198] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Although many cellular processes depend upon enzymatic reactions, protein-protein interactions (PPIs) mediate a large number of important regulatory pathways and thus play a central role in disease development. In order to understand and selectively inhibit cellular signalling pathways, there is a pressing need for small molecules that target PPIs, particularly in the context of pharmaceutical development. This tutorial review will introduce the relevance of PPIs to chemical biology and highlight the key challenges in designing inhibitors. Some of the successes using conventional approaches to the identification of small-molecule PPI inhibitors will be highlighted, and also the reasons why these approaches have not always proven successful. Several general approaches tailored to particular protein topologies are emerging for the design of scaffolds that inhibit PPIs-these will form the major content of this review. Finally a summary of the challenges to be faced in developing inhibitors of PPIs into drug leads and how these challenges may differ from those encountered with enzyme-like targets will be given.
Collapse
Affiliation(s)
- Andrew J Wilson
- School of Chemistry, University of Leeds, Woodhouse Lane, LS2 9JT, Leeds, UK.
| |
Collapse
|
32
|
Abstract
Beta-turns are common conformations that enable proteins to adopt globular structures, and their formation is often rate limiting for folding. Beta-turn mimics, molecules that replace the i + 1 and i + 2 amino acid residues of a beta-turn, are envisioned to act as folding nucleators by preorganizing the pendant polypeptide chains, thereby lowering the activation barrier for beta-sheet formation. However, the crucial kinetic experiments to demonstrate that beta-turn mimics can act as strong nucleators in the context of a cooperatively folding protein have not been reported. We have incorporated 6 beta-turn mimics simulating varied beta-turn types in place of 2 residues in an engineered beta-turn 1 or beta-bulge turn 1 of the Pin 1 WW domain, a three-stranded beta-sheet protein. We present 2 lines of kinetic evidence that the inclusion of beta-turn mimics alters beta-sheet folding rates, enabling us to classify beta-turn mimics into 3 categories: those that are weak nucleators but permit Pin WW folding, native-like nucleators, and strong nucleators. Strong nucleators accelerate folding relative to WW domains incorporating all alpha-amino acid sequences. A solution NMR structure reveals that the native Pin WW beta-sheet structure is retained upon incorporating a strong E-olefin nucleator. These beta-turn mimics can now be used to interrogate protein folding transition state structures and the 2 kinetic analyses presented can be used to assess the nucleation capacity of other beta-turn mimics.
Collapse
|
33
|
Anai T, Nakata E, Koshi Y, Ojida A, Hamachi I. Design of a Hybrid Biosensor for Enhanced Phosphopeptide Recognition Based on a Phosphoprotein Binding Domain Coupled with a Fluorescent Chemosensor. J Am Chem Soc 2007; 129:6232-9. [PMID: 17441721 DOI: 10.1021/ja0693284] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Protein-based fluorescent biosensors with sufficient sensing specificity are useful analytical tools for detection of biologically important substances in complicated biological systems. Here, we present the design of a hybrid biosensor, specific for a bis-phosphorylated peptide, based on a natural phosphoprotein binding domain coupled with an artificial fluorescent chemosensor. The hybrid biosensor consists of a phosphoprotein binding domain, the WW domain, into which has been introduced a fluorescent stilbazole having Zn(II)-dipicolylamine (Dpa) as a phosphate binding motif. It showed strong binding affinity and high sensing selectivity toward a specific bis-phosphorylated peptide in the presence of various phosphate species such as the monophosphorylated peptide, ATP, and others. Detailed fluorescence titration experiments clearly indicate that the binding-induced fluorescence enhancement and the sensing selectivity were achieved by the cooperative action of both binding sites of the hybrid biosensor, i.e., the WW domain and the Zn(II)-Dpa chemosensor unit. Thus, it is clear that the tethered Zn(II)-Dpa-stilbazole unit operated not only as a fluorescence signal transducer, but also as a sub-binding site in the hybrid biosensor. Taking advantage of its selective sensing property, the hybrid biosensor was successfully applied to real-time and label-free fluorescence monitoring of a protein kinase-catalyzed phosphorylation.
Collapse
Affiliation(s)
- Takahiro Anai
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura Campus, Nishikyo-ku, Kyoto 615-8510, Japan
| | | | | | | | | |
Collapse
|
34
|
Li F, Delgado R, Coelho A, Drew MG, Félix V. New dioxadiaza-, trioxadiaza- and hexaaza-macrocycles containing dibenzofuran units. Tetrahedron 2006. [DOI: 10.1016/j.tet.2006.06.073] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
|
35
|
|
36
|
|
37
|
Fotins J, Smithrud DB. Creation and Investigation of Protein-Core Mimetics with Parallel and Antiparallel Aligned Amino Acids. J Org Chem 2005; 70:4452-9. [PMID: 15903324 DOI: 10.1021/jo0479563] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Mimetic protein cores were created that align a set of l-Phe, d-Phe, or l-Leu residues in a parallel or an antiparallel arrangement in chloroform. Not all cores show a single conformation at room temperature. Stable structures require a synergistic relationship between the H-bonding groups and the residues within the core. The spatial arrangement of the side chains dictates whether a zippered or a crossed pattern of H-bonds is observed for these cores. Variable-temperature (1)H NMR experiments were used to determine the strengths of the H-bonds. The existence of H-bonds was verified through FTIR spectroscopic analysis. Large temperature coefficients exist for some protons of aromatic rings that are held in a T-shaped arrangement. A comparison of these temperature coefficients shows that a more stable core is obtained by combining benzenoid and nitrobenzenoid rings as compared to benzenoid rings. Structures were determined using a combination of 2D NMR analysis and molecular modeling.
Collapse
Affiliation(s)
- Juris Fotins
- Department of Chemistry, University of Cincinnati, Cincinnati, OH 45221-0172, USA
| | | |
Collapse
|
38
|
Deechongkit S, Dawson PE, Kelly JW. Toward Assessing the Position-Dependent Contributions of Backbone Hydrogen Bonding to β-Sheet Folding Thermodynamics Employing Amide-to-Ester Perturbations. J Am Chem Soc 2004; 126:16762-71. [PMID: 15612714 DOI: 10.1021/ja045934s] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An amide-to-ester backbone substitution in a protein is accomplished by replacing an alpha-amino acid residue with the corresponding alpha-hydroxy acid, preserving stereochemistry, and conformation of the backbone and the structure of the side chain. This substitution replaces the amide NH (a hydrogen bond donor) with an ester O (which is not a hydrogen bond donor) and the amide carbonyl (a strong hydrogen bond acceptor) with an ester carbonyl (a weaker hydrogen bond acceptor), thus perturbing folding energetics. Amide-to-ester perturbations were used to evaluate the thermodynamic contribution of each hydrogen bond in the PIN WW domain, a three-stranded beta-sheet protein. Our results reveal that removing a hydrogen bond donor destabilizes the native state more than weakening a hydrogen bond acceptor and that the degree of destabilization is strongly dependent on the location of the amide bond replaced. Hydrogen bonds near turns or at the ends of beta-strands are less influential than hydrogen bonds that are protected within a hydrophobic core. Beta-sheet destabilization caused by an amide-to-ester substitution cannot be directly related to hydrogen bond strength because of differences in the solvation and electrostatic interactions of amides and esters. We propose corrections for these differences to obtain approximate hydrogen bond strengths from destabilization energies. These corrections, however, do not alter the trends noted above, indicating that the destabilization energy of an amide-to-ester mutation is a good first-order approximation of the free energy of formation of a backbone amide hydrogen bond.
Collapse
Affiliation(s)
- Songpon Deechongkit
- Department of Chemistry, The Skaggs Institute of Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, BCC 506, La Jolla, CA 92037, USA
| | | | | |
Collapse
|
39
|
Deechongkit S, Nguyen H, Powers ET, Dawson PE, Gruebele M, Kelly JW. Context-dependent contributions of backbone hydrogen bonding to beta-sheet folding energetics. Nature 2004; 430:101-5. [PMID: 15229605 DOI: 10.1038/nature02611] [Citation(s) in RCA: 227] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2004] [Accepted: 04/29/2004] [Indexed: 11/09/2022]
Abstract
Backbone hydrogen bonds (H-bonds) are prominent features of protein structures; however, their role in protein folding remains controversial because they cannot be selectively perturbed by traditional methods of protein mutagenesis. Here we have assessed the contribution of backbone H-bonds to the folding kinetics and thermodynamics of the PIN WW domain, a small beta-sheet protein, by individually replacing its backbone amides with esters. Amide-to-ester mutations site-specifically perturb backbone H-bonds in two ways: a H-bond donor is eliminated by replacing an amide NH with an ester oxygen, and a H-bond acceptor is weakened by replacing an amide carbonyl with an ester carbonyl. We perturbed the 11 backbone H-bonds of the PIN WW domain by synthesizing 19 amide-to-ester mutants. Thermodynamic studies on these variants show that the protein is most destabilized when H-bonds that are enveloped by a hydrophobic cluster are perturbed. Kinetic studies indicate that native-like secondary structure forms in one of the protein's loops in the folding transition state, but the backbone is less ordered elsewhere in the sequence. Collectively, our results provide an unusually detailed picture of the folding of a beta-sheet protein.
Collapse
Affiliation(s)
- Songpon Deechongkit
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, BCC 506, La Jolla, California 92037, USA
| | | | | | | | | | | |
Collapse
|
40
|
Blomberg D, Hedenström M, Kreye P, Sethson I, Brickmann K, Kihlberg J. Synthesis and Conformational Studies of a β-Turn Mimetic Incorporated in Leu-enkephalin. J Org Chem 2004; 69:3500-8. [PMID: 15132562 DOI: 10.1021/jo0356863] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A beta-turn mimetic in which the four amino acids of a beta-turn have been replaced by a 10-membered ring has been designed, synthesized, and subjected to conformational studies. In the mimetic, the intramolecular CO(i)-HN(i)(+3) hydrogen bond that is often found in beta-turns has been replaced by an ethylene bridge. In addition, the amide bond between residues i and i + 1 was exchanged for a methylene ether isoster. Such a beta-turn mimetic, based on the first four residues of Leu-enkephalin (Tyr-Gly-Gly-Phe-Leu), was prepared in 15 steps. The synthesis relied on a beta-azido alcohol prepared in five steps from Cbz-Tyr(tBu)-OH as a key, i-position building block. tert-Butyl bromoacetate, glycine, and a Phe-Leu dipetide were then used as building blocks for positions i + 1, i + 2, and i + 3, respectively. Conformational studies based on (1)H NMR data showed that the beta-turn mimetic was flexible, but that it resembled a type-II beta-turn at low temperature. This low energy conformer closely resembled the structure determined for crystalline Leu-enkephalin.
Collapse
Affiliation(s)
- David Blomberg
- Organic Chemistry, Department of Chemistry, Umeå University, SE-901 87 Umeå, Sweden
| | | | | | | | | | | |
Collapse
|
41
|
|