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Article ; Online: Diversification of Phage-Displayed Peptide Libraries with Noncanonical Amino Acid Mutagenesis and Chemical Modification.

Hampton, J Trae / Liu, Wenshe Ray

2024 Volume 124, Issue 9, Page(s) 6051–6077

Abstract: Sitting on the interface between biologics and small molecules, peptides represent an emerging class of therapeutics. Numerous techniques have been developed in the past 30 years to take advantage of biological methods to generate and screen peptide ... ...

Abstract	Sitting on the interface between biologics and small molecules, peptides represent an emerging class of therapeutics. Numerous techniques have been developed in the past 30 years to take advantage of biological methods to generate and screen peptide libraries for the identification of therapeutic compounds, with phage display being one of the most accessible techniques. Although traditional phage display can generate billions of peptides simultaneously, it is limited to expression of canonical amino acids. Recently, several groups have successfully undergone efforts to apply genetic code expansion to introduce noncanonical amino acids (ncAAs) with novel reactivities and chemistries into phage-displayed peptide libraries. In addition to biological methods, several different chemical approaches have also been used to install noncanonical motifs into phage libraries. This review focuses on these recent advances that have taken advantage of both biological and chemical means for diversification of phage libraries with ncAAs.
MeSH term(s)	Peptide Library ; Amino Acids/chemistry ; Amino Acids/genetics ; Mutagenesis ; Peptides/chemistry ; Peptides/metabolism ; Peptides/genetics
Chemical Substances	Peptide Library ; Amino Acids ; Peptides
Language	English
Publishing date	2024-04-30
Publishing country	United States
Document type	Journal Article ; Review ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ZDB-ID	207949-5
ISSN	1520-6890 ; 0009-2665
ISSN (online)	1520-6890
ISSN	0009-2665
DOI	10.1021/acs.chemrev.4c00004
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Article ; Online: Site Specific Lysine Acetylation of Histones for Nucleosome Reconstitution using Genetic Code Expansion in Escherichia coli.

Rowlett, Chesley Marie / Liu, Wenshe Ray

Journal of visualized experiments : JoVE

2020 , Issue 166

Abstract: Acetylated histone proteins can be easily expressed in Escherichia coli encoding a mutant, ... ...

Abstract	Acetylated histone proteins can be easily expressed in Escherichia coli encoding a mutant, N
MeSH term(s)	Acetylation ; Amino Acyl-tRNA Synthetases/genetics ; Amino Acyl-tRNA Synthetases/metabolism ; DNA/metabolism ; Endopeptidases/metabolism ; Escherichia coli/genetics ; Escherichia coli/metabolism ; Escherichia coli Proteins/metabolism ; Genetic Code ; Histones/metabolism ; Lysine/analogs & derivatives ; Lysine/metabolism ; Methanosarcina/enzymology ; Nucleosomes/metabolism ; Plasmids/genetics ; Protein Multimerization ; Protein Processing, Post-Translational ; RNA, Transfer/metabolism
Chemical Substances	Escherichia coli Proteins ; Histones ; Nucleosomes ; DNA (9007-49-2) ; RNA, Transfer (9014-25-9) ; Endopeptidases (EC 3.4.-) ; TEV protease (EC 3.4.-) ; Amino Acyl-tRNA Synthetases (EC 6.1.1.-) ; pyrrolysine (H3214Y96LP) ; Lysine (K3Z4F929H6)
Language	English
Publishing date	2020-12-26
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Video-Audio Media
ZDB-ID	2259946-0
ISSN	1940-087X ; 1940-087X
ISSN (online)	1940-087X
ISSN	1940-087X
DOI	10.3791/62113
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Article ; Online: Protein Synthesis via Activated Cysteine-Directed Protein Ligation.

Yu, Ge / Qiao, Yuchen / Blankenship, Lauren R / Liu, Wenshe Ray

Methods in molecular biology (Clifton, N.J.)

2022 Volume 2530, Page(s) 159–167

Abstract: Proteins with a functionalized C-terminus are critical to synthesizing large proteins via expressed protein ligation. To overcome the limitations of currently available C-terminus functionalization strategies, we established an approach based on a small ... ...

Abstract	Proteins with a functionalized C-terminus are critical to synthesizing large proteins via expressed protein ligation. To overcome the limitations of currently available C-terminus functionalization strategies, we established an approach based on a small molecule cyanylating reagent that chemically activates a cysteine in a recombinant protein at its N-side amide for undergoing nucleophilic acyl substitution with amines. We demonstrated the versatility of this approach by successfully synthesizing RNAse H with its RNA hydrolyzing activity restored and in vitro nucleosome build with a C-terminal posttranslational modified histone H2A. This technique will expand the landscape of protein chemical synthesis and its application in new research fields significantly.
MeSH term(s)	Cysteine ; Histones ; Nucleosomes ; Protein Biosynthesis ; RNA
Chemical Substances	Histones ; Nucleosomes ; RNA (63231-63-0) ; Cysteine (K848JZ4886)
Language	English
Publishing date	2022-06-27
Publishing country	United States
Document type	Journal Article
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-0716-2489-0_11
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Article ; Online: Evolutionary and Structural Insights about Potential SARS-CoV-2 Evasion of Nirmatrelvir.

Yang, Kai S / Leeuwon, Sunshine Z / Xu, Shiqing / Liu, Wenshe Ray

Journal of medicinal chemistry

2022 Volume 65, Issue 13, Page(s) 8686–8698

Abstract: The U.S. FDA approval of PAXLOVID, a combination therapy of nirmatrelvir and ritonavir has significantly boosted our morale in fighting the COVID-19 pandemic. Nirmatrelvir is an inhibitor of the main protease ( ... ...

Abstract	The U.S. FDA approval of PAXLOVID, a combination therapy of nirmatrelvir and ritonavir has significantly boosted our morale in fighting the COVID-19 pandemic. Nirmatrelvir is an inhibitor of the main protease (M
MeSH term(s)	Coronavirus 3C Proteases ; Humans ; Pandemics ; SARS-CoV-2/genetics ; Viral Nonstructural Proteins/chemistry ; COVID-19 Drug Treatment
Chemical Substances	Viral Nonstructural Proteins ; Coronavirus 3C Proteases (EC 3.4.22.28)
Language	English
Publishing date	2022-06-22
Publishing country	United States
Document type	Journal Article ; Review ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ZDB-ID	218133-2
ISSN	1520-4804 ; 0022-2623
ISSN (online)	1520-4804
ISSN	0022-2623
DOI	10.1021/acs.jmedchem.2c00404
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Article ; Online: The Construction of a Genetically Encoded, Phage-Displayed Cyclic-Peptide Library.

Chen, Peng-Hsun Chase / Liu, Wenshe Ray

Methods in molecular biology (Clifton, N.J.)

2021 Volume 2355, Page(s) 219–230

Abstract: Due to the great potentials of cyclic peptides as therapeutic agents, several phage-displayed peptide libraries in which cyclization is achieved by the covalent linkage of cysteines have been previously demonstrated to identify cyclic-peptide ligands for ...

Abstract	Due to the great potentials of cyclic peptides as therapeutic agents, several phage-displayed peptide libraries in which cyclization is achieved by the covalent linkage of cysteines have been previously demonstrated to identify cyclic-peptide ligands for therapeutic targets. While problems remain in these cysteine conjugation strategies, we have invented a phage display technique in which its displayed peptides are cyclized through a proximity-driven Michael addition reaction between a cysteine and an amber-codon-encoded N
MeSH term(s)	Bacteriophages/genetics ; Cysteine ; Ligands ; Peptide Library ; Peptides/genetics ; Peptides, Cyclic/genetics
Chemical Substances	Ligands ; Peptide Library ; Peptides ; Peptides, Cyclic ; Cysteine (K848JZ4886)
Language	English
Publishing date	2021-08-13
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-0716-1617-8_17
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Article ; Online: Site-Specific Conversion of Cysteine in a Protein to Dehydroalanine Using 2-Nitro-5-thiocyanatobenzoic Acid.

Qiao, Yuchen / Yu, Ge / Leeuwon, Sunshine Z / Liu, Wenshe Ray

Molecules (Basel, Switzerland)

2021 Volume 26, Issue 9

Abstract: Dehydroalanine exists natively in certain proteins and can also be chemically made from the protein cysteine. As a strong Michael acceptor, dehydroalanine in proteins has been explored to undergo reactions with different thiolate reagents for making ... ...

Abstract	Dehydroalanine exists natively in certain proteins and can also be chemically made from the protein cysteine. As a strong Michael acceptor, dehydroalanine in proteins has been explored to undergo reactions with different thiolate reagents for making close analogues of post-translational modifications (PTMs), including a variety of lysine PTMs. The chemical reagent 2-nitro-5-thiocyanatobenzoic acid (NTCB) selectively modifies cysteine to form
MeSH term(s)	Alanine/analogs & derivatives ; Alanine/chemistry ; Chromatography, High Pressure Liquid ; Chromatography, Liquid ; Cysteine/chemistry ; Models, Molecular ; Protein Conformation ; Protein Processing, Post-Translational/drug effects ; Proteins/chemistry ; Recombinant Proteins ; Spectrometry, Mass, Electrospray Ionization ; Thiocyanates/chemistry ; Thiocyanates/pharmacology
Chemical Substances	Proteins ; Recombinant Proteins ; Thiocyanates ; dehydroalanine (98RA387EKY) ; Cysteine (K848JZ4886) ; 2-nitro-5-thiocyanobenzoic acid (O5VCA1GS5O) ; Alanine (OF5P57N2ZX)
Language	English
Publishing date	2021-04-29
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	1413402-0
ISSN	1420-3049 ; 1431-5165 ; 1420-3049
ISSN (online)	1420-3049
ISSN	1431-5165 ; 1420-3049
DOI	10.3390/molecules26092619
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Article: Site specific lysine acetylation of histones for nucleosome reconstitution using genetic code expansion in Escherichia coli

Rowlett, Chesley Marie / Liu, Wenshe Ray

Journal of visualized experiments. 2020 Dec. 26, , no. 166

2020

Abstract: Acetylated histone proteins can be easily expressed in Escherichia coli encoding a mutant, Nε-acetyl-lysine (AcK)-specific Methanosarcina mazi pyrrolysine tRNA-synthetase (MmAcKRS1) and its cognate tRNA (tRNAPyl) to assemble reconstituted mononucleosomes ...

Abstract	Acetylated histone proteins can be easily expressed in Escherichia coli encoding a mutant, Nε-acetyl-lysine (AcK)-specific Methanosarcina mazi pyrrolysine tRNA-synthetase (MmAcKRS1) and its cognate tRNA (tRNAPyl) to assemble reconstituted mononucleosomes with site specific acetylated histones. MmAcKRS1 and tRNAPyl deliver AcK at an amber mutation site in the mRNA of choice during translation in Escherichia coli. This technique has been used extensively to incorporate AcK at H3 lysine sites. Pyrrolysyl-tRNA synthetase (PylRS) can also be easily evolved to incorporate other noncanonical amino acids (ncAAs) for site specific protein modification or functionalization. Here we detail a method to incorporate AcK using the MmAcKRS1 system into histone H3 and integrate acetylated H3 proteins into reconstituted mononucleosomes. Acetylated reconstituted mononucleosomes can be used in biochemical and binding assays, structure determination, and more. Obtaining modified mononucleosomes is crucial for designing experiments related to discovering new interactions and understanding epigenetics.
Keywords	Escherichia coli ; Methanosarcina ; acetylation ; epigenetics ; genetic code ; histones ; lysine ; mutants ; nonsense mutation ; nucleosomes
Language	English
Dates of publication	2020-1226
Size	p. e62113.
Publishing place	Journal of Visualized Experiments
Document type	Article
Note	NAL-AP-2-clean
ZDB-ID	2259946-0
ISSN	1940-087X
ISSN	1940-087X
DOI	10.3791/62113
Database	NAL-Catalogue (AGRICOLA)

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Article: Leveraging a Phage-Encoded Noncanonical Amino Acid: A Novel Pathway to Potent and Selective Epigenetic Reader Protein Inhibitors.

Chen, Peng-Hsun Chase / Guo, Xuejiao Shirley / Zhang, Hanyuan Eric / Dubey, Gopal K / Geng, Zhi Zachary / Fierke, Carol A / Xu, Shiqing / Hampton, J Trae / Liu, Wenshe Ray

ACS central science

2024 Volume 10, Issue 4, Page(s) 782–792

Abstract: Epigenetic reader proteins interpret histone epigenetic marks to regulate gene expression. Given their vital roles and the link between their dysfunction and various diseases, these proteins present compelling targets for therapeutic interventions. ... ...

Abstract	Epigenetic reader proteins interpret histone epigenetic marks to regulate gene expression. Given their vital roles and the link between their dysfunction and various diseases, these proteins present compelling targets for therapeutic interventions. Nevertheless, designing selective inhibitors for these proteins poses significant challenges, primarily due to their unique properties such as shallow binding sites and similarities with homologous proteins. To overcome these challenges, we propose an innovative strategy that uses phage display with a genetically encoded noncanonical amino acid (ncAA) containing an epigenetic mark. This ncAA guides binding to the reader protein's active site, allowing the identification of peptide inhibitors with enhanced affinity and selectivity. In this study, we demonstrate this novel approach's effectiveness by identifying potent inhibitors for the ENL YEATS domain that plays a critical role in leukemogenesis. Our strategy involved genetically incorporating
Language	English
Publishing date	2024-02-28
Publishing country	United States
Document type	Journal Article
ISSN	2374-7943
ISSN	2374-7943
DOI	10.1021/acscentsci.3c01419
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Article: A Designed, Highly Efficient Pyrrolysyl-tRNA Synthetase Mutant Binds o-Chlorophenylalanine Using Two Halogen Bonds

Vatansever, Erol C. / Yang, Kai S. / Geng, Zhi Zachary / Qiao, Yuchen / Li, Pingwei / Xu, Shiqing / Liu, Wenshe Ray

Journal of molecular biology. 2022 Mar. 05,

2022

Abstract: As one of the most valuable tools for genetic code expansion, pyrrolysyl-tRNA synthetase (PylRS) is structurally related to phenylalanyl-tRNA synthetase (PheRS). By introducing mutations that mimic ligand interactions in PheRS into PylRS, we designed a ... ...

Abstract	As one of the most valuable tools for genetic code expansion, pyrrolysyl-tRNA synthetase (PylRS) is structurally related to phenylalanyl-tRNA synthetase (PheRS). By introducing mutations that mimic ligand interactions in PheRS into PylRS, we designed a PylRS mutant. This mutant, designated as oClFRS, recognizes a number of o-substituted phenylalanines for their genetic incorporation at amber codon. Its efficiency in catalyzing genetic incorporation of o-chlorophenylalanine (o-ClF) is better than that for Nᵋ-tert-butyloxycarbonyl-lysine catalyzed by PylRS. The crystal structure of oClFRS bound with o-ClF shows that o-ClF binds deeply into a hydrophobic but catalytically inactive pocket in the active site and involves two halogen bonds to achieve strong interactions. The shift of o-ClF to a catalytically active position in the oClFRS active site will be necessary for its activation. This is the first reported aminoacyl-tRNA synthetase that involves two halogen bonds for ligation recognition and might represent an alternative route to develop aminoacyl-tRNA synthetase mutants that are selective for noncanonical amino acids over native amino acids.
Keywords	active sites ; crystal structure ; genetic code ; halogens ; hydrophobicity ; ligands ; molecular biology ; mutants ; phenylalanine-tRNA ligase ; stop codon
Language	English
Dates of publication	2022-0305
Publishing place	Elsevier Ltd
Document type	Article
Note	Pre-press version
ZDB-ID	80229-3
ISSN	1089-8638 ; 0022-2836
ISSN (online)	1089-8638
ISSN	0022-2836
DOI	10.1016/j.jmb.2022.167534
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Article ; Online: Learning from the Past: Possible Urgent Prevention and Treatment Options for Severe Acute Respiratory Infections Caused by 2019-nCoV.

Morse, Jared S / Lalonde, Tyler / Xu, Shiqing / Liu, Wenshe Ray

Chembiochem : a European journal of chemical biology

2020 Volume 21, Issue 5, Page(s) 730–738

Abstract: With the current trajectory of the 2019-nCoV outbreak unknown, public health and medicinal measures will both be needed to contain spreading of the virus and to optimize patient outcomes. Although little is known about the virus, an examination of the ... ...

Abstract	With the current trajectory of the 2019-nCoV outbreak unknown, public health and medicinal measures will both be needed to contain spreading of the virus and to optimize patient outcomes. Although little is known about the virus, an examination of the genome sequence shows strong homology with its better-studied cousin, SARS-CoV. The spike protein used for host cell infection shows key nonsynonymous mutations that might hamper the efficacy of previously developed therapeutics but remains a viable target for the development of biologics and macrocyclic peptides. Other key drug targets, including RNA-dependent RNA polymerase and coronavirus main proteinase (3CLpro), share a strikingly high (>95 %) homology to SARS-CoV. Herein, we suggest four potential drug candidates (an ACE2-based peptide, remdesivir, 3CLpro-1 and a novel vinylsulfone protease inhibitor) that could be used to treat patients suffering with the 2019-nCoV. We also summarize previous efforts into drugging these targets and hope to help in the development of broad-spectrum anti-coronaviral agents for future epidemics.
MeSH term(s)	Antiviral Agents/chemistry ; Antiviral Agents/therapeutic use ; Betacoronavirus/enzymology ; Betacoronavirus/genetics ; COVID-19 ; Coronavirus 3C Proteases ; Coronavirus Infections/drug therapy ; Coronavirus Infections/prevention & control ; Coronavirus Infections/transmission ; Cysteine Endopeptidases/chemistry ; Cysteine Endopeptidases/genetics ; Cysteine Endopeptidases/metabolism ; Drug Design ; Humans ; Pneumonia, Viral/drug therapy ; Pneumonia, Viral/prevention & control ; Pneumonia, Viral/transmission ; RNA-Dependent RNA Polymerase/chemistry ; RNA-Dependent RNA Polymerase/genetics ; RNA-Dependent RNA Polymerase/metabolism ; SARS-CoV-2 ; COVID-19 Drug Treatment
Chemical Substances	Antiviral Agents ; RNA-Dependent RNA Polymerase (EC 2.7.7.48) ; Cysteine Endopeptidases (EC 3.4.22.-) ; Coronavirus 3C Proteases (EC 3.4.22.28)
Keywords	covid19
Language	English
Publishing date	2020-02-25
Publishing country	Germany
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2020469-3
ISSN	1439-7633 ; 1439-4227
ISSN (online)	1439-7633
ISSN	1439-4227
DOI	10.1002/cbic.202000047
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