1
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Dunham NP, Winston MS, Ray R, Eberle CM, Newman JA, Gao Q, Cao Y, Barrientos RC, Ji Y, Reibarkh MY, Silverman SM. Transaminase-Catalyzed Synthesis of β-Branched Noncanonical Amino Acids Driven by a Lysine Amine Donor. J Am Chem Soc 2024; 146:16306-16313. [PMID: 38804633 DOI: 10.1021/jacs.4c05175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Transaminases are choice biocatalysts for the synthesis of chiral primary amines, including amino acids bearing contiguous stereocenters. In this study, we employ lysine as a "smart" amine donor in transaminase-catalyzed dynamic kinetic resolution reactions to access β-branched noncanonical arylalanines. Our mechanistic investigation demonstrates that, upon transamination, the lysine-derived ketone byproduct readily cyclizes to a six-membered imine, driving the equilibrium in the desired direction and thus alleviating the need to load superstoichiometric quantities of the amine donor or deploy a multienzyme cascade. Lysine also shows good overall compatibility with a panel of wild-type transaminases, a promising hint of its application as a smart donor more broadly. Indeed, by this approach, we furnished a broad scope of β-branched arylalanines, including some bearing hitherto intractable cyclopropyl and isopropyl substituents, with high yields and excellent selectivities.
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Affiliation(s)
- Noah P Dunham
- Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Matthew S Winston
- Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Ritwika Ray
- Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Claire M Eberle
- Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Justin A Newman
- Analytical Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Qi Gao
- Analytical Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Yang Cao
- Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Rodell C Barrientos
- Analytical Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Yining Ji
- Analytical Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Mikhail Y Reibarkh
- Analytical Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Steven M Silverman
- Process Research and Development, Merck & Co., Inc., Rahway, New Jersey 07065, United States
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2
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Werner M, Brinkhofer J, Hammermüller L, Heim T, Pham TL, Huber J, Klein C, Thomas F. Peptide Boronic Acids by Late-Stage Hydroboration on the Solid Phase. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2400640. [PMID: 38810019 DOI: 10.1002/advs.202400640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 05/15/2024] [Indexed: 05/31/2024]
Abstract
Organoboron compounds have a wide range of applications in numerous research fields, and metmhods to incorporate them in biomolecules are much sought after. Here, on-resin chemical syntheses of aliphatic and vinylogous peptide boronic acids are presented by transition metal-catalyzed late-stage hydroboration of alkene and alkyne groups in peptides and peptoids, for example on allyl- and propargylglycine residues, using readily available chemicals. These methods yield peptide boronic acids with much shorter linkers than previously reported on-resin methods. Furthermore, the methods are regio- and stereoselective, compatible with all canonical amino acid residues and can be applied to short, long, and in part even "difficult" peptide sequences. In a feasibility study, the protected peptide vinylboronic acids are further derivatized by the Petasis reaction using salicylaldehyde derivatives. The ability of the obtained peptide boronic acids to reversibly bind to carbohydrates is demonstrated in a catch-release model experiment using a fluorescently labeled peptide boronic acid on cross-linked dextran beads. In summary, this highlights the potential of the target compounds for drug discovery, glycan-specific target recognition, controlled release, and diagnostics.
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Affiliation(s)
- Marius Werner
- Institute of Organic Chemistry, Heidelberg University, Im Neuenheimer Feld 270, 69120, Heidelberg, Germany
- Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University, Im Neuenheimer Feld 364, 69120, Heidelberg, Germany
| | - Julian Brinkhofer
- Institute of Organic Chemistry, Heidelberg University, Im Neuenheimer Feld 270, 69120, Heidelberg, Germany
| | - Leon Hammermüller
- Institute of Organic Chemistry, Heidelberg University, Im Neuenheimer Feld 270, 69120, Heidelberg, Germany
| | - Thomas Heim
- Institute of Organic Chemistry, Heidelberg University, Im Neuenheimer Feld 270, 69120, Heidelberg, Germany
| | - Truc Lam Pham
- Institute of Organic Chemistry, Heidelberg University, Im Neuenheimer Feld 270, 69120, Heidelberg, Germany
| | - Jonas Huber
- Institute of Organic Chemistry, Heidelberg University, Im Neuenheimer Feld 270, 69120, Heidelberg, Germany
| | - Christian Klein
- Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University, Im Neuenheimer Feld 364, 69120, Heidelberg, Germany
| | - Franziska Thomas
- Institute of Organic Chemistry, Heidelberg University, Im Neuenheimer Feld 270, 69120, Heidelberg, Germany
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3
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Dennis DG, Joo Sun Y, Parsons DE, Mahajan VB, Smith M. Identification of highly potent and selective HTRA1 inhibitors. Bioorg Med Chem Lett 2024; 109:129814. [PMID: 38815872 DOI: 10.1016/j.bmcl.2024.129814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 05/17/2024] [Accepted: 05/21/2024] [Indexed: 06/01/2024]
Abstract
High temperature requirement A serine peptidase 1 (HTRA1) is a serine protease involved in an array of signaling pathways. It is also responsible for the regulation of protein aggregates via refolding, translocation, and degradation. It has subsequently been found that runaway proteolytic HTRA1 activity plays a role in a variety of diseases, including Age-Related Macular Degeneration (AMD), osteoarthritis, and Rheumatoid Arthritis. Selective inhibition of serine protease HTRA1 therefore offers a promising new strategy for the treatment of these diseases. Herein we disclose structure-activity-relationship (SAR) studies which identify key interactions responsible for binding affinity of small molecule inhibitors to HTRA1. The study results in highly potent molecules with IC50's less than 15 nM and excellent selectivity following a screen of 35 proteases.
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Affiliation(s)
- David G Dennis
- Medicinal Chemistry Knowledge Center, Sarafan ChEM-H, Stanford University, CA 94305, USA; Molecular Surgery Laboratory, Byers Eye Institute, Department of Ophthalmology, Stanford University, CA 94304, USA
| | - Young Joo Sun
- Molecular Surgery Laboratory, Byers Eye Institute, Department of Ophthalmology, Stanford University, CA 94304, USA
| | - Dylan E Parsons
- Medicinal Chemistry Knowledge Center, Sarafan ChEM-H, Stanford University, CA 94305, USA; Molecular Surgery Laboratory, Byers Eye Institute, Department of Ophthalmology, Stanford University, CA 94304, USA
| | - Vinit B Mahajan
- Molecular Surgery Laboratory, Byers Eye Institute, Department of Ophthalmology, Stanford University, CA 94304, USA; Veterans Affairs Palo Alto Health Care System, CA 94304, USA.
| | - Mark Smith
- Medicinal Chemistry Knowledge Center, Sarafan ChEM-H, Stanford University, CA 94305, USA.
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4
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Jo WS, Curtis BJ, Rehan M, Adrover-Castellano ML, Sherman DH, Healy AR. N-to- S Acyl Transfer as an Enabling Strategy in Asymmetric and Chemoenzymatic Synthesis. JACS AU 2024; 4:2058-2066. [PMID: 38818054 PMCID: PMC11134368 DOI: 10.1021/jacsau.4c00257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 05/01/2024] [Accepted: 05/02/2024] [Indexed: 06/01/2024]
Abstract
The observation of thioester-mediated acyl transfer processes in nature has inspired the development of novel protein synthesis and functionalization methodologies. The chemoselective transfer of an acyl group from S-to-N is the basis of several powerful ligation strategies. In this work, we sought to apply the reverse process, the transfer of an acyl group from N-to-S, as a method to convert stable chiral amides into more reactive thioesters. To this end, we developed a novel cysteine-derived oxazolidinone that serves as both a chiral imide auxiliary and an acyl transfer agent. This auxiliary combines the desirable features of rigid chiral imides as templates for asymmetric transformations with the synthetic applicability of thioesters. We demonstrate that the auxiliary can be applied in a range of highly selective asymmetric transformations. Subsequent intramolecular N-to-S acyl transfer of the chiral product and in situ trapping of the resulting thioester provides access to diverse carboxylic acid derivatives under mild conditions. The oxazolidinone thioester products can also be isolated and used in Pd-mediated transformations to furnish highly valuable chiral scaffolds, such as noncanonical amino acids, cyclic ketones, tetrahydropyrones, and dihydroquinolinones. Finally, we demonstrate that the oxazolidinone thioesters can also serve as a surrogate for SNAC-thioesters, enabling their seamless use as non-native substrates in biocatalytic transformations.
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Affiliation(s)
- Woonkee S Jo
- Chemistry Program, New York University Abu Dhabi (NYUAD), Saadiyat Island, Abu Dhabi 129188, United Arab Emirates (UAE)
| | - Brian J Curtis
- Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI 48109, USA
| | - Mohammad Rehan
- Chemistry Program, New York University Abu Dhabi (NYUAD), Saadiyat Island, Abu Dhabi 129188, United Arab Emirates (UAE)
| | | | - David H Sherman
- Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI 48109, USA
- Departments of Medicinal Chemistry, Chemistry, and Microbiology & Immunology, University of Michigan, Ann Arbor, MI 48109USA
| | - Alan R Healy
- Chemistry Program, New York University Abu Dhabi (NYUAD), Saadiyat Island, Abu Dhabi 129188, United Arab Emirates (UAE)
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5
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Ouyang Y, Page CG, Bilodeau C, Hyster TK. Synergistic Photoenzymatic Catalysis Enables Synthesis of a-Tertiary Amino Acids Using Threonine Aldolases. J Am Chem Soc 2024; 146:13754-13759. [PMID: 38739748 DOI: 10.1021/jacs.4c04661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
a-Tertiary amino acids are essential components of drugs and agrochemicals, yet traditional syntheses are step-intensive and provide access to a limited range of structures with varying levels of enantioselectivity. Here, we report the α-alkylation of unprotected alanine and glycine by pyridinium salts using pyridoxal (PLP)-dependent threonine aldolases with a Rose Bengal photoredox catalyst. The strategy efficiently prepares various a-tertiary amino acids in a single chemical step as a single enantiomer. UV-vis spectroscopy studies reveal a ternary interaction between the pyridinium salt, protein, and photocatalyst, which we hypothesize is responsible for localizing radical formation to the active site. This method highlights the opportunity for combining photoredox catalysts with enzymes to reveal new catalytic functions for known enzymes.
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Affiliation(s)
- Yao Ouyang
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Claire G Page
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Catherine Bilodeau
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Todd K Hyster
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
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6
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Feng Y, Qirjollari A, Fawaz MV, Cancilla MT, Gonzalez RJ, Pearson K. Rapid and Definitive Identification of Cyclic Peptide Soft Spots by Isotope-Labeled Reductive Dimethylation and Mass Spectrometry Fragmentation. Anal Chem 2024; 96:7756-7762. [PMID: 38690743 DOI: 10.1021/acs.analchem.4c01372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2024]
Abstract
Cyclic peptides are an emerging therapeutic modality over the past few decades. To identify drug candidates with sufficient proteolytic stability for oral administration, it is critical to pinpoint the amide bond hydrolysis sites, or soft spots, to better understand their metabolism and provide guidance on further structure optimization. However, the unambiguous characterization of cyclic peptide soft spots remains a significant challenge during early stage discovery studies, as amide bond hydrolysis forms a linearized isobaric sequence with the addition of a water molecule, regardless of the amide hydrolysis location. In this study, an innovative strategy was developed to enable the rapid and definitive identification of cyclic peptide soft spots by isotope-labeled reductive dimethylation and mass spectrometry fragmentation. The dimethylated immonium ion with enhanced MS signal at a distinctive m/z in MS/MS fragmentation spectra reveals the N-terminal amino acid on a linearized peptide sequence definitively and, thus, significantly simplifies the soft spot identification workflow. This approach has been evaluated to demonstrate the potential of isotope-labeled dimethylation to be a powerful analytical tool in cyclic peptide drug discovery and development.
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Affiliation(s)
- Yu Feng
- Nonclinical Drug Safety, MRL, Merck & Co., Inc., 770 Sumneytown Pike, West Point, Pennsylvania 19486, United States
| | - Athanasia Qirjollari
- Nonclinical Drug Safety, MRL, Merck & Co., Inc., 770 Sumneytown Pike, West Point, Pennsylvania 19486, United States
| | - Maria V Fawaz
- Pharmacokinetics, Dynamics, Metabolism, and Bioanalytics, MRL, Merck & Co., Inc., 770 Sumneytown Pike, West Point, Pennsylvania 19486, United States
| | - Mark T Cancilla
- Pharmacokinetics, Dynamics, Metabolism, and Bioanalytics, MRL, Merck & Co., Inc., 770 Sumneytown Pike, West Point, Pennsylvania 19486, United States
| | - Raymond J Gonzalez
- Nonclinical Drug Safety, MRL, Merck & Co., Inc., 770 Sumneytown Pike, West Point, Pennsylvania 19486, United States
| | - Kara Pearson
- Nonclinical Drug Safety, MRL, Merck & Co., Inc., 770 Sumneytown Pike, West Point, Pennsylvania 19486, United States
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7
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Wang TC, Mai BK, Zhang Z, Bo Z, Li J, Liu P, Yang Y. Stereoselective amino acid synthesis by photobiocatalytic oxidative coupling. Nature 2024; 629:98-104. [PMID: 38693411 DOI: 10.1038/s41586-024-07284-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 03/07/2024] [Indexed: 05/03/2024]
Abstract
Photobiocatalysis-where light is used to expand the reactivity of an enzyme-has recently emerged as a powerful strategy to develop chemistries that are new to nature. These systems have shown potential in asymmetric radical reactions that have long eluded small-molecule catalysts1. So far, unnatural photobiocatalytic reactions are limited to overall reductive and redox-neutral processes2-9. Here we report photobiocatalytic asymmetric sp3-sp3 oxidative cross-coupling between organoboron reagents and amino acids. This reaction requires the cooperative use of engineered pyridoxal biocatalysts, photoredox catalysts and an oxidizing agent. We repurpose a family of pyridoxal-5'-phosphate-dependent enzymes, threonine aldolases10-12, for the α-C-H functionalization of glycine and α-branched amino acid substrates by a radical mechanism, giving rise to a range of α-tri- and tetrasubstituted non-canonical amino acids 13-15 possessing up to two contiguous stereocentres. Directed evolution of pyridoxal radical enzymes allowed primary and secondary radical precursors, including benzyl, allyl and alkylboron reagents, to be coupled in an enantio- and diastereocontrolled fashion. Cooperative photoredox-pyridoxal biocatalysis provides a platform for sp3-sp3 oxidative coupling16, permitting the stereoselective, intermolecular free-radical transformations that are unknown to chemistry or biology.
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Affiliation(s)
- Tian-Ci Wang
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, CA, USA
| | - Binh Khanh Mai
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Zheng Zhang
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, CA, USA
| | - Zhiyu Bo
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, CA, USA
| | - Jiedong Li
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, CA, USA
| | - Peng Liu
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA.
| | - Yang Yang
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, CA, USA.
- Biomolecular Science and Engineering (BMSE) Program, University of California Santa Barbara, Santa Barbara, CA, USA.
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8
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Ma X, Beard AM, Burgess SA, Darlak M, Newman JA, Nogle LM, Pietrafitta MJ, Smith DA, Wang X, Yue L. General Synthesis of Conformationally Constrained Noncanonical Amino Acids with C( sp3)-Rich Benzene Bioisosteres. J Org Chem 2024; 89:5010-5018. [PMID: 38532573 DOI: 10.1021/acs.joc.4c00225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/28/2024]
Abstract
Recent years have seen novel modalities emerge for the treatment of human diseases resulting in an increase in beyond rule of 5 (bRo5) chemical matter. As a result, synthetic innovations aiming to enable rapid access to complex bRo5 molecular entities have become increasingly valuable for medicinal chemists' toolkits. Herein, we report the general synthesis of a new class of noncanonical amino acids (ncAA) with a cyclopropyl backbone to achieve conformational constraint and bearing C(sp3)-rich benzene bioisosteres. We also demonstrate preliminary studies toward utilities of these ncAA as building blocks for medicinal chemistry research.
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Affiliation(s)
- Xiaoshen Ma
- Department of Discovery Chemistry, Merck & Co., Inc., 33 Ave. Louis Pasteur, Boston, Massachusetts 02215, United States
| | - Adam M Beard
- Department of Discovery Chemistry, Merck & Co., Inc., 33 Ave. Louis Pasteur, Boston, Massachusetts 02215, United States
| | - Samantha A Burgess
- Analytical Research & Development, Merck & Co., Inc., 33 Ave. Louis Pasteur, Boston, Massachusetts 02215, United States
| | - Miroslawa Darlak
- Department of Discovery Chemistry, Merck & Co., Inc., 33 Ave. Louis Pasteur, Boston, Massachusetts 02215, United States
| | - Justin A Newman
- Analytical Research and Development, Merck & Co., Inc., 126 E. Lincoln Ave., Rahway, New Jersey 07065, United States
| | - Lisa M Nogle
- Department of Discovery Chemistry, Merck & Co., Inc., 33 Ave. Louis Pasteur, Boston, Massachusetts 02215, United States
| | - Mark J Pietrafitta
- Department of Discovery Chemistry, Merck & Co., Inc., 33 Ave. Louis Pasteur, Boston, Massachusetts 02215, United States
| | - David A Smith
- Department of Discovery Chemistry, Merck & Co., Inc., 33 Ave. Louis Pasteur, Boston, Massachusetts 02215, United States
| | - Xiao Wang
- Analytical Research and Development, Merck & Co., Inc., 126 E. Lincoln Ave., Rahway, New Jersey 07065, United States
| | - Lei Yue
- Department of Discovery Chemistry, Merck & Co., Inc., 33 Ave. Louis Pasteur, Boston, Massachusetts 02215, United States
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9
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Nandi S, Bhaduri S, Das D, Ghosh P, Mandal M, Mitra P. Deciphering the Lexicon of Protein Targets: A Review on Multifaceted Drug Discovery in the Era of Artificial Intelligence. Mol Pharm 2024; 21:1563-1590. [PMID: 38466810 DOI: 10.1021/acs.molpharmaceut.3c01161] [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: 03/13/2024]
Abstract
Understanding protein sequence and structure is essential for understanding protein-protein interactions (PPIs), which are essential for many biological processes and diseases. Targeting protein binding hot spots, which regulate signaling and growth, with rational drug design is promising. Rational drug design uses structural data and computational tools to study protein binding sites and protein interfaces to design inhibitors that can change these interactions, thereby potentially leading to therapeutic approaches. Artificial intelligence (AI), such as machine learning (ML) and deep learning (DL), has advanced drug discovery and design by providing computational resources and methods. Quantum chemistry is essential for drug reactivity, toxicology, drug screening, and quantitative structure-activity relationship (QSAR) properties. This review discusses the methodologies and challenges of identifying and characterizing hot spots and binding sites. It also explores the strategies and applications of artificial-intelligence-based rational drug design technologies that target proteins and protein-protein interaction (PPI) binding hot spots. It provides valuable insights for drug design with therapeutic implications. We have also demonstrated the pathological conditions of heat shock protein 27 (HSP27) and matrix metallopoproteinases (MMP2 and MMP9) and designed inhibitors of these proteins using the drug discovery paradigm in a case study on the discovery of drug molecules for cancer treatment. Additionally, the implications of benzothiazole derivatives for anticancer drug design and discovery are deliberated.
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Affiliation(s)
- Suvendu Nandi
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal 721302, India
| | - Soumyadeep Bhaduri
- Centre for Computational and Data Sciences, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal 721302, India
| | - Debraj Das
- Centre for Computational and Data Sciences, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal 721302, India
| | - Priya Ghosh
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal 721302, India
| | - Mahitosh Mandal
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal 721302, India
| | - Pralay Mitra
- Department of Computer Science and Engineering, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal 721302, India
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10
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Bombonato E, Fasano V, Pecorari D, Fornasari L, Castagnini F, Marcaccio M, Ronchi P. Electrochemical Synthesis of Unnatural Amino Acids Embedding 5- and 6-Membered Heteroaromatics. ACS OMEGA 2024; 9:13081-13085. [PMID: 38524423 PMCID: PMC10955561 DOI: 10.1021/acsomega.3c09357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 02/07/2024] [Accepted: 02/21/2024] [Indexed: 03/26/2024]
Abstract
Using a commercially available potentiostat, the electrochemical synthesis of unnatural amino acids bearing heteroaromatics on the lateral chain has been accomplished. This strategy exploits the side-chain decarboxylative arylation of aspartic/glutamic acid, a reaction that becomes challenging with electron-rich coupling partners such as 5- and 6-membered heteroaromatics. These rings are underrepresented in unnatural amino acids, therefore allowing a wider exploration of the chemical space, given the abundance of the aryl bromides employable in this reaction.
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Affiliation(s)
- Elena Bombonato
- Department
of Chemistry “Giacomo Ciamician”, Università di Bologna, Via Selmi, 2, Bologna 40126, Italy
| | - Valerio Fasano
- Department
of Chemistry, Università degli Studi
di Milano, Via Camillo Golgi, 19, Milano 20133, Italy
| | - Daniel Pecorari
- Analytics
and Early Formulations Department, Global Research and Preclinical
Development, Chiesi Farmaceutici S.p.A, Largo Francesco Belloli 11/a, Parma 43122, Italy
| | - Luca Fornasari
- Analytics
and Early Formulations Department, Global Research and Preclinical
Development, Chiesi Farmaceutici S.p.A, Largo Francesco Belloli 11/a, Parma 43122, Italy
| | - Francesco Castagnini
- Department
of Food and Drug Sciences, University of
Parma, Parco area delle scienze, 27/A, Parma 43124, Italy
| | - Massimo Marcaccio
- Department
of Chemistry “Giacomo Ciamician”, Università di Bologna, Via Selmi, 2, Bologna 40126, Italy
| | - Paolo Ronchi
- Medicinal
Chemistry and Drug Design Technologies Department, Global Research
and Preclinical Development, Chiesi Farmaceutici
S.p.A, Largo Francesco
Belloli 11/a, Parma 43122, Italy
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11
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Li R, Lichstrahl MS, Zandi TA, Kahlert L, Townsend CA. The dabABC operon is a marker of C4-alkylated monobactam biosynthesis and responsible for ( 2S, 3R)-diaminobutyrate production. iScience 2024; 27:109202. [PMID: 38433893 PMCID: PMC10906522 DOI: 10.1016/j.isci.2024.109202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 01/12/2024] [Accepted: 02/07/2024] [Indexed: 03/05/2024] Open
Abstract
Non-ribosomal peptide synthetases (NRPSs) assemble metabolites of medicinal and commercial value. Both serine and threonine figure prominently in these processes and separately can be converted to the additional NRPS building blocks 2,3-diaminopropionate (Dap) and 2,3-diaminobutyrate (Dab). Here we bring extensive bioinformatics, in vivo and in vitro experimentation to compose a unified view of the biosynthesis of these widely distributed non-canonical amino acids that both derive by pyridoxal-mediated β-elimination of the activated O-phosphorylated substrates followed by β-addition of an amine donor. By examining monobactam biosynthesis in Pseudomonas and in Burkholderia species where it is silent, we show that (2S,3R)-Dab synthesis depends on an l-threonine kinase (DabA), a β-replacement reaction with l-aspartate (DabB) and an argininosuccinate lyase-like protein (DabC). The growing clinical importance of monobactams to both withstand Ambler Class B metallo-β-lactamases and retain their antibiotic activity make reprogrammed precursor and NRPS synthesis of modified monobactams a feasible and attractive goal.
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Affiliation(s)
- Rongfeng Li
- Department of Chemistry, The Johns Hopkins University, 3400 N Charles St, Baltimore, MD, USA
| | - Michael S. Lichstrahl
- Department of Chemistry, The Johns Hopkins University, 3400 N Charles St, Baltimore, MD, USA
| | - Trevor A. Zandi
- T. C. Jenkins Department of Biophysics, The Johns Hopkins University, Baltimore, MD, USA
| | - Lukas Kahlert
- Department of Chemistry, The Johns Hopkins University, 3400 N Charles St, Baltimore, MD, USA
| | - Craig A. Townsend
- Department of Chemistry, The Johns Hopkins University, 3400 N Charles St, Baltimore, MD, USA
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12
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Patel KP, Chen WT, Delbecq L, Bruner SD. Alternative Linkage Chemistries in the Chemoenzymatic Synthesis of Microviridin-Based Cyclic Peptides. Org Lett 2024; 26:1138-1142. [PMID: 38306609 DOI: 10.1021/acs.orglett.3c04045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2024]
Abstract
Engineering biosynthetic pathways to ribosomally synthesized and post-translationally modified peptides (RiPPs) offers several advantages for both in vivo and in vitro applications. Here we probe the ability of peptide cyclases to generate trimacrocycle microviridin analogs with non-native cross-links. The results demonstrate that diverse chemistries are tolerated by macrocyclases in the ATP-grasp family and allow for the construction of unique cyclic peptide architectures that retain protease inhibition activity. In addition, cocomplex structures of analogs bound to a model protease were determined, illustrating how changes in functional groups maintain peptide conformation and target binding.
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Affiliation(s)
- Krishna P Patel
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Wen-Ting Chen
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Léa Delbecq
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Steven D Bruner
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
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13
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Zhang R, Zhang C, Tan J, He Y, Zhuo D, Zhang J, Luo Z, Li Q, Yao J, Ke C, Tang C, Ye Y, He S, Sheng X, Liao C. Enzymatic Synthesis of Noncanonical α-Amino Acids Containing γ-Tertiary Alcohols. Angew Chem Int Ed Engl 2024; 63:e202318550. [PMID: 38155101 DOI: 10.1002/anie.202318550] [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: 12/04/2023] [Revised: 12/25/2023] [Accepted: 12/28/2023] [Indexed: 12/30/2023]
Abstract
Noncanonical amino acids (ncAAs) containing tertiary alcohols are valuable as precursors of natural products and active pharmaceutical ingredients. However, the assembly of such ncAA scaffolds from simple material by C-C bond formation remains a challenging task due to the presence of multiple stereocenters and large steric hindrance. In this study, we present a novel solution to this problem through highly selective enzymatic decarboxylative aldol addition. This method allows for the streamlined assembly of multifunctionalized ncAAs with γ-tertiary alcohols from readily available materials, such as L -aspartatic acid and isatins, vicinal diones and keto esters. The modularity of electrophiles furnished four classes of ncAAs with decent efficiency as well as excellent site and stereocontrol. Computational modeling was employed to gain detailed insight into the catalytic mechanism and to provide a rationale for the observed selectivities. The method offers a single-step approach to producing multifunctionalized ncAAs, which can be directly utilized in peptide synthesis and bioactivity assessment.
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Affiliation(s)
- Rui Zhang
- State Key Laboratory of Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Chenghua Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- School of Pharmacy, North Sichuan Medical College, Nanchong, 637100, P. R. China
| | - Jiamu Tan
- State Key Laboratory of Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yifan He
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Dan Zhuo
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Jingxuan Zhang
- State Key Laboratory of Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhenzhen Luo
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Qiaoqiao Li
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Jiaying Yao
- Graduate School, Jiangxi University of Chinese Medicine, Nanchang, 330004, China
- Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Changqiang Ke
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Chunping Tang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Yang Ye
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Shijun He
- Innovation Research Institute of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiang Sheng
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
- National Center of Technology Innovation for Synthetic Biology, National Engineering Research Center of Industrial Enzymes and Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin, 300308, P. R. China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Cangsong Liao
- State Key Laboratory of Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, 210023, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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14
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Abstract
Cyclic peptides are fascinating molecules abundantly found in nature and exploited as molecular format for drug development as well as other applications, ranging from research tools to food additives. Advances in peptide technologies made over many years through improved methods for synthesis and drug development have resulted in a steady stream of new drugs, with an average of around one cyclic peptide drug approved per year. Powerful technologies for screening random peptide libraries, and de novo generating ligands, have enabled the development of cyclic peptide drugs independent of naturally derived molecules and now offer virtually unlimited development opportunities. In this review, we feature therapeutically relevant cyclic peptides derived from nature and discuss the unique properties of cyclic peptides, the enormous technological advances in peptide ligand development in recent years, and current challenges and opportunities for developing cyclic peptides that address unmet medical needs.
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Affiliation(s)
- Xinjian Ji
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Alexander L Nielsen
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Christian Heinis
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
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15
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Brown SM, Mayer-Bacon C, Freeland S. Xeno Amino Acids: A Look into Biochemistry as We Do Not Know It. Life (Basel) 2023; 13:2281. [PMID: 38137883 PMCID: PMC10744825 DOI: 10.3390/life13122281] [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: 10/30/2023] [Revised: 11/18/2023] [Accepted: 11/20/2023] [Indexed: 12/24/2023] Open
Abstract
Would another origin of life resemble Earth's biochemical use of amino acids? Here, we review current knowledge at three levels: (1) Could other classes of chemical structure serve as building blocks for biopolymer structure and catalysis? Amino acids now seem both readily available to, and a plausible chemical attractor for, life as we do not know it. Amino acids thus remain important and tractable targets for astrobiological research. (2) If amino acids are used, would we expect the same L-alpha-structural subclass used by life? Despite numerous ideas, it is not clear why life favors L-enantiomers. It seems clearer, however, why life on Earth uses the shortest possible (alpha-) amino acid backbone, and why each carries only one side chain. However, assertions that other backbones are physicochemically impossible have relaxed into arguments that they are disadvantageous. (3) Would we expect a similar set of side chains to those within the genetic code? Many plausible alternatives exist. Furthermore, evidence exists for both evolutionary advantage and physicochemical constraint as explanatory factors for those encoded by life. Overall, as focus shifts from amino acids as a chemical class to specific side chains used by post-LUCA biology, the probable role of physicochemical constraint diminishes relative to that of biological evolution. Exciting opportunities now present themselves for laboratory work and computing to explore how changing the amino acid alphabet alters the universe of protein folds. Near-term milestones include: (a) expanding evidence about amino acids as attractors within chemical evolution; (b) extending characterization of other backbones relative to biological proteins; and (c) merging computing and laboratory explorations of structures and functions unlocked by xeno peptides.
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16
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Koleda O, Prane K, Suna E. Electrochemical Synthesis of Unnatural Amino Acids via Anodic Decarboxylation of N-Acetylamino Malonic Acid Derivatives. Org Lett 2023; 25:7958-7962. [PMID: 37758233 PMCID: PMC10644390 DOI: 10.1021/acs.orglett.3c02687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Indexed: 10/03/2023]
Abstract
Broad application of α,α-disubstituted cyclic amino acid derivatives in medicinal chemistry urges for analogue design with improved pharmacokinetic properties. Herein, we disclose an electrochemical approach toward unnatural THF- and THP-containing amino acid derivatives that relies on anodic decarboxylation-intramolecular etherification of inexpensive and readily available N-acetylamino malonic acid monoesters under Hofer-Moest reaction conditions. The decarboxylative cyclization proceeds under constant current conditions in an undivided cell in an aqueous medium without any added base. A successful bioisosteric replacement of the 1-aminocyclohexane-1-carboxylic acid subunit by the THP-containing amino acid scaffold in cathepsin K inhibitor balicatib helped to reduce lipophilicity while retaining low nanomolar enzyme inhibitory potency and comparable microsomal stability.
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Affiliation(s)
- Olesja Koleda
- Latvian
Institute of Organic Synthesis, Aizkraukles 21, LV-1006 Riga, Latvia
- University
of Latvia, Department of Chemistry, Jelgavas 1, LV-1004 Riga, Latvia
| | - Katrina Prane
- Latvian
Institute of Organic Synthesis, Aizkraukles 21, LV-1006 Riga, Latvia
| | - Edgars Suna
- Latvian
Institute of Organic Synthesis, Aizkraukles 21, LV-1006 Riga, Latvia
- University
of Latvia, Department of Chemistry, Jelgavas 1, LV-1004 Riga, Latvia
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17
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Wang GQ, Wang T, Zhang Y, Zhou YX, Yang D, Han P, Jing LH. Photoredox Metal-Free Synthesis of Unnatural β-Silyl-α-Amino Acids via Hydrosilylation. Chem Asian J 2023:e202300805. [PMID: 37906443 DOI: 10.1002/asia.202300805] [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: 09/16/2023] [Revised: 10/30/2023] [Accepted: 10/31/2023] [Indexed: 11/02/2023]
Abstract
An efficient, practical and metal-free methodology for the synthesis of β-silyl-α-amino acid motifs via photoredox and hydrogen atom transfer (HAT) process is described. This protocol enables the direct hydrosilylation of dehydroalanine derivatives and tolerates a wide array of functional groups and synthetic handles, leading to valuable β-silyl-α-amino acids with moderate to good yields.
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Affiliation(s)
- Guo-Qin Wang
- Chemical Synthesis and Pollution Control Key Laboratory of Sichuan Province, College of Chemistry and Chemical Engineering, China West Normal University, Nanchong, 637002, P.R. China
| | - Ting Wang
- Chemical Synthesis and Pollution Control Key Laboratory of Sichuan Province, College of Chemistry and Chemical Engineering, China West Normal University, Nanchong, 637002, P.R. China
| | - Yue Zhang
- Chemical Synthesis and Pollution Control Key Laboratory of Sichuan Province, College of Chemistry and Chemical Engineering, China West Normal University, Nanchong, 637002, P.R. China
| | - Yuan-Xia Zhou
- Chemical Synthesis and Pollution Control Key Laboratory of Sichuan Province, College of Chemistry and Chemical Engineering, China West Normal University, Nanchong, 637002, P.R. China
| | - Dan Yang
- Chemical Synthesis and Pollution Control Key Laboratory of Sichuan Province, College of Chemistry and Chemical Engineering, China West Normal University, Nanchong, 637002, P.R. China
| | - Pan Han
- Chemical Synthesis and Pollution Control Key Laboratory of Sichuan Province, College of Chemistry and Chemical Engineering, China West Normal University, Nanchong, 637002, P.R. China
| | - Lin-Hai Jing
- Chemical Synthesis and Pollution Control Key Laboratory of Sichuan Province, College of Chemistry and Chemical Engineering, China West Normal University, Nanchong, 637002, P.R. China
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18
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Chen Z, Lim YW, Neo JY, Ting Chan RS, Koh LQ, Yuen TY, Lim YH, Johannes CW, Gates ZP. De Novo Sequencing of Synthetic Bis-cysteine Peptide Macrocycles Enabled by "Chemical Linearization" of Compound Mixtures. Anal Chem 2023; 95:14870-14878. [PMID: 37724843 PMCID: PMC10569172 DOI: 10.1021/acs.analchem.3c01742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Accepted: 09/04/2023] [Indexed: 09/21/2023]
Abstract
A "chemical linearization" approach was applied to synthetic peptide macrocycles to enable their de novo sequencing from mixtures using nanoliquid chromatography-tandem mass spectrometry (nLC-MS/MS). This approach─previously applied to individual macrocycles but not to mixtures─involves cleavage of the peptide backbone at a defined position to give a product capable of generating sequence-determining fragment ions. Here, we first established the compatibility of "chemical linearization" by Edman degradation with a prominent macrocycle scaffold based on bis-Cys peptides cross-linked with the m-xylene linker, which are of major significance in therapeutics discovery. Then, using macrocycle libraries of known sequence composition, the ability to recover accurate de novo assignments to linearized products was critically tested using performance metrics unique to mixtures. Significantly, we show that linearized macrocycles can be sequenced with lower recall compared to linear peptides but with similar accuracy, which establishes the potential of using "chemical linearization" with synthetic libraries and selection procedures that yield compound mixtures. Sodiated precursor ions were identified as a significant source of high-scoring but inaccurate assignments, with potential implications for improving automated de novo sequencing more generally.
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Affiliation(s)
- Zhi’ang Chen
- Institute
of Molecular and Cell Biology (IMCB), Agency
for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore 138673, Republic of Singapore
- Institute
of Sustainability for Chemicals, Energy and Environment (ISCE), Agency for Science, Technology
and Research (A*STAR), 8 Biomedical Grove, #07-01 Neuros, Singapore 138665, Republic
of Singapore
| | - Yi Wee Lim
- Institute
of Sustainability for Chemicals, Energy and Environment (ISCE), Agency for Science, Technology
and Research (A*STAR), 8 Biomedical Grove, #07-01 Neuros, Singapore 138665, Republic
of Singapore
| | - Jin Yong Neo
- Institute
of Sustainability for Chemicals, Energy and Environment (ISCE), Agency for Science, Technology
and Research (A*STAR), 8 Biomedical Grove, #07-01 Neuros, Singapore 138665, Republic
of Singapore
| | - Rachel Shu Ting Chan
- Institute
of Sustainability for Chemicals, Energy and Environment (ISCE), Agency for Science, Technology
and Research (A*STAR), 8 Biomedical Grove, #07-01 Neuros, Singapore 138665, Republic
of Singapore
| | - Li Quan Koh
- Institute
of Molecular and Cell Biology (IMCB), Agency
for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore 138673, Republic of Singapore
- Institute
of Sustainability for Chemicals, Energy and Environment (ISCE), Agency for Science, Technology
and Research (A*STAR), 8 Biomedical Grove, #07-01 Neuros, Singapore 138665, Republic
of Singapore
| | - Tsz Ying Yuen
- Institute
of Sustainability for Chemicals, Energy and Environment (ISCE), Agency for Science, Technology
and Research (A*STAR), 8 Biomedical Grove, #07-01 Neuros, Singapore 138665, Republic
of Singapore
| | - Yee Hwee Lim
- Institute
of Sustainability for Chemicals, Energy and Environment (ISCE), Agency for Science, Technology
and Research (A*STAR), 8 Biomedical Grove, #07-01 Neuros, Singapore 138665, Republic
of Singapore
| | - Charles W. Johannes
- Institute
of Molecular and Cell Biology (IMCB), Agency
for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore 138673, Republic of Singapore
| | - Zachary P. Gates
- Institute
of Molecular and Cell Biology (IMCB), Agency
for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, Singapore 138673, Republic of Singapore
- Institute
of Sustainability for Chemicals, Energy and Environment (ISCE), Agency for Science, Technology
and Research (A*STAR), 8 Biomedical Grove, #07-01 Neuros, Singapore 138665, Republic
of Singapore
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19
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Zmich A, Perkins LJ, Bingman C, Acheson JF, Buller AR. Multiplexed Assessment of Promiscuous Non-Canonical Amino Acid Synthase Activity in a Pyridoxal Phosphate-Dependent Protein Family. ACS Catal 2023; 13:11644-11655. [PMID: 37720819 PMCID: PMC10501158 DOI: 10.1021/acscatal.3c02498] [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] [Indexed: 09/19/2023]
Abstract
Pyridoxal phosphate (PLP)-dependent enzymes afford access to a variety of non-canonical amino acids (ncAAs), which are premier buildings blocks for the construction of complex bioactive molecules. The vinylglycine ketimine (VGK) subfamily of PLP-dependent enzymes plays a critical role in sulfur metabolism and is home to a growing set of secondary metabolic enzymes that synthesize γ-substituted ncAAs. Identification of VGK enzymes for biocatalysis faces a distinct challenge because the subfamily contains both desirable synthases as well as lyases that break down ncAAs. Some enzymes have both activities, which may contribute to pervasive mis-annotation. To navigate this complex functional landscape, we used a substrate multiplexed screening approach to rapidly measure the substrate promiscuity of 40 homologs in the VGK subfamily. We found that enzymes involved in transsulfuration are less likely to have promiscuous activities and often possess undesirable lyase activity. Enzymes from direct sulfuration and secondary metabolism generally had a high degree of substrate promiscuity. From this cohort, we identified an exemplary γ-synthase from Caldicellulosiruptor hydrothermalis (CahyGS). This enzyme is thermostable and has high expression (~400 mg protein per L culture), enabling preparative scale synthesis of thioether containing ncAAs. When assayed with l-allylglycine, CahyGS catalyzes a stereoselective γ-addition reaction to afford access to a unique set of γ-methyl branched ncAAs. We determined high-resolution crystal structures of this enzyme that define an open-close transition associated with ligand binding and set the stage for future engineering within this enzyme subfamily.
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Affiliation(s)
- Anna Zmich
- Department of Biochemistry, University of Wisconsin−Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Lydia J. Perkins
- Department of Chemistry, University of Wisconsin−Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Craig Bingman
- Department of Biochemistry, University of Wisconsin−Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Justin F Acheson
- Department of Biochemistry, University of Wisconsin−Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Andrew R. Buller
- Department of Biochemistry, University of Wisconsin−Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
- Department of Chemistry, University of Wisconsin−Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
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