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Kuehm OP, Hayden JA, Bearne SL. A Phenylboronic Acid-Based Transition State Analogue Yields Nanomolar Inhibition of Mandelate Racemase. Biochemistry 2023. [PMID: 37285384 DOI: 10.1021/acs.biochem.3c00143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Mandelate racemase (MR) catalyzes the Mg2+-dependent interconversion of (R)- and (S)-mandelate by stabilizing the altered substrate in the transition state (TS) by ∼26 kcal/mol. The enzyme has been employed as a model to explore the limits to which the free energy of TS stabilization may be captured by TS analogues to effect strong binding. Herein, we determined the thermodynamic parameters accompanying binding of a series of bromo-, chloro-, and fluoro-substituted phenylboronic acids (PBAs) by MR and found that binding was predominately driven by favorable entropy changes. 3,4-Dichloro-PBA was discovered to be the most potent inhibitor yet identified for MR, binding with a Kdapp value of 11 ± 2 nM and exceeding the binding of the substrate by ∼72,000-fold. The ΔCp value accompanying binding (-488 ± 18 cal·mol-1 K-1) suggested that dispersion forces contribute significantly to the binding. The pH-dependence of the inhibition revealed that MR preferentially binds the anionic, tetrahedral form of 3,4-dichloro-PBA with a pH-independent Ki value of 5.7 ± 0.5 nM, which was consistent with the observed upfield shift of the 11B NMR signal. The linear free energy relationship between log(kcat/Km) and log(1/Ki) for wild-type and 11 MR variants binding 3,4-dichloro-PBA had a slope of 0.8 ± 0.2, indicating that MR recognizes the inhibitor as an analogue of the TS. Hence, halogen substitution may be utilized to capture additional free energy of TS stabilization arising from dispersion forces to enhance the binding of boronic acid inhibitors by MR.
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Affiliation(s)
- Oliver P Kuehm
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Joshua A Hayden
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Stephen L Bearne
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada
- Department of Chemistry, Dalhousie University, Halifax, NS B3H 4R2, Canada
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Bearne SL, Hayden JA. Application of circular dichroism-based assays to racemases and epimerases: Recognition and catalysis of reactions of chiral substrates by mandelate racemase. Methods Enzymol 2023; 685:127-169. [PMID: 37245900 DOI: 10.1016/bs.mie.2023.03.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Racemases and epimerases have attracted much interest because of their astonishing ability to catalyze the rapid α-deprotonation of carbon acid substrates with high pKa values (∼13-30) leading to the formation of d-amino acids or various carbohydrate diastereomers that serve important roles in both normal physiology and pathology. Enzymatic assays to measure the initial rates of reactions catalyzed by these enzymes are discussed using mandelate racemase (MR) as an example. For MR, a convenient, rapid, and versatile circular dichroism (CD)-based assay has been used to determine the kinetic parameters accompanying the MR-catalyzed racemization of mandelate and alternative substrates. This direct, continuous assay permits real time monitoring of reaction progress, the rapid determination of initial velocities, and immediate recognition of anomalous behaviors. MR recognizes chiral substrates primarily through interactions of the phenyl ring of (R)- or (S)-mandelate with the hydrophobic R- or S-pocket at the active site, respectively. During catalysis, the carboxylate and α-hydroxyl groups of the substrate remain fixed in place through interactions with the Mg2+ ion and multiple H-bonding interactions, while the phenyl ring moves between the R- and S-pockets. The minimal requirements for the substrate appear to be the presence of a glycolate or glycolamide moiety, and a hydrophobic group of limited size that can stabilize the carbanionic intermediate through resonance or strong inductive effects. Similar CD-based assays may be applied to determine the activity of other racemases or epimerases with proper consideration of the molar ellipticity, wavelength, overall absorbance of the sample, and the light pathlength.
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Affiliation(s)
- Stephen L Bearne
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada; Department of Chemistry, Dalhousie University, Halifax, NS, Canada.
| | - Joshua A Hayden
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada
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Bearne SL. Capturing the free energy of transition state stabilization: insights from the inhibition of mandelate racemase. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220041. [PMID: 36633273 PMCID: PMC9835602 DOI: 10.1098/rstb.2022.0041] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Mandelate racemase (MR) catalyses the Mg2+-dependent interconversion of (R)- and (S)-mandelate. To effect catalysis, MR stabilizes the altered substrate in the transition state (TS) by approximately 26 kcal mol-1 (-ΔGtx), such that the upper limit of the virtual dissociation constant of the enzyme-TS complex is 2 × 10-19 M. Designing TS analogue inhibitors that capture a significant amount of ΔGtx for binding presents a challenge since there are a limited number of protein binding determinants that interact with the substrate and the structural simplicity of mandelate constrains the number of possible isostructural variations. Indeed, current intermediate/TS analogue inhibitors of MR capture less than or equal to 30% of ΔGtx because they fail to fully capitalize on electrostatic interactions with the metal ion, and the strength and number of all available electrostatic and H-bond interactions with binding determinants present at the TS. Surprisingly, phenylboronic acid (PBA), 2-formyl-PBA, and para-chloro-PBA capture 31-38% of ΔGtx. The boronic acid group interacts with the Mg2+ ion and multiple binding determinants that effect TS stabilization. Inhibitors capable of forming multiple interactions can exploit the cooperative interactions that contribute to optimum binding of the TS. Hence, maximizing interactions with multiple binding determinants is integral to effective TS analogue inhibitor design. This article is part of the theme issue 'Reactivity and mechanism in chemical and synthetic biology'.
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Affiliation(s)
- Stephen L. Bearne
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada B3H 4R2,Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada B3H 4R2
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Zheng Y, Yan W, Dou C, Zhou D, Chen Y, Jin Y, Yang L, Zeng X, Cheng W. Structural insights into the catalytic and inhibitory mechanisms of the flavin transferase FmnB in Listeria monocytogenes. MedComm (Beijing) 2022; 3:e99. [PMID: 35281791 PMCID: PMC8906456 DOI: 10.1002/mco2.99] [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: 08/29/2021] [Revised: 10/05/2021] [Accepted: 10/20/2021] [Indexed: 02/05/2023] Open
Abstract
Listeria monocytogenes, a food-borne Gram-positive pathogen, often causes diseases such as gastroenteritis, bacterial sepsis, and meningitis. Newly discovered extracellular electron transfer (EET) from L. monocytogenes plays critical roles in the generation of redox molecules as electron carriers in bacteria. A Mg2+-dependent protein flavin mononucleotide (FMN) transferase (FmnB; UniProt: LMRG_02181) in EET is responsible for the transfer of electrons from intracellular to extracellular by hydrolyzing cofactor flavin adenine dinucleotide (FAD) and transferring FMN. FmnB homologs have been investigated in Gram-negative bacteria but have been less well studied in Gram-positive bacteria. In particular, the catalytic and inhibitory mechanisms of FmnB homologs remain elusive. Here, we report a series of crystal structures of apo-FmnB and FmnB complexed with substrate FAD, three inhibitors AMP, ADP, and ATP, revealing the unusual catalytic triad center (Asp301-Ser257-His273) of FmnB. The three inhibitors indeed inhibited the activity of FmnB in varying degrees by occupying the binding site of the FAD substrate. The key residue Arg262 of FmnB was profoundly affected by ADP but not AMP or ATP. Overall, our studies not only provide insights into the promiscuous ligand recognition behavior of FmnB but also shed light on its catalytic and inhibitory mechanisms.
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Affiliation(s)
- Yanhui Zheng
- Division of Respiratory and Critical Care MedicineRespiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease‐Related Molecular NetworkState Key Laboratory of BiotherapyWest China Hospital of Sichuan UniversityChengduChina
| | - Weizhu Yan
- Division of Respiratory and Critical Care MedicineRespiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease‐Related Molecular NetworkState Key Laboratory of BiotherapyWest China Hospital of Sichuan UniversityChengduChina
| | - Chao Dou
- Division of Respiratory and Critical Care MedicineRespiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease‐Related Molecular NetworkState Key Laboratory of BiotherapyWest China Hospital of Sichuan UniversityChengduChina
| | - Dan Zhou
- Division of Respiratory and Critical Care MedicineRespiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease‐Related Molecular NetworkState Key Laboratory of BiotherapyWest China Hospital of Sichuan UniversityChengduChina
| | - Yunying Chen
- Division of Respiratory and Critical Care MedicineRespiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease‐Related Molecular NetworkState Key Laboratory of BiotherapyWest China Hospital of Sichuan UniversityChengduChina
| | - Ying Jin
- Division of Respiratory and Critical Care MedicineRespiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease‐Related Molecular NetworkState Key Laboratory of BiotherapyWest China Hospital of Sichuan UniversityChengduChina
| | - Lulu Yang
- Division of Respiratory and Critical Care MedicineRespiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease‐Related Molecular NetworkState Key Laboratory of BiotherapyWest China Hospital of Sichuan UniversityChengduChina
| | - Xiaotao Zeng
- Division of Respiratory and Critical Care MedicineRespiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease‐Related Molecular NetworkState Key Laboratory of BiotherapyWest China Hospital of Sichuan UniversityChengduChina
| | - Wei Cheng
- Division of Respiratory and Critical Care MedicineRespiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease‐Related Molecular NetworkState Key Laboratory of BiotherapyWest China Hospital of Sichuan UniversityChengduChina
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Douglas CD, Grandinetti L, Easton NM, Kuehm OP, Hayden JA, Hamilton MC, St Maurice M, Bearne SL. Slow-Onset, Potent Inhibition of Mandelate Racemase by 2-Formylphenylboronic Acid. An Unexpected Adduct Clasps the Catalytic Machinery. Biochemistry 2021; 60:2508-2518. [PMID: 34339165 DOI: 10.1021/acs.biochem.1c00374] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
o-Carbonyl arylboronic acids such as 2-formylphenylboronic acid (2-FPBA) are employed in biocompatible conjugation reactions with the resulting iminoboronate adduct stabilized by an intramolecular N-B interaction. However, few studies have utilized these reagents as active site-directed enzyme inhibitors. We show that 2-FPBA is a potent reversible, slow-onset inhibitor of mandelate racemase (MR), an enzyme that has served as a valuable paradigm for understanding enzyme-catalyzed abstraction of an α-proton from a carbon acid substrate with a high pKa. Kinetic analysis of the progress curves for the slow onset of inhibition of wild-type MR using a two-step kinetic mechanism gave Ki and Ki* values of 5.1 ± 1.8 and 0.26 ± 0.08 μM, respectively. Hence, wild-type MR binds 2-FPBA with an affinity that exceeds that for the substrate by ∼3000-fold. K164R MR was inhibited by 2-FPBA, while K166R MR was not inhibited, indicating that Lys 166 was essential for inhibition. Unexpectedly, mass spectrometric analysis of the NaCNBH3-treated enzyme-inhibitor complex did not yield evidence of an iminoboronate adduct. 11B nuclear magnetic resonance spectroscopy of the MR·2-FPBA complex indicated that the boron atom was sp3-hybridized (δ 6.0), consistent with dative bond formation. Surprisingly, X-ray crystallography revealed the formation of an Nζ-B dative bond between Lys 166 and 2-FPBA with intramolecular cyclization to form a benzoxaborole, rather than the expected iminoboronate. Thus, when o-carbonyl arylboronic acid reagents are employed to modify proteins, the structure of the resulting product depends on the protein architecture at the site of modification.
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Affiliation(s)
- Colin D Douglas
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Lia Grandinetti
- Department of Biological Sciences, Marquette University, Milwaukee, Wisconsin 53201-1881, United States
| | - Nicole M Easton
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Oliver P Kuehm
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Joshua A Hayden
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Meghan C Hamilton
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Martin St Maurice
- Department of Biological Sciences, Marquette University, Milwaukee, Wisconsin 53201-1881, United States
| | - Stephen L Bearne
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada
- Department of Chemistry, Dalhousie University, Halifax, NS B3H 4R2, Canada
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Immel JR, Chilamari M, Bloom S. Combining flavin photocatalysis with parallel synthesis: a general platform to optimize peptides with non-proteinogenic amino acids. Chem Sci 2021; 12:10083-10091. [PMID: 34377401 PMCID: PMC8317666 DOI: 10.1039/d1sc02562g] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 06/28/2021] [Indexed: 02/06/2023] Open
Abstract
Most peptide drugs contain non-proteinogenic amino acids (NPAAs), born out through extensive structure-activity relationship (SAR) studies using solid-phase peptide synthesis (SPPS). Synthetically laborious and expensive to manufacture, NPAAs also can have poor coupling efficiencies allowing only a small fraction to be sampled by conventional SPPS. To gain general access to NPAA-containing peptides, we developed a first-generation platform that merges contemporary flavin photocatalysis with parallel synthesis to simultaneously make, purify, quantify, and even test up to 96 single-NPAA peptide variants via the unique combination of boronic acids and a dehydroalanine residue in a peptide. We showcase the power of our newly minted platform to introduce NPAAs of diverse chemotypes-aliphatic, aromatic, heteroaromatic-directly into peptides, including 15 entirely new residues, and to evolve a simple proteinogenic peptide into an unnatural inhibitor of thrombin by non-classical peptide SAR.
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Affiliation(s)
- Jacob R Immel
- Department of Medicinal Chemistry, The University of Kansas Integrated Science Building Lawrence KS 66045 USA
| | - Maheshwerreddy Chilamari
- Department of Medicinal Chemistry, The University of Kansas Integrated Science Building Lawrence KS 66045 USA
| | - Steven Bloom
- Department of Medicinal Chemistry, The University of Kansas Integrated Science Building Lawrence KS 66045 USA
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