1
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Byerly-Duke J, Donovan A, O'Brien EA, Sharma KK, Ibrahim R, Stanley LM, VanVeller B. Complementary Strategies for Installation of Thioimidates into Peptide Backbones. J Org Chem 2024. [PMID: 39364858 DOI: 10.1021/acs.joc.4c01386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/05/2024]
Abstract
Thioimidates are a precursor and synthetic branch point to access either thioamide or amidine isosteres of the native amide (peptide bond). Previous syntheses of thioimidate-containing peptides were prone to side reactivity and required slow, cumbersome steps that were difficult to monitor. We describe a more efficient approach to directly couple thioimidates onto the growing peptide chain. This work also outlines optimal conditions for thioimidate formation on solid support and identifies potential off-target sites for alkylation that impact the choice of protecting group.
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Affiliation(s)
- Jacob Byerly-Duke
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
| | - Aaron Donovan
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
| | - Emily A O'Brien
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
| | - Krishna K Sharma
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
| | - Rida Ibrahim
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
| | - Levi M Stanley
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
| | - Brett VanVeller
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
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2
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Byerly-Duke J, O'Brien EA, Wall BJ, VanVeller B. Thioimidates provide general access to thioamide, amidine, and imidazolone peptide-bond isosteres. Methods Enzymol 2024; 698:27-55. [PMID: 38886036 DOI: 10.1016/bs.mie.2024.04.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2024]
Abstract
Thioamides, amidines, and heterocycles are three classes of modifications that can act as peptide-bond isosteres to alter the peptide backbone. Thioimidate protecting groups can address many of the problematic synthetic issues surrounding installation of these groups. Historically, amidines have received little attention in peptides due to limitations in methods to access them. The first robust and general procedure for the introduction of amidines into peptide backbones exploits the utility of thioimidate protecting groups as a means to side-step reactivity that ultimately renders existing methods unsuitable for the installation of amidines along the main-chain of peptides. Further, amidines formed on-resin can be reacted to form (4H)-imidazolone heteorcycles which have recently been shown to act as cis-amide isosteres. General methods for heterocyclic installation capable of geometrically restricting peptide conformation are also under-developed. This work is significant because it describes a generally applicable and divergent approach to access unexplored peptide designs and architectures.
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Affiliation(s)
- Jacob Byerly-Duke
- Department of Chemistry, Iowa State University, Ames, IA, United States
| | - Emily A O'Brien
- Department of Chemistry, Iowa State University, Ames, IA, United States
| | - Brendan J Wall
- Department of Chemistry, Iowa State University, Ames, IA, United States
| | - Brett VanVeller
- Department of Chemistry, Iowa State University, Ames, IA, United States.
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3
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Byerly-Duke J, VanVeller B. Thioimidate Solutions to Thioamide Problems during Thionopeptide Deprotection. Org Lett 2024; 26:1452-1457. [PMID: 38341867 PMCID: PMC11031844 DOI: 10.1021/acs.orglett.4c00035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/13/2024]
Abstract
Thioamides have structural and chemical similarity to peptide bonds, offering valuable insights when probing peptide backbone interactions, but are prone to side reactions during solid-phase peptide synthesis (SPPS). Thioimidates have been demonstrated to be effective protecting groups for thioamides during peptide elongation. We further demonstrate how thioimidates can assist thioamides through the most yield-crippling step of thionopeptide deprotection, allowing for the first isolation of an important benchmark α-helical peptide that had previously eluded synthesis and isolation.
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Affiliation(s)
- Jacob Byerly-Duke
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
| | - Brett VanVeller
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
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4
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Hansen TN, Olsen CA. Contemporary Applications of Thioamides and Methods for Their Synthesis. Chemistry 2024; 30:e202303770. [PMID: 38088462 DOI: 10.1002/chem.202303770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Indexed: 12/23/2023]
Abstract
Thioamides are naturally occurring isosteres of amide bonds in which the chalcogen atom of the carbonyl is changed from oxygen to sulfur. This substitution gives rise to altered nucleophilicity and hydrogen bonding properties with importance for both chemical reactivity and non-covalent interactions. As such, thioamides have been introduced into biologically active compounds to achieve improved target affinity and/or stability towards hydrolytic enzymes but have also been applied as probes of protein and peptide folding and dynamics. Recently, a series of new methods have been developed for the synthesis of thioamides as well as their utilization in peptide chemistry. Further, novel strategies for the incorporation of thioamides into proteins have been developed, enabling both structural and functional studies to be performed. In this Review, we highlight the recent developments in the preparation of thioamides and their applications for peptide modification and study of protein function.
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Affiliation(s)
- Tobias N Hansen
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 160, 2100, Copenhagen, Denmark
| | - Christian A Olsen
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 160, 2100, Copenhagen, Denmark
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5
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Gibadullin R, Morris RK, Niu J, Sidney J, Sette A, Gellman SH. Thioamide Analogues of MHC I Antigen Peptides. J Am Chem Soc 2023; 145:25559-25569. [PMID: 37968794 PMCID: PMC10782604 DOI: 10.1021/jacs.3c05300] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2023]
Abstract
Short, synthetic peptides that are displayed by major histocompatibility complex I (MHC I) can stimulate CD8 T cells in vivo to destroy virus-infected or cancer cells. The development of such peptides as vaccines that provide protective immunity, however, is limited by rapid proteolytic degradation. Introduction of unnatural amino acid residues can suppress MHC I antigen proteolysis, but the modified peptides typically display lower affinity for MHC I and/or diminished ability to activate CD8 T cells relative to native antigen. Here, we report a new strategy for modifying MHC I antigens to enhance resistance to proteolysis while preserving MHC I affinity and T cell activation properties. This approach, replacing backbone amide groups with thioamides, was evaluated in two well-characterized antigens presented by HLA-A2, a common human MHC I. For each antigen, singly modified thioamide analogues retained affinity for HLA-A2 and activated T cells specific for the native antigen, as measured via interferon-γ secretion. In each system, we identified a highly potent triply substituted thioamide antigen ("thio-antigen") that displayed substantial resistance to proteolytic cleavage. Collectively, our results suggest that thio-antigens may represent a general and readily accessible source of potent vaccine candidates that resist degradation.
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Affiliation(s)
- Ruslan Gibadullin
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
- Present address: Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Rylie K. Morris
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Jiani Niu
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - John Sidney
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, California 92037, United States
| | - Alessandro Sette
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, California 92037, United States
- Department of Medicine, University of California, San Diego, California 92093, United States
| | - Samuel H. Gellman
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
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6
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Ghosh P, Raj N, Verma H, Patel M, Chakraborti S, Khatri B, Doreswamy CM, Anandakumar SR, Seekallu S, Dinesh MB, Jadhav G, Yadav PN, Chatterjee J. An amide to thioamide substitution improves the permeability and bioavailability of macrocyclic peptides. Nat Commun 2023; 14:6050. [PMID: 37770425 PMCID: PMC10539501 DOI: 10.1038/s41467-023-41748-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 09/06/2023] [Indexed: 09/30/2023] Open
Abstract
Solvent shielding of the amide hydrogen bond donor (NH groups) through chemical modification or conformational control has been successfully utilized to impart membrane permeability to macrocyclic peptides. We demonstrate that passive membrane permeability can also be conferred by masking the amide hydrogen bond acceptor (>C = O) through a thioamide substitution (>C = S). The membrane permeability is a consequence of the lower desolvation penalty of the macrocycle resulting from a concerted effect of conformational restriction, local desolvation of the thioamide bond, and solvent shielding of the amide NH groups. The enhanced permeability and metabolic stability on thioamidation improve the bioavailability of a macrocyclic peptide composed of hydrophobic amino acids when administered through the oral route in rats. Thioamidation of a bioactive macrocyclic peptide composed of polar amino acids results in analogs with longer duration of action in rats when delivered subcutaneously. These results highlight the potential of O to S substitution as a stable backbone modification in improving the pharmacological properties of peptide macrocycles.
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Affiliation(s)
- Pritha Ghosh
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, Karnataka, India
| | - Nishant Raj
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, Karnataka, India
| | - Hitesh Verma
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, Karnataka, India
| | - Monika Patel
- Neuroscience & Ageing Biology, CSIR-CDRI, Lucknow, 226031, Uttar Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Sohini Chakraborti
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, Karnataka, India
| | - Bhavesh Khatri
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, Karnataka, India
| | - Chandrashekar M Doreswamy
- Department of Pre-clinical Research, Anthem Biosciences Pvt. Ltd., Bangalore, 560099, Karnataka, India
| | - S R Anandakumar
- Department of Pre-clinical Research, Anthem Biosciences Pvt. Ltd., Bangalore, 560099, Karnataka, India
| | - Srinivas Seekallu
- Department of Pre-clinical Research, Anthem Biosciences Pvt. Ltd., Bangalore, 560099, Karnataka, India
| | - M B Dinesh
- Central Animal Facility, Indian Institute of Science, Bangalore, 560012, Karnataka, India
| | - Gajanan Jadhav
- Eurofins Advinus Biopharma Services India Pvt. Ltd., Bangalore, 560058, Karnataka, India
| | - Prem Narayan Yadav
- Neuroscience & Ageing Biology, CSIR-CDRI, Lucknow, 226031, Uttar Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Jayanta Chatterjee
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, Karnataka, India.
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7
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Zhang J, Zhao H, Li G, Zhu X, Shang L, He Y, Liu X, Ma Y, Szostak M. Transamidation of thioamides with nucleophilic amines: thioamide N-C(S) activation by ground-state-destabilization. Org Biomol Chem 2022; 20:5981-5988. [PMID: 35441645 DOI: 10.1039/d2ob00412g] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Thioamides are 'single-atom' isosteres of amide bonds that have found broad applications in organic synthesis, biochemistry and drug discovery. In this New Talent themed issue, we present a general strategy for activation of N-C(S) thioamide bonds by ground-state-destabilization. This concept is outlined in the context of a full study on transamidation of thioamides with nucleophilic amines, and relies on (1) site-selective N-activation of the thioamide bond to decrease resonance and (2) highly chemoselective nucleophilic acyl addition to the thioamide CS bond. The follow-up collapse of the tetrahedral intermediate is favored by the electronic properties of the amine leaving group. The ground-state-destabilization concept of thioamides enables weakening of the N-C(S) bond and rationally modifies the properties of valuable thioamide isosteres for the development of new methods in organic synthesis. We fully expect that in analogy to the burgeoning field of destabilized amides introduced by our group in 2015, the thioamide bond ground-state-destabilization activation concept will find broad applications in various facets of chemical science, including metal-free, metal-catalyzed and metal-promoted reaction pathways.
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Affiliation(s)
- Jin Zhang
- College of Chemistry and Chemical Engineering, Key Laboratory of Chemical Additives for China National Light Industry, Shaanxi University of Science and Technology, Xi'an 710021, China. .,Department of Chemistry, Rutgers University, 73 Warren Street, Newark, NJ 07102, USA.
| | - Hui Zhao
- College of Chemistry and Chemical Engineering, Key Laboratory of Chemical Additives for China National Light Industry, Shaanxi University of Science and Technology, Xi'an 710021, China.
| | - Guangchen Li
- Department of Chemistry, Rutgers University, 73 Warren Street, Newark, NJ 07102, USA.
| | - Xinhao Zhu
- College of Chemistry and Chemical Engineering, Key Laboratory of Chemical Additives for China National Light Industry, Shaanxi University of Science and Technology, Xi'an 710021, China.
| | - Linqin Shang
- College of Chemistry and Chemical Engineering, Key Laboratory of Chemical Additives for China National Light Industry, Shaanxi University of Science and Technology, Xi'an 710021, China.
| | - Yang He
- College of Chemistry and Chemical Engineering, Key Laboratory of Chemical Additives for China National Light Industry, Shaanxi University of Science and Technology, Xi'an 710021, China.
| | - Xin Liu
- College of Chemistry and Chemical Engineering, Key Laboratory of Chemical Additives for China National Light Industry, Shaanxi University of Science and Technology, Xi'an 710021, China.
| | - Yangmin Ma
- College of Chemistry and Chemical Engineering, Key Laboratory of Chemical Additives for China National Light Industry, Shaanxi University of Science and Technology, Xi'an 710021, China.
| | - Michal Szostak
- Department of Chemistry, Rutgers University, 73 Warren Street, Newark, NJ 07102, USA.
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8
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Li G, Xing Y, Zhao H, Zhang J, Hong X, Szostak M. Chemoselective Transamidation of Thioamides by Transition-Metal-Free N-C(S) Transacylation. Angew Chem Int Ed Engl 2022; 61:e202200144. [PMID: 35122374 PMCID: PMC8983593 DOI: 10.1002/anie.202200144] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Indexed: 01/13/2023]
Abstract
Thioamides represent highly valuable isosteric in the strictest sense "single-atom substitution" analogues of amides that have found broad applications in chemistry and biology. A long-standing challenge is the direct transamidation of thioamides, a process which would convert one thioamide bond (R-C(S)-NR1 R2 ) into another (R-C(S)-NR3 N4 ). Herein, we report the first general method for the direct transamidation of thioamides by highly chemoselective N-C(S) transacylation. The method relies on site-selective N-tert-butoxycarbonyl activation of 2° and 1° thioamides, resulting in ground-state-destabilization of thioamides, thus enabling to rationally manipulate nucleophilic addition to the thioamide bond. This method showcases a remarkably broad scope including late-stage functionalization (>100 examples). We further present extensive DFT studies that provide insight into the chemoselectivity and provide guidelines for the development of transamidation methods of the thioamide bond.
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Affiliation(s)
- Guangchen Li
- Department of Chemistry, Rutgers University, 73 Warren Street, Newark, NJ 07102, USA
| | - Yangyang Xing
- Center of Chemistry for Frontier Technologies, Department of Chemistry, State Key Laboratory of Clean Energy Utilization, Zhejiang University, Hangzhou, 310027, China
| | - Hui Zhao
- College of Chemistry and Chemical Engineering, Key Laboratory of Chemical Additives for China National Light Industry, Shaanxi University of Science and Technology, Xi'an, 710021, China
| | - Jin Zhang
- College of Chemistry and Chemical Engineering, Key Laboratory of Chemical Additives for China National Light Industry, Shaanxi University of Science and Technology, Xi'an, 710021, China
| | - Xin Hong
- Center of Chemistry for Frontier Technologies, Department of Chemistry, State Key Laboratory of Clean Energy Utilization, Zhejiang University, Hangzhou, 310027, China.,Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, School of Science, Westlake University, 18 Shilongshan Road, Hangzhou, 310024, Zhejiang Province, China.,Beijing National Laboratory for Molecular Sciences, Zhongguancun North First Street NO. 2, Beijing, 100190, PR China
| | - Michal Szostak
- Department of Chemistry, Rutgers University, 73 Warren Street, Newark, NJ 07102, USA
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9
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Li G, Xing Y, Zhao H, Zhang J, Hong X, Szostak M. Chemoselective Transamidation of Thioamides by Transition‐Metal‐Free N–C(S) Transacylation. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202200144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Guangchen Li
- Rutgers University: Rutgers The State University of New Jersey Chemistry UNITED STATES
| | | | - Hui Zhao
- Shaanxi University of Science and Technology Xi\'an Campus: Shaanxi University of Science and Technology Chemistry CHINA
| | - Jin Zhang
- Shaanxi University of Science and Technology Chemistry CHINA
| | - Xin Hong
- Zhejiang University Department of Chemistry CHINA
| | - Michal Szostak
- Rutgers University Department of Chemistry 73 Warren St. 07102 Newark UNITED STATES
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10
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Bellat V, Michel AO, Thomas C, Stokol T, Choi B, Law B. A urinary drug-disposing approach as an alternative to intravesical chemotherapy for treating non-muscle invasive bladder cancer. Cancer Res 2022; 82:1409-1422. [PMID: 35039320 DOI: 10.1158/0008-5472.can-21-2897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 10/22/2021] [Accepted: 01/12/2022] [Indexed: 11/16/2022]
Abstract
The standard treatment of non-muscle invasive bladder cancer (NMIBC) is transurethral resection of the tumors, followed by intravesical therapy (IT), which comprises a direct instillation of a solution of Bacillus Calmette-Guérin vaccine or chemotherapy into the bladder. However, the recurrence rate in this disease remains unacceptably high. IT is a local treatment that fails to reach tumors developed in the upper urinary tract (ureter and renal pelvis). The catheterization procedure required for IT is invasive, painful, and poses an increased infection risk resulting in poor patient quality of life and compliance. There is an unmet need for a potent, comprehensive, and non-invasive option. Without chemical modifications, peptides are rapidly removed by renal clearance. This "shortcoming" can be advantageous when used as a drug carrier for directing therapy to NMIBC. Here we develop a urinary drug-disposing (UDD) approach to improve NMIBC treatment. A 12-amino acid bio-inert peptide (Bdd) that can be exclusively eliminated via renal filtration was generated for delivering the microtubule inhibitor DM1 to NMIBC with minimal non-specific accumulation in other organs. The UDD approach prolonged survival of mice bearing human bladder tumors. Unlike IT, the treatment was given non-invasively (intravenously). Furthermore, it was more effective at suppressing tumor growth than clinically used IT (mitomycin) and safer than free DM1. The application of this urinary drug-disposing approach to treat kidney tumors and deliver other drugs such as doxorubicin was also demonstrated. Overall, the rapid renal clearance of peptides can be exploited to direct cancer therapies to the urinary system.
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Affiliation(s)
- Vanessa Bellat
- Molecular Imaging Innovations Institute, Department of Radiology, Weill Cornell Medicine
| | | | | | - Tracy Stokol
- Population Medicine and Diagnostic Sciences, Cornell University
| | | | - Benedict Law
- Molecular Imaging Innovations Institute, Department of Radiology, Weill Cornell Medicine
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11
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Lampkin BJ, VanVeller B. Hydrogen Bond and Geometry Effects of Thioamide Backbone Modifications. J Org Chem 2021; 86:18287-18291. [PMID: 34851645 DOI: 10.1021/acs.joc.1c02373] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Thioamide substitution of backbone peptide bonds can probe interactions along the main chain of proteins. Despite theoretical predictions of the enhanced hydrogen bonding propensities of thioamides, previous studies often do not consider the geometric constraints imposed by folded peptide secondary structure. This work addresses drawbacks in previous studies that ignored the geometry dependence and local dielectric properties of thioamide hydrogen bonding and identifies cases where thioamides may be either stronger or weaker hydrogen-bonding partners than amides.
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Affiliation(s)
- Bryan J Lampkin
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
| | - Brett VanVeller
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
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12
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Phan HAT, Giannakoulias SG, Barrett TM, Liu C, Petersson EJ. Rational design of thioamide peptides as selective inhibitors of cysteine protease cathepsin L. Chem Sci 2021; 12:10825-10835. [PMID: 35355937 PMCID: PMC8901119 DOI: 10.1039/d1sc00785h] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 06/30/2021] [Indexed: 12/24/2022] Open
Abstract
Aberrant levels of cathepsin L (Cts L), a ubiquitously expressed endosomal cysteine protease, have been implicated in many diseases such as cancer and diabetes. Significantly, Cts L has been identified as a potential target for the treatment of COVID-19 due to its recently unveiled critical role in SARS-CoV-2 entry into the host cells. However, there are currently no clinically approved specific inhibitors of Cts L, as it is often challenging to obtain specificity against the many highly homologous cathepsin family cysteine proteases. Peptide-based agents are often promising protease inhibitors as they offer high selectivity and potency, but unfortunately are subject to degradation in vivo. Thioamide substitution, a single-atom O-to-S modification in the peptide backbone, has been shown to improve the proteolytic stability of peptides addressing this issue. Utilizing this approach, we demonstrate herein that good peptidyl substrates can be converted into sub-micromolar inhibitors of Cts L by a single thioamide substitution in the peptide backbone. We have designed and scanned several thioamide stabilized peptide scaffolds, in which one peptide, RS 1A, was stabilized against proteolysis by all five cathepsins (Cts L, Cts V, Cts K, Cts S, and Cts B) while inhibiting Cts L with >25-fold specificity against the other cathepsins. We further showed that this stabilized RS 1A peptide could inhibit Cts L in human liver carcinoma lysates (IC50 = 19 μM). Our study demonstrates that one can rationally design a stabilized, specific peptidyl protease inhibitor by strategic placement of a thioamide and reaffirms the place of this single-atom modification in the toolbox of peptide-based rational drug design.
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Affiliation(s)
- Hoang Anh T Phan
- Department of Chemistry, University of Pennsylvania Philadelphia Pennsylvania 19104 USA
| | - Sam G Giannakoulias
- Department of Chemistry, University of Pennsylvania Philadelphia Pennsylvania 19104 USA
| | - Taylor M Barrett
- Department of Chemistry, University of Pennsylvania Philadelphia Pennsylvania 19104 USA
| | - Chunxiao Liu
- Department of Chemistry, University of Pennsylvania Philadelphia Pennsylvania 19104 USA
- Key Laboratory for Northern Urban Agriculture of Ministry of Agriculture and Rural Affairs, Beijing University of Agriculture Beijing 102206 P. R. China
| | - E James Petersson
- Department of Chemistry, University of Pennsylvania Philadelphia Pennsylvania 19104 USA
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13
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Schmitthenner HF, Barrett TM, Beach SA, Heese LE, Weidman C, Dobson DE, Mahoney ER, Schug NC, Jones KG, Durmaz C, Otasowie O, Aronow S, Lee YP, Ophardt HD, Becker AE, Hornak JP, Evans IM, Ferran MC. Modular Synthesis of Peptide-Based Single- and Multimodal Targeted Molecular Imaging Agents. ACS APPLIED BIO MATERIALS 2021; 4:5435-5448. [PMID: 35006725 PMCID: PMC9633131 DOI: 10.1021/acsabm.1c00157] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A practical, modular synthesis of targeted molecular imaging agents (TMIAs) containing near-infrared dyes for optical molecular imaging (OMI) or chelated metals for magnetic resonance imaging (MRI) and single-photon emission correlation tomography (SPECT) or positron emission tomography (PET) has been developed. In the method, imaging modules are formed early in the synthesis by attaching imaging agents to the side chain of protected lysines. These modules may be assembled to provide a given set of single- or dual-modal imaging agents, which may be conjugated in the last steps of the synthesis under mild conditions to linkers and targeting groups. A key discovery was the ability of a metal such as gadolinium, useful in MRI, to serve as a protecting group for the chelator, 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid (DOTA). It was further discovered that two lanthanide metals, La and Ce, can double as protecting groups and placeholder metals, which may be transmetalated under mild conditions by metals used for PET in the final step. The modular method enabled the synthesis of discrete targeted probes with two of the same or different dyes, two same or different metals, or mixtures of dyes and metals. The approach was exemplified by the synthesis of single- or dual-modal imaging modules for MRI-OMI, PET-OMI, and PET-MRI, followed by conjugation to the integrin-seeking peptide, c(RGDyK). For Gd modules, their efficacy for MRI was verified by measuring the NMR spin-lattice relaxivity. To validate functional imaging of TMIAs, dual-modal agents containing Cy5.5 were shown to target A549 cancer cells by confocal fluorescence microscopy.
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Affiliation(s)
- Hans F Schmitthenner
- School of Chemistry and Materials Science, Rochester Institute of Technology, Rochester, New York 14623, United States
| | - Taylor M Barrett
- School of Chemistry and Materials Science, Rochester Institute of Technology, Rochester, New York 14623, United States
| | - Stephanie A Beach
- School of Chemistry and Materials Science, Rochester Institute of Technology, Rochester, New York 14623, United States
| | - Lauren E Heese
- School of Chemistry and Materials Science, Rochester Institute of Technology, Rochester, New York 14623, United States
| | - Chelsea Weidman
- School of Chemistry and Materials Science, Rochester Institute of Technology, Rochester, New York 14623, United States
| | - Damien E Dobson
- School of Chemistry and Materials Science, Rochester Institute of Technology, Rochester, New York 14623, United States
| | - Emily R Mahoney
- School of Chemistry and Materials Science, Rochester Institute of Technology, Rochester, New York 14623, United States
| | - Nicholas C Schug
- School of Chemistry and Materials Science, Rochester Institute of Technology, Rochester, New York 14623, United States
| | - Kelsea G Jones
- School of Chemistry and Materials Science, Rochester Institute of Technology, Rochester, New York 14623, United States
| | - Ceyda Durmaz
- School of Chemistry and Materials Science, Rochester Institute of Technology, Rochester, New York 14623, United States
| | - Osarhuwense Otasowie
- School of Chemistry and Materials Science, Rochester Institute of Technology, Rochester, New York 14623, United States
| | - Sean Aronow
- Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, New York 14623, United States
| | - Yin Peng Lee
- Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, New York 14623, United States
| | - Henry D Ophardt
- Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, New York 14623, United States
| | - Amy E Becker
- Chester Carlson Center for Imaging Science, Rochester Institute of Technology, Rochester, New York 14623, United States
| | - Joseph P Hornak
- School of Chemistry and Materials Science, Rochester Institute of Technology, Rochester, New York 14623, United States
- Chester Carlson Center for Imaging Science, Rochester Institute of Technology, Rochester, New York 14623, United States
| | - Irene M Evans
- Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, New York 14623, United States
| | - Maureen C Ferran
- Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, New York 14623, United States
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14
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Song S, Hyodo T, Ikeda H, Vu KAL, Tang Y, Chan ES, Otani Y, Inagaki S, Yamaguchi K, Ohwada T. Contribution of Solvents to Geometrical Preference in the Z/ E Equilibrium of N-Phenylthioacetamide. J Org Chem 2021; 87:1641-1660. [PMID: 34082529 DOI: 10.1021/acs.joc.1c00801] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We studied the Z/E preference of N-phenylthioacetamide (thioacetanilide) derivatives in various solvents by means of 1H NMR spectroscopy, as well as molecular dynamics (MD) and other computational analyses. Our experimental results indicate that the Z/E isomer preference of secondary (NH)thioamides of N-phenylthioacetamides shows substantial solvent dependency, whereas the corresponding amides do not show solvent dependency of the Z/E isomer ratios. Detailed study of the solvent effects based on molecular dynamics simulations revealed that there are two main modes of hydrogen (H)-bond formation between solvent and (NH)thioacetamide, which influence the Z/E isomer preference of (NH)thioamides. DFT calculations of NH-thioamide in the presence of one or two explicit solvent molecules in the continuum solvent model can effectively mimic the solvation by multiple solvent molecules surrounding the thioamide in MD simulations and shed light on the precise nature of the interactions between thioamide and solvent. Orbital interaction analysis showed that, counterintuitively, the Z/E preference of NH-thioacetamides is mainly determined by steric repulsion, while that of sterically congested N-methylthioacetamides is mainly determined by thioamide conjugation.
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Affiliation(s)
- Shuyi Song
- Graduate School of Pharmaceutical Sciences, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Tadashi Hyodo
- Faculty of Pharmaceutical Sciences at Kagawa Campus, Tokushima Bunri University, 1314-1 Shido, Sanuki, Kagawa 769-2193, Japan
| | - Hirotaka Ikeda
- Graduate School of Pharmaceutical Sciences, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Kim Anh L Vu
- Graduate School of Pharmaceutical Sciences, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.,NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore, 119077.,Cancer Science Institute of Singapore, National University of Singapore, Singapore, 117599
| | - Yulan Tang
- Graduate School of Pharmaceutical Sciences, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Erika S Chan
- Graduate School of Pharmaceutical Sciences, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.,Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, 160 Frelinghuysen Road, Piscataway, New Jersey 08854, United States
| | - Yuko Otani
- Graduate School of Pharmaceutical Sciences, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Satoshi Inagaki
- Graduate School of Pharmaceutical Sciences, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Kentaro Yamaguchi
- Faculty of Pharmaceutical Sciences at Kagawa Campus, Tokushima Bunri University, 1314-1 Shido, Sanuki, Kagawa 769-2193, Japan
| | - Tomohiko Ohwada
- Graduate School of Pharmaceutical Sciences, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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15
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Khatri B, Raj N, Chatterjee J. Opportunities and challenges in the synthesis of thioamidated peptides. Methods Enzymol 2021; 656:27-57. [PMID: 34325789 DOI: 10.1016/bs.mie.2021.04.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Chemical modifications of peptides hold great promise for modulating their pharmacological properties. In the last few decades amide to thioamide substitution has been widely explored to modulate the conformation, non-covalent interactions, and proteolytic stability of peptides. Despite widespread utilization, there are some potential limitations including epimerization and degradation under basic and acidic conditions, respectively. In this chapter, we present the synthetic method to build thio-precursors, their site-specific incorporation onto a growing peptide chain, and troubleshooting during the elongation of thioamidated peptides. This highly efficient, rapid, and robust method can be used for positional scanning of the thioamide bond.
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Affiliation(s)
- Bhavesh Khatri
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | - Nishant Raj
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | - Jayanta Chatterjee
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India.
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16
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Fiore KE, Phan HAT, Robkis DM, Walters CR, Petersson EJ. Incorporating thioamides into proteins by native chemical ligation. Methods Enzymol 2021; 656:295-339. [PMID: 34325791 PMCID: PMC8617429 DOI: 10.1016/bs.mie.2021.04.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The thioamide is a versatile replacement of the peptide backbone with altered hydrogen bonding and conformational preferences, as well the ability participate in energy and electron transfer processes. Semi-synthetic incorporation of a thioamide into a protein can be used to study protein folding or protein/protein interactions using these properties. Semi-synthesis also provides the opportunity to study the role of thioamides in natural proteins. Here we outline the semi-synthesis of a model protein, the B1 domain of protein G (GB1) with a thioamide at the N-terminus or the C-terminus. The thioamide is synthetically incorporated into a fragment by solid-phase peptide synthesis, whereas the remainder of the protein is recombinantly expressed. Then, the two fragments are joined by native chemical ligation. The explicit protocol for GB1 synthesis is accompanied by examples of applications with GB1 and other proteins in structural biology and protein misfolding studies.
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Affiliation(s)
- Kristen E Fiore
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, United States
| | - Hoang Anh T Phan
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, United States
| | - D Miklos Robkis
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, United States; Biochemistry and Molecular Biophysics Graduate Group, University of Pennsylvania, Philadelphia, PA, United States
| | - Christopher R Walters
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, United States
| | - E James Petersson
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, United States.
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17
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Novel formulations and drug delivery systems to administer biological solids. Adv Drug Deliv Rev 2021; 172:183-210. [PMID: 33705873 DOI: 10.1016/j.addr.2021.02.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 01/28/2021] [Accepted: 02/18/2021] [Indexed: 12/13/2022]
Abstract
Recent advances in formulation sciences have expanded the previously limited design space for biological modalities, including peptide, protein, and vaccine products. At the same time, the discovery and application of new modalities, such as cellular therapies and gene therapies, have presented formidable challenges to formulation scientists. We explore these challenges and highlight the opportunities to overcome them through the development of novel formulations and drug delivery systems as biological solids. We review the current progress in both industry and academic laboratories, and we provide expert perspectives in those settings. Formulation scientists have made a tremendous effort to accommodate the needs of these novel delivery routes. These include stability-preserving formulations and dehydration processes as well as dosing regimes and dosage forms that improve patient compliance.
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18
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Robkis DM, Hoang EM, Po P, Deutsch CJ, Petersson EJ. Side-chain thioamides as fluorescence quenching probes. Biopolymers 2021; 112:e23384. [PMID: 32740927 PMCID: PMC7744324 DOI: 10.1002/bip.23384] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 05/22/2020] [Accepted: 05/22/2020] [Indexed: 12/11/2022]
Abstract
Thioamides, single atom oxygen-to-sulfur substitutions of canonical amide bonds, can be valuable probes for protein folding and protease studies. Here, we investigate the fluorescence quenching properties of thioamides incorporated into the side-chains of amino acids. We synthesize and incorporate Fmoc-protected, solid-phase peptide synthesis building blocks for introducing Nε -thioacetyl-lysine and γ-thioasparagine. Using rigid model peptides, we demonstrate the distance-dependent fluorescence quenching of these thioamides. Furthermore, we describe attempts to incorporate of Nε -thioacetyl-lysine into proteins expressed in Escherichia coli using amber codon suppression.
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Affiliation(s)
- D Miklos Robkis
- Department of Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Eileen M Hoang
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Pengse Po
- Department of Physiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Carol J Deutsch
- Department of Physiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - E James Petersson
- Department of Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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19
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Boaro A, Ageitos L, Torres M, Bartoloni FH, de la Fuente-Nunez C. Light-Emitting Probes for Labeling Peptides. CELL REPORTS. PHYSICAL SCIENCE 2020; 1:100257. [PMID: 34396352 PMCID: PMC8360326 DOI: 10.1016/j.xcrp.2020.100257] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Peptides are versatile biopolymers composed of 2-100 amino acid residues that present a wide range of biological functions and constitute potential therapies for numerous diseases, partly due to their ability to penetrate cell membranes. However, their mechanisms of action have not been fully elucidated due to the lack of appropriate tools. Existing light-emitting probes are limited by their cytotoxicity and large size, which can alter peptide structure and function. Here, we describe the available fluorescent, bioluminescent, and chemiluminescent probes for labeling peptides, with a focus on minimalistic options.
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Affiliation(s)
- Andreia Boaro
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, and Department of Bioengineering, University of Pennsylvania, 3610 Hamilton Walk, Philadelphia, PA 19104, USA
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Avenida dos Estados, 5001, Santo André, São Paulo 09210-580, Brazil
| | - Lucía Ageitos
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, and Department of Bioengineering, University of Pennsylvania, 3610 Hamilton Walk, Philadelphia, PA 19104, USA
- Centro de Investigacións Científicas Avanzadas (CICA) e Departamento de Química, Facultade de Ciencias, Universidade da Coruña, Calle de la Maestranza, 9, A Coruña 15071, Spain
| | - Marcelo Torres
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, and Department of Bioengineering, University of Pennsylvania, 3610 Hamilton Walk, Philadelphia, PA 19104, USA
| | - Fernando Heering Bartoloni
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Avenida dos Estados, 5001, Santo André, São Paulo 09210-580, Brazil
| | - Cesar de la Fuente-Nunez
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, and Department of Bioengineering, University of Pennsylvania, 3610 Hamilton Walk, Philadelphia, PA 19104, USA
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20
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Zhang J, Liu Z, Yin Z, Yang X, Ma Y, Szostak R, Szostak M. Preference of cis-Thioamide Structure in N-Thioacyl-N-methylanilines. Org Lett 2020; 22:9500-9505. [DOI: 10.1021/acs.orglett.0c03512] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Jin Zhang
- College of Chemistry and Chemical Engineering, Key Laboratory of Chemical Additives for China National Light Industry, Shaanxi University of Science and Technology, Xi’an 710021, China
| | - Zhulin Liu
- College of Chemistry and Chemical Engineering, Key Laboratory of Chemical Additives for China National Light Industry, Shaanxi University of Science and Technology, Xi’an 710021, China
| | - Zheng Yin
- College of Chemistry and Chemical Engineering, Key Laboratory of Chemical Additives for China National Light Industry, Shaanxi University of Science and Technology, Xi’an 710021, China
| | - Xiufang Yang
- College of Chemistry and Chemical Engineering, Key Laboratory of Chemical Additives for China National Light Industry, Shaanxi University of Science and Technology, Xi’an 710021, China
| | - Yangmin Ma
- College of Chemistry and Chemical Engineering, Key Laboratory of Chemical Additives for China National Light Industry, Shaanxi University of Science and Technology, Xi’an 710021, China
| | - Roman Szostak
- Department of Chemistry, Wroclaw University, F. Joliot-Curie 14, Wroclaw 50-383, Poland
| | - Michal Szostak
- Department of Chemistry, Rutgers University, 73 Warren Street, Newark, New Jersey 07102, United States
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21
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Giannakoulias S, Shringari SR, Liu C, Phan HAT, Barrett TM, Ferrie JJ, Petersson EJ. Rosetta Machine Learning Models Accurately Classify Positional Effects of Thioamides on Proteolysis. J Phys Chem B 2020; 124:8032-8041. [PMID: 32869996 DOI: 10.1021/acs.jpcb.0c05981] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Thioamide substitutions of the peptide backbone have been shown to stabilize therapeutic and imaging peptides toward proteolysis. In order to rationally design thioamide modifications, we have developed a novel Rosetta custom score function to classify thioamide positional effects on proteolysis in substrates of serine and cysteine proteases. Peptides of interest were docked into proteases using the FlexPepDock application in Rosetta. Docked complexes were modified to contain thioamides parametrized through the creation of custom atom types in Rosetta based on ab intio simulations. Thioamide complexes were simulated, and the resultant structural complexes provided features for machine learning classification as the decomposed values of the Rosetta score function. An ensemble, majority voting model was developed to be a robust predictor of previously unpublished thioamide proteolysis holdout data. Theoretical control simulations with pseudo-atoms that modulate only one physical characteristic of the thioamide show differential effects on prediction accuracy by the optimized voting classification model. These pseudo-atom model simulations, as well as statistical analyses of the full thioamide simulations, implicate steric effects on peptide binding as being primarily responsible for thioamide positional effects on proteolytic resistance.
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Affiliation(s)
- Sam Giannakoulias
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Sumant R Shringari
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Chunxiao Liu
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Hoang Anh T Phan
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Taylor M Barrett
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - John J Ferrie
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - E James Petersson
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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