1
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Jacobs LMC, Consol P, Chen Y. Drug Discovery in the Field of β-Lactams: An Academic Perspective. Antibiotics (Basel) 2024; 13:59. [PMID: 38247618 PMCID: PMC10812508 DOI: 10.3390/antibiotics13010059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 12/21/2023] [Accepted: 12/23/2023] [Indexed: 01/23/2024] Open
Abstract
β-Lactams are the most widely prescribed class of antibiotics that inhibit penicillin-binding proteins (PBPs), particularly transpeptidases that function in peptidoglycan synthesis. A major mechanism of antibiotic resistance is the production of β-lactamase enzymes, which are capable of hydrolyzing β-lactam antibiotics. There have been many efforts to counter increasing bacterial resistance against β-lactams. These studies have mainly focused on three areas: discovering novel inhibitors against β-lactamases, developing new β-lactams less susceptible to existing resistance mechanisms, and identifying non-β-lactam inhibitors against cell wall transpeptidases. Drug discovery in the β-lactam field has afforded a range of research opportunities for academia. In this review, we summarize the recent new findings on both β-lactamases and cell wall transpeptidases because these two groups of enzymes are evolutionarily and functionally connected. Many efforts to develop new β-lactams have aimed to inhibit both transpeptidases and β-lactamases, while several promising novel β-lactamase inhibitors have shown the potential to be further developed into transpeptidase inhibitors. In addition, the drug discovery progress against each group of enzymes is presented in three aspects: understanding the targets, screening methodology, and new inhibitor chemotypes. This is to offer insights into not only the advancement in this field but also the challenges, opportunities, and resources for future research. In particular, cyclic boronate compounds are now capable of inhibiting all classes of β-lactamases, while the diazabicyclooctane (DBO) series of small molecules has led to not only new β-lactamase inhibitors but potentially a new class of antibiotics by directly targeting PBPs. With the cautiously optimistic successes of a number of new β-lactamase inhibitor chemotypes and many questions remaining to be answered about the structure and function of cell wall transpeptidases, non-β-lactam transpeptidase inhibitors may usher in the next exciting phase of drug discovery in this field.
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Affiliation(s)
| | | | - Yu Chen
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA; (L.M.C.J.); (P.C.)
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2
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Lebrette H, Srinivas V, John J, Aurelius O, Kumar R, Lundin D, Brewster AS, Bhowmick A, Sirohiwal A, Kim IS, Gul S, Pham C, Sutherlin KD, Simon P, Butryn A, Aller P, Orville AM, Fuller FD, Alonso-Mori R, Batyuk A, Sauter NK, Yachandra VK, Yano J, Kaila VRI, Sjöberg BM, Kern J, Roos K, Högbom M. Structure of a ribonucleotide reductase R2 protein radical. Science 2023; 382:109-113. [PMID: 37797025 PMCID: PMC7615503 DOI: 10.1126/science.adh8160] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 08/30/2023] [Indexed: 10/07/2023]
Abstract
Aerobic ribonucleotide reductases (RNRs) initiate synthesis of DNA building blocks by generating a free radical within the R2 subunit; the radical is subsequently shuttled to the catalytic R1 subunit through proton-coupled electron transfer (PCET). We present a high-resolution room temperature structure of the class Ie R2 protein radical captured by x-ray free electron laser serial femtosecond crystallography. The structure reveals conformational reorganization to shield the radical and connect it to the translocation path, with structural changes propagating to the surface where the protein interacts with the catalytic R1 subunit. Restructuring of the hydrogen bond network, including a notably short O-O interaction of 2.41 angstroms, likely tunes and gates the radical during PCET. These structural results help explain radical handling and mobilization in RNR and have general implications for radical transfer in proteins.
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Affiliation(s)
- Hugo Lebrette
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, Stockholm, Sweden
- Laboratoire de Microbiologie et Génétique Moléculaires, Centre de Biologie Intégrative, CNRS, Université Toulouse III, Toulouse, France
| | - Vivek Srinivas
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, Stockholm, Sweden
| | - Juliane John
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, Stockholm, Sweden
| | - Oskar Aurelius
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, Stockholm, Sweden
- MAX IV Laboratory, Lund University, Lund, Sweden
| | - Rohit Kumar
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, Stockholm, Sweden
| | - Daniel Lundin
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, Stockholm, Sweden
| | - Aaron S. Brewster
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Asmit Bhowmick
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Abhishek Sirohiwal
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, Stockholm, Sweden
| | - In-Sik Kim
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Sheraz Gul
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Cindy Pham
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Kyle D. Sutherlin
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Philipp Simon
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Agata Butryn
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, United Kingdom
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, United Kingdom
| | - Pierre Aller
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, United Kingdom
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, United Kingdom
| | - Allen M. Orville
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, United Kingdom
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, United Kingdom
| | | | | | | | - Nicholas K. Sauter
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Vittal K. Yachandra
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Junko Yano
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Ville R. I. Kaila
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, Stockholm, Sweden
| | - Britt-Marie Sjöberg
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, Stockholm, Sweden
| | - Jan Kern
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Katarina Roos
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Martin Högbom
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, Stockholm, Sweden
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3
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Motai K, Koishihara N, Narimatsu T, Ohtsu H, Kawano M, Wada Y, Akisawa K, Okuwaki K, Mori T, Kim JS, Mochizuki Y, Hayamizu Y. Correction to "Bifurcated Hydrogen Bonds in a Peptide Crystal Unveiled by X-ray Diffraction and Polarized Raman Spectroscopy". CRYSTAL GROWTH & DESIGN 2023; 23:6988. [PMID: 37692335 PMCID: PMC10485815 DOI: 10.1021/acs.cgd.3c00787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Indexed: 09/12/2023]
Abstract
[This corrects the article DOI: 10.1021/acs.cgd.3c00302.].
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4
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Brunetti F, Ghiglione B, Gudeta DD, Gutkind G, Guardabassi L, Klinke S, Power P. Biochemical and Structural Characterization of CRH-1, a Carbapenemase from Chromobacterium haemolyticum Related to KPC β-Lactamases. Antimicrob Agents Chemother 2023; 67:e0006123. [PMID: 37272821 PMCID: PMC10353377 DOI: 10.1128/aac.00061-23] [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: 01/12/2023] [Accepted: 05/10/2023] [Indexed: 06/06/2023] Open
Abstract
KPC-2 is one of the most relevant serine-carbapenemases among the carbapenem-resistant Enterobacterales. We previously isolated from the environmental species Chromobacterium haemolyticum a class A CRH-1 β-lactamase displaying 69% amino acid sequence identity with KPC-2. The objective of this study was to analyze the kinetic behavior and crystallographic structure of this β-lactamase. Our results showed that CRH-1 can hydrolyze penicillins, cephalosporins (except ceftazidime), and carbapenems with similar efficacy compared to KPC-2. Inhibition kinetics showed that CRH-1 is not well inhibited by clavulanic acid, in contrast to efficient inhibition by avibactam (AVI). The high-resolution crystal of the apoenzyme showed that CRH-1 has a similar folding compared to other class A β-lactamases. The CRH-1/AVI complex showed that AVI adopts a chair conformation, stabilized by hydrogen bonds to Ser70, Ser237, Asn132, and Thr235. Our findings highlight the biochemical and structural similarities of CRH-1 and KPC-2 and the potential clinical impact of this carbapenemase in the event of recruitment by pathogenic bacterial species.
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Affiliation(s)
- Florencia Brunetti
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Barbara Ghiglione
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Dereje D. Gudeta
- Division of Microbiology, U.S. Food and Drug Administration, National Center for Toxicological Research, Jefferson, Arkansas, USA
| | - Gabriel Gutkind
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Luca Guardabassi
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Sebastián Klinke
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Fundación Instituto Leloir, Buenos Aires, Argentina
- Plataforma Argentina de Biología Estructural y Metabolómica PLABEM, Buenos Aires, Argentina
| | - Pablo Power
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
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5
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Judge A, Hu L, Sankaran B, Van Riper J, Venkataram Prasad BV, Palzkill T. Mapping the determinants of catalysis and substrate specificity of the antibiotic resistance enzyme CTX-M β-lactamase. Commun Biol 2023; 6:35. [PMID: 36635385 PMCID: PMC9837174 DOI: 10.1038/s42003-023-04422-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 01/04/2023] [Indexed: 01/14/2023] Open
Abstract
CTX-M β-lactamases are prevalent antibiotic resistance enzymes and are notable for their ability to rapidly hydrolyze the extended-spectrum cephalosporin, cefotaxime. We hypothesized that the active site sequence requirements of CTX-M-mediated hydrolysis differ between classes of β-lactam antibiotics. Accordingly, we use codon randomization, antibiotic selection, and deep sequencing to determine the CTX-M active-site residues required for hydrolysis of cefotaxime and the penicillin, ampicillin. The study reveals positions required for hydrolysis of all β-lactams, as well as residues controlling substrate specificity. Further, CTX-M enzymes poorly hydrolyze the extended-spectrum cephalosporin, ceftazidime. We further show that the sequence requirements for ceftazidime hydrolysis follow those of cefotaxime, with the exception that key active-site omega loop residues are not required, and may be detrimental, for ceftazidime hydrolysis. These results provide insights into cephalosporin hydrolysis and demonstrate that changes to the active-site omega loop are likely required for the evolution of CTX-M-mediated ceftazidime resistance.
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Affiliation(s)
- Allison Judge
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Liya Hu
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Banumathi Sankaran
- Department of Molecular Biophysics and Integrated Bioimaging, Berkeley Center for Structural Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Justin Van Riper
- Graduate Program in Chemical, Physical, and Structural Biology, Baylor College of Medicine, Houston, TX, USA
| | - B V Venkataram Prasad
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Timothy Palzkill
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA.
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX, USA.
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6
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Rossi MA, Palzkill T, Almeida FCL, Vila AJ. Slow Protein Dynamics Elicits New Enzymatic Functions by Means of Epistatic Interactions. Mol Biol Evol 2022; 39:6711538. [PMID: 36136729 PMCID: PMC9547502 DOI: 10.1093/molbev/msac194] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Protein evolution depends on the adaptation of these molecules to different functional challenges. This occurs by tuning their biochemical, biophysical, and structural traits through the accumulation of mutations. While the role of protein dynamics in biochemistry is well recognized, there are limited examples providing experimental evidence of the optimization of protein dynamics during evolution. Here we report an NMR study of four variants of the CTX-M β-lactamases, in which the interplay of two mutations outside the active site enhances the activity against a cephalosporin substrate, ceftazidime. The crystal structures of these enzymes do not account for this activity enhancement. By using NMR, here we show that the combination of these two mutations increases the backbone dynamics in a slow timescale and the exposure to the solvent of an otherwise buried β-sheet. The two mutations located in this β-sheet trigger conformational changes in loops located at the opposite side of the active site. We postulate that the most active variant explores alternative conformations that enable binding of the more challenging substrate ceftazidime. The impact of the mutations in the dynamics is context-dependent, in line with the epistatic effect observed in the catalytic activity of the different variants. These results reveal the existence of a dynamic network in CTX-M β-lactamases that has been exploited in evolution to provide a net gain-of-function, highlighting the role of alternative conformations in protein evolution.
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Affiliation(s)
- Maria-Agustina Rossi
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR), Ocampo and Esmeralda, Rosario, Argentina
| | - Timothy Palzkill
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, USA,Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, USA
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7
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Strong proton transfer from phenolic ring to imine functionality in 1D azido and dicyanamido bridged Mn(II) coordination polymers: Synthesis, crystal structure and magnetic studies. Inorganica Chim Acta 2022. [DOI: 10.1016/j.ica.2022.121005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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8
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Yang J, Li Y, Qiu Q, Wang R, Yan W, Yu Y, Niu L, Pei H, Wei H, Ouyang L, Ye H, Xu D, Wei Y, Chen Q, Chen L. Small Molecules Promote Selective Denaturation and Degradation of Tubulin Heterodimers through a Low-Barrier Hydrogen Bond. J Med Chem 2022; 65:9159-9173. [PMID: 35762925 DOI: 10.1021/acs.jmedchem.2c00379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Here, we report a novel mechanism to selectively degrade target proteins. 3-(3-Phenoxybenzyl)amino-β-carboline (PAC), a tubulin inhibitor, promotes selective degradation of αβ-tubulin heterodimers. Biochemical studies have revealed that PAC specifically denatures tubulin, making it prone to aggregation that predisposes it to ubiquitinylation and then degradation. The degradation is mediated by a single hydrogen bond formed between the pyridine nitrogen of PAC and βGlu198, which is identified as a low-barrier hydrogen bond (LBHB). In contrast, another two tubulin inhibitors that only form normal hydrogen bonds with βGlu198 exhibit no degradation effect. Thus, the LBHB accounts for the degradation. We then screened for compounds capable of forming an LBHB with βGlu198 and demonstrated that BML284, a Wnt signaling activator, also promotes tubulin heterodimer degradation through the LBHB. Our study provided a unique example of LBHB function and identified a novel approach to obtain tubulin degraders.
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Affiliation(s)
- Jianhong Yang
- Laboratory of Natural and Targeted Small Molecule Drugs, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Yong Li
- Laboratory of Natural and Targeted Small Molecule Drugs, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Qiang Qiu
- Laboratory of Natural and Targeted Small Molecule Drugs, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Ruihan Wang
- MOE Key Laboratory of Green Chemistry and Technology, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, China
| | - Wei Yan
- Laboratory of Natural and Targeted Small Molecule Drugs, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Yamei Yu
- Laboratory of Natural and Targeted Small Molecule Drugs, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Lu Niu
- Laboratory of Natural and Targeted Small Molecule Drugs, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Heying Pei
- Laboratory of Natural and Targeted Small Molecule Drugs, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Haoche Wei
- Laboratory of Natural and Targeted Small Molecule Drugs, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Liang Ouyang
- Laboratory of Natural and Targeted Small Molecule Drugs, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Haoyu Ye
- Laboratory of Natural and Targeted Small Molecule Drugs, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Dingguo Xu
- MOE Key Laboratory of Green Chemistry and Technology, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, China
| | - Yuquan Wei
- Laboratory of Natural and Targeted Small Molecule Drugs, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Qiang Chen
- Laboratory of Natural and Targeted Small Molecule Drugs, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Lijuan Chen
- Laboratory of Natural and Targeted Small Molecule Drugs, State Key Laboratory of Biotherapy and Cancer Center, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
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9
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True-atomic-resolution insights into the structure and functional role of linear chains and low-barrier hydrogen bonds in proteins. Nat Struct Mol Biol 2022; 29:440-450. [PMID: 35484235 DOI: 10.1038/s41594-022-00762-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 03/14/2022] [Indexed: 12/21/2022]
Abstract
Hydrogen bonds are fundamental to the structure and function of biological macromolecules and have been explored in detail. The chains of hydrogen bonds (CHBs) and low-barrier hydrogen bonds (LBHBs) were proposed to play essential roles in enzyme catalysis and proton transport. However, high-resolution structural data from CHBs and LBHBs is limited. The challenge is that their 'visualization' requires ultrahigh-resolution structures of the ground and functionally important intermediate states to identify proton translocation events and perform their structural assignment. Our true-atomic-resolution structures of the light-driven proton pump bacteriorhodopsin, a model in studies of proton transport, show that CHBs and LBHBs not only serve as proton pathways, but also are indispensable for long-range communications, signaling and proton storage in proteins. The complete picture of CHBs and LBHBs discloses their multifunctional roles in providing protein functions and presents a consistent picture of proton transport and storage resolving long-standing debates and controversies.
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10
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Structural basis to repurpose boron-based proteasome inhibitors Bortezomib and Ixazomib as β-lactamase inhibitors. Sci Rep 2022; 12:5510. [PMID: 35365689 PMCID: PMC8976068 DOI: 10.1038/s41598-022-09392-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 03/21/2022] [Indexed: 12/23/2022] Open
Abstract
β-lactamases are a major cause of rapidly emerging and spreading antibiotic resistance. Currently β-lactamase inhibitors (BLIs) in clinical use act only on Ambler Class A, C and some class D lactamases. The urgent need to identify new BLIs recently lead to FDA approval of boron-based compounds BLIs, e.g. Vaborbactam. The boron-based proteasome inhibitors Bortezomib and Ixazomib are used in cancer therapy as multiple myeloma drugs but they also bind to Ser-/Thr- proteases. In this study we show the crystal structures of the β-lactamase CTX-M-14 with covalently bound Bortezomib and Ixazomib at high resolutions of 1.3 and 1.1 Å, respectively. Ixazomib is well defined in electron density whereas Bortezomib show some disorder which corresponds to weaker inhibition efficiency observed for Ixazomib. Both inhibitors mimic the deacylation transition state of β-lactam hydrolysis, because they replace the deacylating water molecule. We further investigate differences in binding of Bortezomib/Ixazomib to CTX-M-14 and its target proteases as well as known β-lactamase drugs. Our findings can help to use Bortezomib/Ixazomib as lead compounds for development of new BLIs.
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11
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Zhou S, Liu Y, Wang S, Wang L. Effective prediction of short hydrogen bonds in proteins via machine learning method. Sci Rep 2022; 12:469. [PMID: 35013487 PMCID: PMC8748993 DOI: 10.1038/s41598-021-04306-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 12/20/2021] [Indexed: 12/11/2022] Open
Abstract
Short hydrogen bonds (SHBs), whose donor and acceptor heteroatoms lie within 2.7 Å, exhibit prominent quantum mechanical characters and are connected to a wide range of essential biomolecular processes. However, exact determination of the geometry and functional roles of SHBs requires a protein to be at atomic resolution. In this work, we analyze 1260 high-resolution peptide and protein structures from the Protein Data Bank and develop a boosting based machine learning model to predict the formation of SHBs between amino acids. This model, which we name as machine learning assisted prediction of short hydrogen bonds (MAPSHB), takes into account 21 structural, chemical and sequence features and their interaction effects and effectively categorizes each hydrogen bond in a protein to a short or normal hydrogen bond. The MAPSHB model reveals that the type of the donor amino acid plays a major role in determining the class of a hydrogen bond and that the side chain Tyr-Asp pair demonstrates a significant probability of forming a SHB. Combining electronic structure calculations and energy decomposition analysis, we elucidate how the interplay of competing intermolecular interactions stabilizes the Tyr-Asp SHBs more than other commonly observed combinations of amino acid side chains. The MAPSHB model, which is freely available on our web server, allows one to accurately and efficiently predict the presence of SHBs given a protein structure with moderate or low resolution and will facilitate the experimental and computational refinement of protein structures.
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Affiliation(s)
- Shengmin Zhou
- Department of Chemistry and Chemical Biology, Institute for Quantitative Biomedicine, Rutgers University, Piscataway, NJ, 08854, USA
| | - Yuanhao Liu
- Department of Statistics, Institute for Quantitative Biomedicine, Rutgers University, Piscataway, NJ, 08854, USA
| | - Sijian Wang
- Department of Statistics, Institute for Quantitative Biomedicine, Rutgers University, Piscataway, NJ, 08854, USA
| | - Lu Wang
- Department of Chemistry and Chemical Biology, Institute for Quantitative Biomedicine, Rutgers University, Piscataway, NJ, 08854, USA.
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12
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Kemp MT, Nichols DA, Zhang X, Defrees K, Na I, Renslo AR, Chen Y. Mutation of the conserved Asp-Asp pair impairs the structure, function, and inhibition of CTX-M Class A β-lactamase. FEBS Lett 2021; 595:2981-2994. [PMID: 34704263 DOI: 10.1002/1873-3468.14215] [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: 09/14/2021] [Revised: 10/07/2021] [Accepted: 10/21/2021] [Indexed: 11/07/2022]
Abstract
The Asp233-Asp246 pair is highly conserved in Class A β-lactamases, which hydrolyze β-lactam antibiotics. Here, we characterize its function using CTX-M-14 β-lactamase. The D233N mutant displayed decreased activity that is substrate-dependent, with reductions in kcat /Km ranging from 20% for nitrocefin to 6-fold for cefotaxime. In comparison, the mutation reduced the binding of a known reversible inhibitor by 10-fold. The mutant structures showed movement of the 213-219 loop and the loss of the Thr216-Thr235 hydrogen bond, which was restored by inhibitor binding. Mutagenesis of Thr216 further highlighted its contribution to CTX-M activity. These results demonstrate the importance of the aspartate pair to CTX-M hydrolysis of substrates with bulky side chains, while suggesting increased protein flexibility as a means to evolve drug resistance.
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Affiliation(s)
- M Trent Kemp
- Department of Molecular Medicine, University of South Florida College of Medicine, Tampa, FL, USA
| | - Derek A Nichols
- Department of Molecular Medicine, University of South Florida College of Medicine, Tampa, FL, USA
| | - Xiujun Zhang
- Department of Molecular Medicine, University of South Florida College of Medicine, Tampa, FL, USA
| | - Kyle Defrees
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Insung Na
- Department of Molecular Medicine, University of South Florida College of Medicine, Tampa, FL, USA
| | - Adam R Renslo
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Yu Chen
- Department of Molecular Medicine, University of South Florida College of Medicine, Tampa, FL, USA
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13
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Shi Y, Xing J, Li J, Zhu F, Fan X, Zhang Y. The alcohol catalytic mechanism for Schiff base 1,3-proton transfer. COMPUT THEOR CHEM 2021. [DOI: 10.1016/j.comptc.2021.113419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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14
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Protonation Equilibrium in the Active Site of the Photoactive Yellow Protein. Molecules 2021; 26:molecules26072025. [PMID: 33918211 PMCID: PMC8037372 DOI: 10.3390/molecules26072025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 03/30/2021] [Accepted: 03/30/2021] [Indexed: 11/17/2022] Open
Abstract
The role and existence of low-barrier hydrogen bonds (LBHBs) in enzymatic and protein activity has been largely debated. An interesting case is that of the photoactive yellow protein (PYP). In this protein, two short HBs adjacent to the chromophore, p-coumaric acid (pCA), have been identified by X-ray and neutron diffraction experiments. However, there is a lack of agreement on the chemical nature of these H-bond interactions. Additionally, no consensus has been reached on the presence of LBHBs in the active site of the protein, despite various experimental and theoretical studies having been carried out to investigate this issue. In this work, we perform a computational study that combines classical and density functional theory (DFT)-based quantum mechanical/molecular mechanical (QM/MM) simulations to shed light onto this controversy. Furthermore, we aim to deepen our understanding of the chemical nature and dynamics of the protons involved in the two short hydrogen bonds that, in the dark state of PYP, connect pCA with the two binding pocket residues (E46 and Y42). Our results support the existence of a strong LBHB between pCA and E46, with the H fully delocalized and shared between both the carboxylic oxygen of E46 and the phenolic oxygen of pCA. Additionally, our findings suggest that the pCA interaction with Y42 can be suitably described as a typical short ionic H-bond of moderate strength that is fully localized on the phenolic oxygen of Y42.
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15
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Structural and Biochemical Characterization of the Novel CTX-M-151 Extended-Spectrum β-Lactamase and Its Inhibition by Avibactam. Antimicrob Agents Chemother 2021; 65:AAC.01757-20. [PMID: 33431411 DOI: 10.1128/aac.01757-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 12/28/2020] [Indexed: 12/11/2022] Open
Abstract
The diazabicyclooctane (DBO) inhibitor avibactam (AVI) reversibly inactivates most serine β-lactamases, including the CTX-M β-lactamases. Currently, more than 230 unique CTX-M members distributed in five clusters with less than 5% amino acid sequence divergence within each group have been described. Recently, a variant named CTX-M-151 was isolated from a Salmonella enterica subsp. enterica serovar Choleraesuis strain in Japan. This variant possesses a low degree of amino acid identity with the other CTX-Ms (63.2% to 69.7% with respect to the mature proteins), and thus it may represent a new subgroup within the family. CTX-M-151 hydrolyzes ceftriaxone better than ceftazidime (k cat/K m values 6,000-fold higher), as observed with CTX-Ms. CTX-M-151 is well inhibited by mechanism-based inhibitors like clavulanic acid (inactivation rate [k inact]/inhibition constant [Ki ] = 0.15 μM-1 · s-1). For AVI, the apparent inhibition constant (Ki app), 0.4 μM, was comparable to that of KPC-2; the acylation rate (k2/K) (37,000 M-1 · s-1) was lower than that for CTX-M-15, while the deacylation rate (k off) (0.0015 s-1) was 2- to 14-fold higher than those of other class A β-lactamases. The structure of the CTX-M-151/AVI complex (1.32 Å) reveals that AVI adopts a chair conformation with hydrogen bonds between the AVI carbamate and Ser70 and Ser237 at the oxyanion hole. Upon acylation, the side chain of Lys73 points toward Ser130, which is associated with the protonation of Glu166, supporting the role of Lys73 in the proton relay pathway and Glu166 as the general base in deacylation. To our knowledge, this is the first chromosomally encoded CTX-M in Salmonella Choleraesuis that shows similar hydrolytic preference toward cefotaxime (CTX) and ceftriaxone (CRO) to that toward ceftazidime (CAZ).
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16
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Yodsin N, Sakagami H, Udagawa T, Ishimoto T, Jungsuttiwong S, Tachikawa M. Metal-doped carbon nanocones as highly efficient catalysts for hydrogen storage: Nuclear quantum effect on hydrogen spillover mechanism. MOLECULAR CATALYSIS 2021. [DOI: 10.1016/j.mcat.2021.111486] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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17
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Li Z, Wang Y, Baryshnikov G, Shen S, Zhang M, Zou Q, Ågren H, Zhu L. Lighting up solid states using a rubber. Nat Commun 2021; 12:908. [PMID: 33568677 PMCID: PMC7876014 DOI: 10.1038/s41467-021-21253-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 01/13/2021] [Indexed: 11/10/2022] Open
Abstract
It is crucial and desirable to develop green and high-efficient strategies to regulate solid-state structures and their related material properties. However, relative to solution, it is more difficult to break and generate chemical bonds in solid states. In this work, a rubbing-induced photoluminescence on the solid states of ortho-pyridinil phenol family was achieved. This rubbing response relied on an accurately designed topochemical tautomerism, where a negative charge, exactly provided by the triboelectric effect of a rubber, can induce a proton transfer in a double H-bonded dimeric structure. This process instantaneously led to a bright-form tautomer that can be stabilized in the solid-state settings, leading to an up to over 450-fold increase of the fluorescent quantum yield of the materials. The property can be repeatedly used due to the reversibility of the tautomerism, enabling encrypted applications. Moreover, a further modification to the structure can be accomplished to achieve different properties, opening up more possibilities for the design of new-generation smart materials. Changes in molecular properties due to stimuli response are critically important for the development of new materials. However, most processes are slow or inefficient in the solid state. Here the authors demonstrate property switching in the solid state using a rubbing-induced tautomerism in multiple hydrogen-bonded donor-acceptor couples.
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Affiliation(s)
- Zhongyu Li
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai, China
| | - Yanjie Wang
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai, China
| | - Gleb Baryshnikov
- Division of Theoretical Chemistry and Biology School of Biotechnology, KTH Royal Institute of Technology, Stockholm, Sweden.,Tomsk State University, Tomsk, Russia
| | - Shen Shen
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai, China
| | - Man Zhang
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai, China
| | - Qi Zou
- Shanghai Key Laboratory of Materials Protection and Advanced Materials in Electric Power, Shanghai University of Electric Power, Shanghai, China
| | - Hans Ågren
- Tomsk State University, Tomsk, Russia.,Department of Physics and Astronomy, Uppsala University, Uppsala, Sweden
| | - Liangliang Zhu
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai, China.
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18
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Santra S, Giri S, Jana M. Unraveling the origin of interactions of hydroxychloroquine with the receptor-binding domain of SARS-CoV-2 in aqueous medium. Chem Phys Lett 2021; 764:138280. [PMID: 33362291 PMCID: PMC7748971 DOI: 10.1016/j.cplett.2020.138280] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 12/13/2020] [Accepted: 12/14/2020] [Indexed: 12/23/2022]
Abstract
Interactions of hydroxychloroquin (HCQ) with the receptor binding domain (RBD) of SARS-CoV-2 were studied from atomistic simulation and ONIOM techniques. The key-residues of RBD responsible for the human transmission are recognized to be blocked in a heterogeneous manner with the favorable formation of key-residue:HCQ (1:1) complex. Such heterogeneity in binding was identified to be governed by the differential life-time of the hydrogen bonded water network anchoring HCQ and the key-residues. The intermolecular proton transfer facilitates the most favorable Lys417:HCQ complexation. The study demonstrates that off-target bindings of HCQ need to be minimized to efficiently prevent the transmission of SARS-CoV-2.
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Affiliation(s)
- Santanu Santra
- Molecular Simulation Laboratory, Department of Chemistry, National Institute of Technology, Rourkela 769008, India
| | - Santanab Giri
- School of Applied Science and Humanities, Haldia Institute of Technology, Haldia 721657, India
| | - Madhurima Jana
- Molecular Simulation Laboratory, Department of Chemistry, National Institute of Technology, Rourkela 769008, India,Corresponding author
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19
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Kumar P, Agarwal PK, Cuneo MJ. On the Case of the Misplaced Hydrogens. Chembiochem 2021; 22:288-297. [PMID: 32706524 PMCID: PMC7952024 DOI: 10.1002/cbic.202000376] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 07/21/2020] [Indexed: 12/30/2022]
Abstract
Few other elements play a more central role in biology than hydrogen. The interactions, bonding and movement of hydrogen atoms are central to biological catalysis, structure and function. Yet owing to the elusive nature of a single hydrogen atom few experimental and computational techniques can precisely determine its location. This is exemplified in short hydrogen bonds (SHBs) where the location of the hydrogen atom is indicative of the underlying strength of the bonds, which can vary from 1-5 kcal/mol in canonical hydrogen bonds, to an almost covalent nature in single-well hydrogen bonds. Owing to the often-times inferred position of hydrogen, the role of SHBs in biology has remained highly contested and debated. This has also led to discrepancies in computational, biochemical and structural studies of proteins thought to use SHBs in performing chemistry and stabilizing interactions. Herein, we discuss in detail two distinct examples, namely the conserved catalytic triad and the photoreceptor, photoactive yellow protein, where studies of these SHB-containing systems have permitted contextualization of the role these unique hydrogen bonds play in biology.
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Affiliation(s)
- Prashasti Kumar
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Pratul K Agarwal
- Arium BioLabs LLC, Knoxville, TN, 37932, USA
- Department of Physiological Sciences and High-Performance Computing Center, Oklahoma State University, Stillwater, OK 74078, USA
| | - Matthew J Cuneo
- Department of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Pl, Memphis, TN, 38103, USA
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20
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Kemp MT, Lewandowski EM, Chen Y. Low barrier hydrogen bonds in protein structure and function. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2021; 1869:140557. [PMID: 33148530 PMCID: PMC7736181 DOI: 10.1016/j.bbapap.2020.140557] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 10/17/2020] [Accepted: 10/22/2020] [Indexed: 01/05/2023]
Abstract
Low-barrier hydrogen bonds (LBHBs) are a special type of short hydrogen bond (HB) that is characterized by the equal sharing of a hydrogen atom. The existence and catalytic role of LBHBs in proteins has been intensely contested. Advancements in X-ray and neutron diffraction methods has revealed delocalized hydrogen atoms involved in potential LBHBs in a number of proteins, while also demonstrating that short HBs are not necessarily LBHBs. More importantly, a series of experiments on ketosteroid isomerase (KSI) have suggested that LBHBs are significantly stronger than standard HBs in the protein microenvironment in terms of enthalpy, but not free energy. The discrepancy between the enthalpy and free energy of LBHBs offers clues to the challenges, and potential solutions, of the LBHB debate, where the unique strength of LBHBs plays a special role in the kinetic processes of enzyme function and structure, together with other molecular forces in a pre-organized environment.
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Affiliation(s)
- M Trent Kemp
- Department of Molecular Medicine, University of South Florida Morsani College of Medicine, 12901 Bruce B. Downs Blvd, MDC 3522, Tampa, Florida 33612, United States
| | - Eric M Lewandowski
- Department of Molecular Medicine, University of South Florida Morsani College of Medicine, 12901 Bruce B. Downs Blvd, MDC 3522, Tampa, Florida 33612, United States
| | - Yu Chen
- Department of Molecular Medicine, University of South Florida Morsani College of Medicine, 12901 Bruce B. Downs Blvd, MDC 3522, Tampa, Florida 33612, United States.
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21
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Soeung V, Lu S, Hu L, Judge A, Sankaran B, Prasad BVV, Palzkill T. A drug-resistant β-lactamase variant changes the conformation of its active-site proton shuttle to alter substrate specificity and inhibitor potency. J Biol Chem 2020; 295:18239-18255. [PMID: 33109613 DOI: 10.1074/jbc.ra120.016103] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 10/22/2020] [Indexed: 11/06/2022] Open
Abstract
Lys234 is one of the residues present in class A β-lactamases that is under selective pressure due to antibiotic use. Located adjacent to proton shuttle residue Ser130, it is suggested to play a role in proton transfer during catalysis of the antibiotics. The mechanism underpinning how substitutions in this position modulate inhibitor efficiency and substrate specificity leading to drug resistance is unclear. The K234R substitution identified in several inhibitor-resistant β-lactamase variants is associated with decreased potency of the inhibitor clavulanic acid, which is used in combination with amoxicillin to overcome β-lactamase-mediated antibiotic resistance. Here we show that for CTX-M-14 β-lactamase, whereas Lys234 is required for hydrolysis of cephalosporins such as cefotaxime, either lysine or arginine is sufficient for hydrolysis of ampicillin. Further, by determining the acylation and deacylation rates for cefotaxime hydrolysis, we show that both rates are fast, and neither is rate-limiting. The K234R substitution causes a 1500-fold decrease in the cefotaxime acylation rate but a 5-fold increase in kcat for ampicillin, suggesting that the K234R enzyme is a good penicillinase but a poor cephalosporinase due to slow acylation. Structural results suggest that the slow acylation by the K234R enzyme is due to a conformational change in Ser130, and this change also leads to decreased inhibition potency of clavulanic acid. Because other inhibitor resistance mutations also act through changes at Ser130 and such changes drastically reduce cephalosporin but not penicillin hydrolysis, we suggest that clavulanic acid paired with an oxyimino-cephalosporin rather than penicillin would impede the evolution of resistance.
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Affiliation(s)
- Victoria Soeung
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Shuo Lu
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Liya Hu
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Allison Judge
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Banumathi Sankaran
- Department of Molecular Biophysics and Integrated Bioimaging, Berkeley Center for Structural Biology, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - B V Venkataram Prasad
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, USA; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Timothy Palzkill
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, Texas, USA; Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, USA; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA.
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22
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Structural Basis and Binding Kinetics of Vaborbactam in Class A β-Lactamase Inhibition. Antimicrob Agents Chemother 2020; 64:AAC.00398-20. [PMID: 32778546 DOI: 10.1128/aac.00398-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 07/31/2020] [Indexed: 12/20/2022] Open
Abstract
Class A β-lactamases are a major cause of β-lactam resistance in Gram-negative bacteria. The recently FDA-approved cyclic boronate vaborbactam is a reversible covalent inhibitor of class A β-lactamases, including CTX-M extended-spectrum β-lactamase and KPC carbapenemase, both frequently observed in the clinic. Intriguingly, vaborbactam displayed different binding kinetics and cell-based activity for these two enzymes, despite their similarity. A 1.0-Å crystal structure of CTX-M-14 demonstrated that two catalytic residues, K73 and E166, are positively charged and neutral, respectively. Meanwhile, a 1.25-Å crystal structure of KPC-2 revealed a more compact binding mode of vaborbactam versus CTX-M-14, as well as alternative conformations of W105. Together with kinetic analysis of W105 mutants, the structures demonstrate the influence of this residue and the unusual conformation of the β3 strand on the inactivation rate, as well as the stability of the reversible covalent bond with S70. Furthermore, studies of KPC-2 S130G mutant shed light on the different impacts of S130 in the binding of vaborbactam versus avibactam, another recently approved β-lactamase inhibitor. Taken together, these new data provide valuable insights into the inhibition mechanism of vaborbactam and future development of cyclic boronate inhibitors.
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23
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Nakanishi T, Hori Y, Wu S, Sato H, Okazawa A, Kojima N, Horie Y, Okajima H, Sakamoto A, Shiota Y, Yoshizawa K, Sato O. Three-Step Spin State Transition and Hysteretic Proton Transfer in the Crystal of an Iron(II) Hydrazone Complex. Angew Chem Int Ed Engl 2020; 59:14781-14787. [PMID: 32452130 DOI: 10.1002/anie.202006763] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Indexed: 11/06/2022]
Abstract
A proton-electron coupling system, exhibiting unique bistability or multistability of the protonated state, is an attractive target for developing new switchable materials based on proton dynamics. Herein, we present an iron(II) hydrazone crystalline compound, which displays the stepwise transition and bistability of proton transfer at the crystal level. These phenomena are realized through the coupling with spin transition. Although the multi-step transition with hysteresis has been observed in various systems, the corresponding behavior of proton transfer has not been reported in crystalline systems; thus, the described iron(II) complex is the first example. Furthermore, because proton transfer occurs only in one of the two ligands and π electrons redistribute in it, the dipole moment of the iron(II) complexes changes with the proton transfer, wherein the total dipole moment in the crystal was canceled out owing to the antiferroelectric-like arrangement.
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Affiliation(s)
- Takumi Nakanishi
- Institute for Materials Chemistry and Engineering & IRCCS, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Yuta Hori
- Institute for Materials Chemistry and Engineering & IRCCS, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan.,Center for Computational Sciences, University of Tsukuba, Tsukuba, 305-8577, Japan
| | - Shuqi Wu
- Institute for Materials Chemistry and Engineering & IRCCS, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Hiroyasu Sato
- Rigaku Corporation, 3-9-12 Matsubaracho, Akishima, Tokyo, 196-8666, Japan
| | - Atsushi Okazawa
- Department of Basic Science, Graduation School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo, 153-8902, Japan.,Current address: Division of Chemistry, Institution of Liberal Education, Nihon University School of Medicine, 30-1 Oyaguchi Uemachi, Itabashi-ku, Tokyo, 173-8610, Japan
| | - Norimichi Kojima
- Department of Basic Science, Graduation School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo, 153-8902, Japan
| | - Yusuke Horie
- Graduate School of Science and Engineering, Aoyama Gakuin University, 5-10-1 Fuchinobe, Chuo-ku, Sagamihara, Kanagawa, 252-5258, Japan
| | - Hajime Okajima
- Graduate School of Science and Engineering, Aoyama Gakuin University, 5-10-1 Fuchinobe, Chuo-ku, Sagamihara, Kanagawa, 252-5258, Japan
| | - Akira Sakamoto
- Graduate School of Science and Engineering, Aoyama Gakuin University, 5-10-1 Fuchinobe, Chuo-ku, Sagamihara, Kanagawa, 252-5258, Japan
| | - Yoshihito Shiota
- Institute for Materials Chemistry and Engineering & IRCCS, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Kazunari Yoshizawa
- Institute for Materials Chemistry and Engineering & IRCCS, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Osamu Sato
- Institute for Materials Chemistry and Engineering & IRCCS, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
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24
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Durand-Réville TF, Comita-Prevoir J, Zhang J, Wu X, May-Dracka TL, Romero JAC, Wu F, Chen A, Shapiro AB, Carter NM, McLeod SM, Giacobbe RA, Verheijen JC, Lahiri SD, Sacco MD, Chen Y, O'Donnell JP, Miller AA, Mueller JP, Tommasi RA. Discovery of an Orally Available Diazabicyclooctane Inhibitor (ETX0282) of Class A, C, and D Serine β-Lactamases. J Med Chem 2020; 63:12511-12525. [PMID: 32658473 PMCID: PMC7927146 DOI: 10.1021/acs.jmedchem.0c00579] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
![]()
Multidrug
resistant Gram-negative bacterial infections are an increasing
public health threat due to rapidly rising resistance toward β-lactam
antibiotics. The hydrolytic enzymes called β-lactamases are
responsible for a large proportion of the resistance phenotype. β-Lactamase
inhibitors (BLIs) can be administered in combination with β-lactam
antibiotics to negate the action of the β-lactamases, thereby
restoring activity of the β-lactam. Newly developed BLIs offer
some advantage over older BLIs in terms of enzymatic spectrum but
are limited to the intravenous route of administration. Reported here
is a novel, orally bioavailable diazabicyclooctane (DBO) β-lactamase
inhibitor. This new DBO, ETX1317, contains an endocyclic carbon–carbon
double bond and a fluoroacetate activating group and exhibits broad
spectrum activity against class A, C, and D serine β-lactamases.
The ester prodrug of ETX1317, ETX0282, is orally bioavailable and,
in combination with cefpodoxime proxetil, is currently in development
as an oral therapy for multidrug resistant and carbapenem-resistant Enterobacterales infections.
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Affiliation(s)
| | | | - Jing Zhang
- Entasis Therapeutics, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Xiaoyun Wu
- Entasis Therapeutics, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Tricia L May-Dracka
- Infection Discovery, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | | | - Frank Wu
- Entasis Therapeutics, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - April Chen
- Entasis Therapeutics, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Adam B Shapiro
- Entasis Therapeutics, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Nicole M Carter
- Entasis Therapeutics, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Sarah M McLeod
- Entasis Therapeutics, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Robert A Giacobbe
- Infection Discovery, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Jeroen C Verheijen
- Infection Discovery, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Sushmita D Lahiri
- Infection Discovery, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Michael D Sacco
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Boulevard, Tampa, Florida 33612, United States
| | - Yu Chen
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Boulevard, Tampa, Florida 33612, United States
| | - John P O'Donnell
- Entasis Therapeutics, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Alita A Miller
- Entasis Therapeutics, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - John P Mueller
- Entasis Therapeutics, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Rubén A Tommasi
- Entasis Therapeutics, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
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25
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Nakanishi T, Hori Y, Wu S, Sato H, Okazawa A, Kojima N, Horie Y, Okajima H, Sakamoto A, Shiota Y, Yoshizawa K, Sato O. Three‐Step Spin State Transition and Hysteretic Proton Transfer in the Crystal of an Iron(II) Hydrazone Complex. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202006763] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Takumi Nakanishi
- Institute for Materials Chemistry and Engineering & IRCCS Kyushu University 744 Motooka Nishi-ku Fukuoka 819-0395 Japan
| | - Yuta Hori
- Institute for Materials Chemistry and Engineering & IRCCS Kyushu University 744 Motooka Nishi-ku Fukuoka 819-0395 Japan
- Center for Computational Sciences University of Tsukuba Tsukuba 305-8577 Japan
| | - Shuqi Wu
- Institute for Materials Chemistry and Engineering & IRCCS Kyushu University 744 Motooka Nishi-ku Fukuoka 819-0395 Japan
| | - Hiroyasu Sato
- Rigaku Corporation 3-9-12 Matsubaracho Akishima Tokyo 196-8666 Japan
| | - Atsushi Okazawa
- Department of Basic Science Graduation School of Arts and Sciences The University of Tokyo 3-8-1 Komaba, Meguro-ku Tokyo 153-8902 Japan
- Current address: Division of Chemistry Institution of Liberal Education Nihon University School of Medicine 30-1 Oyaguchi Uemachi Itabashi-ku Tokyo 173-8610 Japan
| | - Norimichi Kojima
- Department of Basic Science Graduation School of Arts and Sciences The University of Tokyo 3-8-1 Komaba, Meguro-ku Tokyo 153-8902 Japan
| | - Yusuke Horie
- Graduate School of Science and Engineering Aoyama Gakuin University 5-10-1 Fuchinobe, Chuo-ku Sagamihara Kanagawa 252-5258 Japan
| | - Hajime Okajima
- Graduate School of Science and Engineering Aoyama Gakuin University 5-10-1 Fuchinobe, Chuo-ku Sagamihara Kanagawa 252-5258 Japan
| | - Akira Sakamoto
- Graduate School of Science and Engineering Aoyama Gakuin University 5-10-1 Fuchinobe, Chuo-ku Sagamihara Kanagawa 252-5258 Japan
| | - Yoshihito Shiota
- Institute for Materials Chemistry and Engineering & IRCCS Kyushu University 744 Motooka Nishi-ku Fukuoka 819-0395 Japan
| | - Kazunari Yoshizawa
- Institute for Materials Chemistry and Engineering & IRCCS Kyushu University 744 Motooka Nishi-ku Fukuoka 819-0395 Japan
| | - Osamu Sato
- Institute for Materials Chemistry and Engineering & IRCCS Kyushu University 744 Motooka Nishi-ku Fukuoka 819-0395 Japan
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26
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Das CK, Nair NN. Elucidating the Molecular Basis of Avibactam‐Mediated Inhibition of Class A β‐Lactamases. Chemistry 2020; 26:9639-9651. [DOI: 10.1002/chem.202001261] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 04/10/2020] [Indexed: 12/25/2022]
Affiliation(s)
- Chandan Kumar Das
- Department of ChemistryIndian Institute of Technology Kanpur Kanpur 208016 India
- Current Address: Lehrstuhl für Theoretische ChemieRuhr Universität Bochum 44780 Bochum Germany
| | - Nisanth N. Nair
- Department of ChemistryIndian Institute of Technology Kanpur Kanpur 208016 India
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27
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He Y, Lei J, Pan X, Huang X, Zhao Y. The hydrolytic water molecule of Class A β-lactamase relies on the acyl-enzyme intermediate ES* for proper coordination and catalysis. Sci Rep 2020; 10:10205. [PMID: 32576842 PMCID: PMC7311446 DOI: 10.1038/s41598-020-66431-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 01/06/2020] [Indexed: 11/16/2022] Open
Abstract
Serine-based β-lactamases of Class A, C and D all rely on a key water molecule to hydrolyze and inactivate β-lactam antibiotics. This process involves two conserved catalytic steps. In the first acylation step, the β-lactam antibiotic forms an acyl-enzyme intermediate (ES*) with the catalytic serine residue. In the second deacylation step, an activated water molecule serves as nucleophile (WAT_Nu) to attack ES* and release the inactivated β-lactam. The coordination and activation of WAT_Nu is not fully understood. Using time-resolved x-ray crystallography and QM/MM simulations, we analyzed three intermediate structures of Class A β-lactamase PenP as it slowly hydrolyzed cephaloridine. WAT_Nu is centrally located in the apo structure but becomes slightly displaced away by ES* in the post-acylation structure. In the deacylation structure, WAT_Nu moves back and is positioned along the Bürgi–Dunitz trajectory with favorable energetic profile to attack ES*. Unexpectedly, WAT_Nu is also found to adopt a catalytically incompetent conformation in the deacylation structure forming a hydrogen bond with ES*. Our results reveal that ES* plays a significant role in coordinating and activating WAT_Nu through subtle yet distinct interactions at different stages of the catalytic process. These interactions may serve as potential targets to circumvent β-lactamase-mediated antibiotic resistance.
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Affiliation(s)
- Yunjiao He
- The Hong Kong Polytechnic University Shenzhen Research Institute, Shenzhen, P. R. China.,Department of Applied Biology and Chemical Technology, State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, P. R. China
| | - Jinping Lei
- Department of Chemistry, Center of Systems Biology and Human Health, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, P. R. China.,School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou, P. R. China
| | - Xuehua Pan
- The Hong Kong Polytechnic University Shenzhen Research Institute, Shenzhen, P. R. China.,Department of Applied Biology and Chemical Technology, State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, P. R. China
| | - Xuhui Huang
- Department of Chemistry, Center of Systems Biology and Human Health, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, P. R. China.
| | - Yanxiang Zhao
- The Hong Kong Polytechnic University Shenzhen Research Institute, Shenzhen, P. R. China. .,Department of Applied Biology and Chemical Technology, State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, P. R. China.
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28
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Kędzierski P, Zaczkowska M, Sokalski WA. Extreme Catalytic Power of Ketosteroid Isomerase Related to the Reversal of Proton Dislocations in Hydrogen-Bond Network. J Phys Chem B 2020; 124:3661-3666. [PMID: 32293890 PMCID: PMC7467711 DOI: 10.1021/acs.jpcb.0c01489] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Dynamic
electrostatic catalytic field (DECF) vectors derived from
transition state and reactant wavefunctions for the two-step reaction
occurring within ketosteroid isomerase (KSI) have been calculated
using MP2/aug-cc-pVTZ and lower theory levels to determine the magnitude
of the catalytic effect and the optimal directions of proton transfers
in the KSI hydrogen-bond network. The most surprising and meaningful
finding is that the KSI catalytic activity is enhanced by proton dislocations
proceeding in opposite directions for each of the two consecutive
reaction steps in the same hydrogen network. Such a mechanism allows
an ultrafast switching of the catalytic proton wire environment, possibly
related to the exceptionally high KSI catalytic power.
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Affiliation(s)
- Paweł Kędzierski
- Department of Chemistry, Wrocław University of Science and Technology, Wyb. Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Maria Zaczkowska
- Department of Chemistry, Wrocław University of Science and Technology, Wyb. Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - W Andrzej Sokalski
- Department of Chemistry, Wrocław University of Science and Technology, Wyb. Wyspiańskiego 27, 50-370 Wrocław, Poland
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29
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Mechanism of proton transfer in class A β-lactamase catalysis and inhibition by avibactam. Proc Natl Acad Sci U S A 2020; 117:5818-5825. [PMID: 32123084 DOI: 10.1073/pnas.1922203117] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Gram-negative bacteria expressing class A β-lactamases pose a serious health threat due to their ability to inactivate all β-lactam antibiotics. The acyl-enzyme intermediate is a central milestone in the hydrolysis reaction catalyzed by these enzymes. However, the protonation states of the catalytic residues in this complex have never been fully analyzed experimentally due to inherent difficulties. To help unravel the ambiguity surrounding class A β-lactamase catalysis, we have used ultrahigh-resolution X-ray crystallography and the recently approved β-lactamase inhibitor avibactam to trap the acyl-enzyme complex of class A β-lactamase CTX-M-14 at varying pHs. A 0.83-Å-resolution CTX-M-14 complex structure at pH 7.9 revealed a neutral state for both Lys73 and Glu166. Furthermore, the avibactam hydroxylamine-O-sulfonate group conformation varied according to pH, and this conformational switch appeared to correspond to a change in the Lys73 protonation state at low pH. In conjunction with computational analyses, our structures suggest that Lys73 has a perturbed acid dissociation constant (pKa) compared with acyl-enzyme complexes with β-lactams, hindering its function to deprotonate Glu166 and the initiation of the deacylation reaction. Further NMR analysis demonstrated Lys73 pKa to be ∼5.2 to 5.6. Together with previous ultrahigh-resolution crystal structures, these findings enable us to follow the proton transfer process of the entire acylation reaction and reveal the critical role of Lys73. They also shed light on the stability and reversibility of the avibactam carbamoyl acyl-enzyme complex, highlighting the effect of substrate functional groups in influencing the protonation states of catalytic residues and subsequently the progression of the reaction.
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30
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β-Lactamase of Mycobacterium tuberculosis Shows Dynamics in the Active Site That Increase upon Inhibitor Binding. Antimicrob Agents Chemother 2020; 64:AAC.02025-19. [PMID: 31871087 DOI: 10.1128/aac.02025-19] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 12/19/2019] [Indexed: 12/11/2022] Open
Abstract
The Mycobacterium tuberculosis β-lactamase BlaC is a broad-spectrum β-lactamase that can convert a range of β-lactam antibiotics. Enzymes with low specificity are expected to exhibit active-site flexibility. To probe the motions in BlaC, we studied the dynamic behavior in solution using nuclear magnetic resonance (NMR) spectroscopy. 15N relaxation experiments show that BlaC is mostly rigid on the pico- to nanosecond timescale. Saturation transfer experiments indicate that also on the high-millisecond timescale BlaC is not dynamic. Using relaxation dispersion experiments, clear evidence was obtained for dynamics in the low-millisecond range, with an exchange rate of ca. 860 s-1 The dynamic amide groups are localized in the active site. Upon formation of an adduct with the inhibitor avibactam, extensive line broadening occurs, indicating an increase in magnitude of the active-site dynamics. Furthermore, the rate of the motions increases significantly. Upon reaction with the inhibitor clavulanic acid, similar line broadening is accompanied by duplication of NMR signals, indicative of at least one additional, slower exchange process (exchange rate, k ex, of <100 s-1), while for this inhibitor also loss of pico- to nanosecond timescale rigidity is observed for some amides in the α domain. Possible sources of the observed dynamics, such as motions in the omega loop and rearrangements of active-site residues, are discussed. The increase in dynamics upon ligand binding argues against a model of inhibitor binding through conformational selection. Rather, the induced dynamics may serve to maximize the likelihood of sampling the optimal conformation for hydrolysis of the bound ligand.
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31
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Berta D, Buigues PJ, Badaoui M, Rosta E. Cations in motion: QM/MM studies of the dynamic and electrostatic roles of H + and Mg 2+ ions in enzyme reactions. Curr Opin Struct Biol 2020; 61:198-206. [PMID: 32065923 DOI: 10.1016/j.sbi.2020.01.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 01/04/2020] [Accepted: 01/06/2020] [Indexed: 12/17/2022]
Abstract
Here we discuss current trends in the simulations of enzymatic reactions focusing on phosphate catalysis. The mechanistic details of the proton transfers coupled to the phosphate cleavage is one of the key challenges in QM/MM calculations of these and other enzyme catalyzed reactions. The lack of experimental information offers both an opportunity for computations as well as often unresolved controversies. We discuss the example of small GTPases including the important human Ras protein. The high dimensionality and chemical complexity of these reactions demand carefully chosen computational techniques both in terms of the underlying quantum chemical theory and the sampling of the conformational ensemble. We also point out the important role of Mg2+ ions, and recent advances in their transient involvement in the catalytic mechanisms.
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Affiliation(s)
- Dénes Berta
- Department of Chemistry, King's College London, London, SE1 1DB, United Kingdom
| | - Pedro J Buigues
- Department of Chemistry, King's College London, London, SE1 1DB, United Kingdom
| | - Magd Badaoui
- Department of Chemistry, King's College London, London, SE1 1DB, United Kingdom
| | - Edina Rosta
- Department of Chemistry, King's College London, London, SE1 1DB, United Kingdom.
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32
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Akhtar A, Pemberton OA, Chen Y. Structural Basis for Substrate Specificity and Carbapenemase Activity of OXA-48 Class D β-Lactamase. ACS Infect Dis 2020; 6:261-271. [PMID: 31872762 DOI: 10.1021/acsinfecdis.9b00304] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Carbapenem-hydrolyzing class D β-lactamases (CHDLs) are a diverse family of enzymes that are rapidly becoming the predominant cause of bacterial resistance against β-lactam antibiotics in many regions of the world. OXA-48, an atypical member of CHDLs, is one of the most frequently observed in the clinic and exhibits a unique substrate profile. We applied X-ray crystallography to OXA-48 complexes with multiple β-lactam antibiotics to elucidate this enzyme's carbapenemase activity and its preference of imipenem over meropenem and other substrates such as cefotaxime. In particular, we obtained acyl-enzyme complexes of OXA-48 with imipenem, meropenem, faropenem, cefotaxime, and cefoxitin, and a product complex with imipenem. Importantly, the product complex captures a key reaction milestone with the newly generated carboxylate group still in the oxyanion hole, and represents the first such complex with a wild-type serine β-lactamase. A potential hydrogen bond is observed between the two carboxylate groups from the product and the carbamylated Lys73, representing the stage immediately after the breakage of the acyl-enzyme bond where the product carboxylate would be neutral. The placement of the product carboxylate also illustrates the approximate transient location of the deacylation water that has long eluded structural characterization in class D β-lactamases. Additionally, comparing the product complex with the acyl-enzyme intermediates provides new insights into the various mechanisms by which specific side chain groups hinder the access of the deacylation water to the acyl-enzyme linkage, especially in meropenem. Taken together, these data offer valuable information on the substrate specificity of OXA-48 and the catalytic mechanism of CHDLs.
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Affiliation(s)
- Afroza Akhtar
- Department of Molecular Medicine, University of South Florida Morsani College of Medicine, 12901 Bruce B. Downs Boulevard, MDC 3522, Tampa, Florida 33612, United States
| | - Orville A. Pemberton
- Department of Molecular Medicine, University of South Florida Morsani College of Medicine, 12901 Bruce B. Downs Boulevard, MDC 3522, Tampa, Florida 33612, United States
| | - Yu Chen
- Department of Molecular Medicine, University of South Florida Morsani College of Medicine, 12901 Bruce B. Downs Boulevard, MDC 3522, Tampa, Florida 33612, United States
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33
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Langan PS, Sullivan B, Weiss KL, Coates L. Probing the role of the conserved residue Glu166 in a class A β-lactamase using neutron and X-ray protein crystallography. Acta Crystallogr D Struct Biol 2020; 76:118-123. [PMID: 32038042 PMCID: PMC7008513 DOI: 10.1107/s2059798319016334] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 12/03/2019] [Indexed: 11/10/2022] Open
Abstract
The amino-acid sequence of the Toho-1 β-lactamase contains several conserved residues in the active site, including Ser70, Lys73, Ser130 and Glu166, some of which coordinate a catalytic water molecule. This catalytic water molecule is essential in the acylation and deacylation parts of the reaction mechanism through which Toho-1 inactivates specific antibiotics and provides resistance to its expressing bacterial strains. To investigate the function of Glu166 in the acylation part of the catalytic mechanism, neutron and X-ray crystallographic studies were performed on a Glu166Gln mutant. The structure of this class A β-lactamase mutant provides several insights into its previously reported reduced drug-binding kinetic rates. A joint refinement of both X-ray and neutron diffraction data was used to study the effects of the Glu166Gln mutation on the active site of Toho-1. This structure reveals that while the Glu166Gln mutation has a somewhat limited impact on the positions of the conserved amino acids within the active site, it displaces the catalytic water molecule from the active site. These subtle changes offer a structural explanation for the previously observed decreases in the binding of non-β-lactam inhibitors such as the recently developed diazobicyclooctane inhibitor avibactam.
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Affiliation(s)
- Patricia S. Langan
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Brendan Sullivan
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Kevin L. Weiss
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Leighton Coates
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
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34
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Zhou S, Wang L. Symmetry and 1H NMR chemical shifts of short hydrogen bonds: impact of electronic and nuclear quantum effects. Phys Chem Chem Phys 2020; 22:4884-4895. [DOI: 10.1039/c9cp06840f] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Electronic and nuclear quantum effects determine the symmetry and highly downfield 1H NMR chemical shifts of short hydrogen bonds.
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Affiliation(s)
- Shengmin Zhou
- Department of Chemistry and Chemical Biology
- Institute for Quantitative Biomedicine
- Rutgers University
- Piscataway
- USA
| | - Lu Wang
- Department of Chemistry and Chemical Biology
- Institute for Quantitative Biomedicine
- Rutgers University
- Piscataway
- USA
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35
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Tai H, Nishikawa K, Higuchi Y, Mao ZW, Hirota S. Cysteine SH and Glutamate COOH Contributions to [NiFe] Hydrogenase Proton Transfer Revealed by Highly Sensitive FTIR Spectroscopy. Angew Chem Int Ed Engl 2019; 58:13285-13290. [PMID: 31343102 DOI: 10.1002/anie.201904472] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 07/10/2019] [Indexed: 11/12/2022]
Abstract
A [NiFe] hydrogenase (H2 ase) is a proton-coupled electron transfer enzyme that catalyses reversible H2 oxidation; however, its fundamental proton transfer pathway remains unknown. Herein, we observed the protonation of Cys546-SH and Glu34-COOH near the Ni-Fe site with high-sensitivity infrared difference spectra by utilizing Ni-C-to-Ni-L and Ni-C-to-Ni-SIa photoconversions. Protonated Cys546-SH in the Ni-L state was verified by the observed SH stretching frequency (2505 cm-1 ), whereas Cys546 was deprotonated in the Ni-C and Ni-SIa states. Glu34-COOH was double H-bonded in the Ni-L state, as determined by the COOH stretching frequency (1700 cm-1 ), and single H-bonded in the Ni-C and Ni-SIa states. Additionally, a stretching mode of an ordered water molecule was observed in the Ni-L and Ni-C states. These results elucidate the organized proton transfer pathway during the catalytic reaction of a [NiFe] H2 ase, which is regulated by the H-bond network of Cys546, Glu34, and an ordered water molecule.
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Affiliation(s)
- Hulin Tai
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara, 630-0192, Japan.,MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Koji Nishikawa
- Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo, 678-1297, Japan
| | - Yoshiki Higuchi
- Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo, 678-1297, Japan
| | - Zong-Wan Mao
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Shun Hirota
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara, 630-0192, Japan
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36
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Tai H, Nishikawa K, Higuchi Y, Mao Z, Hirota S. Cysteine SH and Glutamate COOH Contributions to [NiFe] Hydrogenase Proton Transfer Revealed by Highly Sensitive FTIR Spectroscopy. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201904472] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Hulin Tai
- Division of Materials Science Graduate School of Science and Technology Nara Institute of Science and Technology 8916-5 Takayama, Ikoma Nara 630-0192 Japan
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry School of Chemistry Sun Yat-Sen University Guangzhou 510275 China
| | - Koji Nishikawa
- Graduate School of Life Science University of Hyogo 3-2-1 Koto Kamigori-cho, Ako-gun Hyogo 678-1297 Japan
| | - Yoshiki Higuchi
- Graduate School of Life Science University of Hyogo 3-2-1 Koto Kamigori-cho, Ako-gun Hyogo 678-1297 Japan
| | - Zong‐wan Mao
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry School of Chemistry Sun Yat-Sen University Guangzhou 510275 China
| | - Shun Hirota
- Division of Materials Science Graduate School of Science and Technology Nara Institute of Science and Technology 8916-5 Takayama, Ikoma Nara 630-0192 Japan
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37
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Xu Z, Zhang Q, Shi J, Zhu W. Underestimated Noncovalent Interactions in Protein Data Bank. J Chem Inf Model 2019; 59:3389-3399. [PMID: 31294978 DOI: 10.1021/acs.jcim.9b00258] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Noncovalent interactions (NCIs) play essential roles in the structure and function of biomacromolecules. There are various NCIs, e.g., hydrogen bonds (HBs), cation-π and π-π interactions, and ionic bonds, among which HBs are the most widespread and well-studied. By utilizing the ratio of the observed HBs over pseudo HBs (1.0 Å longer than the HB distance criteria without angle constraints), we demonstrated that HBs in both protein-ligand and protein-protein interfaces are overlooked in structures deposited in PDB. After the QM/MM optimization of 12 protein-ligand complexes, we showed that the overlooked HBs could be recovered. With a systematic search in the PDB, we found that the HB number per residue (NHB/R) in proteins decreases as structural resolution becomes lower, implying that HBs are overlooked even today, regardless of the type of refinement approach used. Similarly, cation-π, π-π, and ionic interactions were found to be significantly lost, manifesting the universal underestimation of various NCIs. Considering the vital role of NCIs, it is important to recover the NCIs to facilitate drug design, to explore protein-protein interaction, and to study protein structure and function.
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Affiliation(s)
- Zhijian Xu
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center , Shanghai Institute of Materia Medica, Chinese Academy of Sciences , Shanghai 201203 , China
| | - Qian Zhang
- Department of Computer Science and Technology , East China Normal University , Shanghai 200241 , China
| | - Jiye Shi
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center , Shanghai Institute of Materia Medica, Chinese Academy of Sciences , Shanghai 201203 , China
| | - Weiliang Zhu
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center , Shanghai Institute of Materia Medica, Chinese Academy of Sciences , Shanghai 201203 , China.,Open Studio for Druggability Research of Marine Natural Products , Pilot National Laboratory for Marine Science and Technology (Qingdao) , Qingdao 266237 , China
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38
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Zhou S, Wang L. Unraveling the structural and chemical features of biological short hydrogen bonds. Chem Sci 2019; 10:7734-7745. [PMID: 31588321 PMCID: PMC6764281 DOI: 10.1039/c9sc01496a] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 06/30/2019] [Indexed: 02/06/2023] Open
Abstract
Short hydrogen bonds are ubiquitous in biological macromolecules and exhibit distinctive proton potential energy surfaces and proton sharing properties.
The three-dimensional architecture of biomolecules often creates specialized structural elements, notably short hydrogen bonds that have donor–acceptor separations below 2.7 Å. In this work, we statistically analyze 1663 high-resolution biomolecular structures from the Protein Data Bank and demonstrate that short hydrogen bonds are prevalent in proteins, protein–ligand complexes and nucleic acids. From these biological macromolecules, we characterize the preferred location, connectivity and amino acid composition in short hydrogen bonds and hydrogen bond networks, and assess their possible functional importance. Using electronic structure calculations, we further uncover how the interplay of the structural and chemical features determines the proton potential energy surfaces and proton sharing conditions in biological short hydrogen bonds.
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Affiliation(s)
- Shengmin Zhou
- Department of Chemistry and Chemical Biology , Institute for Quantitative Biomedicine , Rutgers University , Piscataway , NJ 08854 , USA .
| | - Lu Wang
- Department of Chemistry and Chemical Biology , Institute for Quantitative Biomedicine , Rutgers University , Piscataway , NJ 08854 , USA .
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39
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Shurina BA, Page RC. Influence of substrates and inhibitors on the structure of Klebsiella pneumoniae carbapenemase-2. Exp Biol Med (Maywood) 2019; 244:1596-1604. [PMID: 31161945 DOI: 10.1177/1535370219854322] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The hydrolysis of last resort carbapenem antibiotics by Klebsiella pneumoniae carbapenemase-2 (KPC-2) presents a significant danger to global health. Combined with horizontal gene transfer, the emergence KPC-2 threatens to quickly expand carbapenemase activity to ever increasing numbers of pathogens. Our understanding of KPC-2 has greatly increased over the past decade thanks, in great part, to 20 crystal structures solved by groups around the world. These include apo KPC-2 structures, along with structures featuring a library of 10 different inhibitors representing diverse structural and functional classes. Herein we focus on cataloging the available KPC-2 structures and presenting a discussion of key aspects of each structure and important relationships between structures. Although the available structures do not provide information on dynamic motions with KPC-2, and the family of structures indicates small conformational changes across a wide array of bound inhibitors, substrates, and products, the structures provide a strong foundation for additional studies in the coming years to discover new KPC-2 inhibitors. Impact statement The work herein is important to the field as it provides a clear and succinct accounting of available KPC-2 structures. The work advances the field by collecting and analyzing differences and similarities across the available structures. This work features new analyses and interpretations of the existing structures which will impact the field in a positive way by making structural insights more widely available among the beta-lactamase community.
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Affiliation(s)
- Ben A Shurina
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
| | - Richard C Page
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
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40
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DeFrees K, Kemp MT, ElHilali-Pollard X, Zhang X, Mohamed A, Chen Y, Renslo AR. An Empirical Study of Amide-Heteroarene π-Stacking Interactions Using Reversible Inhibitors of a Bacterial Serine Hydrolase. Org Chem Front 2019; 6:1749-1756. [PMID: 32774871 DOI: 10.1039/c9qo00342h] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Compared to aryl-aryl π-stacking interactions, the analogous stacking of heteroarenes on amide π systems is less well understood and vastly underutilized in structure-based drug design. Recent theoretical studies have delineated the important geometric coordinates of the interaction, some of which have been confirmed with synthetic model systems based on Rebek imides. Unfortunately, a broadly useful and tractable protein-ligand model system of this interaction has remained elusive. Here we employed a known inhibitor scaffold to study π-stacking of diverse heteroarene substituents on the amide face of Gly238 in the cephalosporinases CTX-M-14 and CTX-M-27. Biochemical inhibition constants (K i) and biophysical binding constants (K d) were determined for nineteen new analogues against both enzymes, while multiple high-resolution co-crystal structures revealed remarkably consistent placement of the probe heteroarene on Gly238. The data presented support the predicted importance of opposing dipoles in amide-heteroarene interactions and should be useful for evaluating other theoretical predictions concerning these interactions.
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Affiliation(s)
- Kyle DeFrees
- Department of Pharmaceutical Chemistry, University of California San Francisco, 600 16th St., San Francisco, California 94158, United States
| | - M Trent Kemp
- Department of Molecular Medicine, University of South Florida College of Medicine, 12901, Bruce B. Downs Blvd, MDC 3522, Tampa, Florida 33612, United States
| | - Xochina ElHilali-Pollard
- Department of Pharmaceutical Chemistry, University of California San Francisco, 600 16th St., San Francisco, California 94158, United States
| | - Xiujun Zhang
- Department of Molecular Medicine, University of South Florida College of Medicine, 12901, Bruce B. Downs Blvd, MDC 3522, Tampa, Florida 33612, United States
| | - Ahmed Mohamed
- Department of Pharmaceutical Chemistry, University of California San Francisco, 600 16th St., San Francisco, California 94158, United States
| | - Yu Chen
- Department of Molecular Medicine, University of South Florida College of Medicine, 12901, Bruce B. Downs Blvd, MDC 3522, Tampa, Florida 33612, United States
| | - Adam R Renslo
- Department of Pharmaceutical Chemistry, University of California San Francisco, 600 16th St., San Francisco, California 94158, United States
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Tooke CL, Hinchliffe P, Bragginton EC, Colenso CK, Hirvonen VHA, Takebayashi Y, Spencer J. β-Lactamases and β-Lactamase Inhibitors in the 21st Century. J Mol Biol 2019; 431:3472-3500. [PMID: 30959050 PMCID: PMC6723624 DOI: 10.1016/j.jmb.2019.04.002] [Citation(s) in RCA: 427] [Impact Index Per Article: 85.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 03/27/2019] [Accepted: 04/01/2019] [Indexed: 12/31/2022]
Abstract
The β-lactams retain a central place in the antibacterial armamentarium. In Gram-negative bacteria, β-lactamase enzymes that hydrolyze the amide bond of the four-membered β-lactam ring are the primary resistance mechanism, with multiple enzymes disseminating on mobile genetic elements across opportunistic pathogens such as Enterobacteriaceae (e.g., Escherichia coli) and non-fermenting organisms (e.g., Pseudomonas aeruginosa). β-Lactamases divide into four classes; the active-site serine β-lactamases (classes A, C and D) and the zinc-dependent or metallo-β-lactamases (MBLs; class B). Here we review recent advances in mechanistic understanding of each class, focusing upon how growing numbers of crystal structures, in particular for β-lactam complexes, and methods such as neutron diffraction and molecular simulations, have improved understanding of the biochemistry of β-lactam breakdown. A second focus is β-lactamase interactions with carbapenems, as carbapenem-resistant bacteria are of grave clinical concern and carbapenem-hydrolyzing enzymes such as KPC (class A) NDM (class B) and OXA-48 (class D) are proliferating worldwide. An overview is provided of the changing landscape of β-lactamase inhibitors, exemplified by the introduction to the clinic of combinations of β-lactams with diazabicyclooctanone and cyclic boronate serine β-lactamase inhibitors, and of progress and strategies toward clinically useful MBL inhibitors. Despite the long history of β-lactamase research, we contend that issues including continuing unresolved questions around mechanism; opportunities afforded by new technologies such as serial femtosecond crystallography; the need for new inhibitors, particularly for MBLs; the likely impact of new β-lactam:inhibitor combinations and the continuing clinical importance of β-lactams mean that this remains a rewarding research area.
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Affiliation(s)
- Catherine L Tooke
- School of Cellular and Molecular Medicine, University of Bristol Biomedical Sciences Building, University Walk, Bristol BS8 1TD, United Kingdom
| | - Philip Hinchliffe
- School of Cellular and Molecular Medicine, University of Bristol Biomedical Sciences Building, University Walk, Bristol BS8 1TD, United Kingdom
| | - Eilis C Bragginton
- School of Cellular and Molecular Medicine, University of Bristol Biomedical Sciences Building, University Walk, Bristol BS8 1TD, United Kingdom
| | - Charlotte K Colenso
- School of Cellular and Molecular Medicine, University of Bristol Biomedical Sciences Building, University Walk, Bristol BS8 1TD, United Kingdom
| | - Viivi H A Hirvonen
- School of Cellular and Molecular Medicine, University of Bristol Biomedical Sciences Building, University Walk, Bristol BS8 1TD, United Kingdom
| | - Yuiko Takebayashi
- School of Cellular and Molecular Medicine, University of Bristol Biomedical Sciences Building, University Walk, Bristol BS8 1TD, United Kingdom
| | - James Spencer
- School of Cellular and Molecular Medicine, University of Bristol Biomedical Sciences Building, University Walk, Bristol BS8 1TD, United Kingdom.
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Antibacterial Spectrum of a Tetrazole-Based Reversible Inhibitor of Serine β-Lactamases. Antimicrob Agents Chemother 2018; 62:AAC.02563-17. [PMID: 29844038 DOI: 10.1128/aac.02563-17] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 05/13/2018] [Indexed: 11/20/2022] Open
Abstract
CTX-M is the most prevalent family of extended-spectrum β-lactamases. We recently developed a tetrazole-derived noncovalent inhibitor of CTX-M-9. Here, we present the biochemical and microbiological activity of this inhibitor across a representative panel of serine β-lactamases and Gram-negative bacteria. The compound displayed significant activity against all major subgroups of CTX-M, including CTX-M-15, while it exhibited some low-level inhibition of other serine β-lactamases. Complex crystal structures with the CTX-M-14 S237A mutant and CTX-M-27 illustrate the binding contribution of specific active-site residues on the β3 strand. In vitro pharmacokinetic studies revealed drug-like properties and positive prospects for further optimization. These studies suggest that tetrazole-based compounds can provide novel chemotypes for future serine β-lactamase inhibitor discovery.
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Langan PS, Vandavasi VG, Cooper CJ, Weiss KL, Ginell SL, Parks JM, Coates L. Substrate Binding Induces Conformational Changes in a Class A β-lactamase That Prime It for Catalysis. ACS Catal 2018. [DOI: 10.1021/acscatal.7b04114] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Patricia S. Langan
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Venu Gopal Vandavasi
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Connor J. Cooper
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Kevin L. Weiss
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Stephan L. Ginell
- Structural Biology Center, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, Illinois 60439, United States
| | - Jerry M. Parks
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, Tennessee 37996, United States
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6309, United States
| | - Leighton Coates
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
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Wei Y, Li Q, Scheiner S. The π-Tetrel Bond and its Influence on Hydrogen Bonding and Proton Transfer. Chemphyschem 2018; 19:736-743. [DOI: 10.1002/cphc.201701136] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 11/27/2017] [Indexed: 12/18/2022]
Affiliation(s)
- Yuanxin Wei
- Laboratory of Theoretical and Computational Chemistry and School of Chemistry and Chemical Engineering; Yantai University; Yantai 264005 China), Fax: (+86) 535-6902063
| | - Qingzhong Li
- Laboratory of Theoretical and Computational Chemistry and School of Chemistry and Chemical Engineering; Yantai University; Yantai 264005 China), Fax: (+86) 535-6902063
| | - Steve Scheiner
- Department of Chemistry and Biochemistry; Utah State University; Logan UT 84322-0300 USA
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46
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Sugiura K, Tachikawa M, Udagawa T. Nuclear quantum effect and H/D isotope effect on Cl· + (H2O)n → HCl + OH·(H2O)n−1 (n = 1–3) reactions. RSC Adv 2018; 8:17191-17201. [PMID: 35539263 PMCID: PMC9080416 DOI: 10.1039/c8ra02679c] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 05/03/2018] [Indexed: 11/26/2022] Open
Abstract
Cl· + (H2O)n → HCl + OH·(H2O)n−1 (n = 1–3) reactions are fundamental and important ones in atmospheric chemistry. In this study, we focused on the nuclear quantum effect (NQE) of the hydrogen nucleus on these reactions with the aid of the multicomponent quantum mechanics (MC_QM) method, which can directly take account of NQE of light nuclei. Our study reveals that the NQE of the hydrogen nucleus lowers the activation barriers of the reactions and enhances the catalytic effects of second and third water molecules. In particular, we find that (i) the NQE of the proton removes the activation barrier of the reverse reaction of HCl + OH· → Cl· + H2O, and (ii) the catalytic effect of the third water molecule appears in only our MC_QM calculation. We also analyze the H/D isotope effects on these reactions by using the MC_QM method. Cl·+ (H2O)n → HCl + OH(H2O)n−1 (n = 1–3) reactions have been investigated using multicomponent quantum mechanics method, which can take account of the nuclear quantum effect of proton and deuteron.![]()
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Affiliation(s)
- Keita Sugiura
- Department of Chemistry and Biomolecular Science
- Faculty of Engineering
- Gifu University
- Gifu 501-1193
- Japan
| | - Masanori Tachikawa
- Quantum Chemistry Division
- Graduate School of NanoBioScience
- Yokohama City University
- Yokohama
- Japan
| | - Taro Udagawa
- Department of Chemistry and Biomolecular Science
- Faculty of Engineering
- Gifu University
- Gifu 501-1193
- Japan
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Lewandowski EM, Lethbridge KG, Sanishvili R, Skiba J, Kowalski K, Chen Y. Mechanisms of proton relay and product release by Class A β-lactamase at ultrahigh resolution. FEBS J 2017; 285:87-100. [PMID: 29095570 DOI: 10.1111/febs.14315] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 09/15/2017] [Accepted: 10/28/2017] [Indexed: 01/25/2023]
Abstract
The β-lactam antibiotics inhibit penicillin-binding proteins (PBPs) by forming a stable, covalent, acyl-enzyme complex. During the evolution from PBPs to Class A β-lactamases, the β-lactamases acquired Glu166 to activate a catalytic water and cleave the acyl-enzyme bond. Here we present three product complex crystal structures of CTX-M-14 Class A β-lactamase with a ruthenocene-conjugated penicillin-a 0.85 Å resolution structure of E166A mutant complexed with the penilloate product, a 1.30 Å resolution complex structure of the same mutant with the penicilloate product, and a 1.18 Å resolution complex structure of S70G mutant with a penicilloate product epimer-shedding light on the catalytic mechanisms and product inhibition of PBPs and Class A β-lactamases. The E166A-penilloate complex captured the hydrogen bonding network following the protonation of the leaving group and, for the first time, unambiguously show that the ring nitrogen donates a proton to Ser130, which in turn donates a proton to Lys73. These observations indicate that in the absence of Glu166, the equivalent lysine would be neutral in PBPs and therefore capable of serving as the general base to activate the catalytic serine. Together with previous results, this structure suggests a common proton relay network shared by Class A β-lactamases and PBPs, from the catalytic serine to the lysine, and ultimately to the ring nitrogen. Additionally, the E166A-penicilloate complex reveals previously unseen conformational changes of key catalytic residues during the release of the product, and is the first structure to capture the hydrolyzed product in the presence of an unmutated catalytic serine. DATABASE Structural data are available in the PDB database under the accession numbers 5TOP, 5TOY, and 5VLE.
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Affiliation(s)
- Eric M Lewandowski
- Department of Molecular Medicine, University of South Florida College of Medicine, Tampa, FL, USA
| | - Kathryn G Lethbridge
- Department of Molecular Medicine, University of South Florida College of Medicine, Tampa, FL, USA
| | - Ruslan Sanishvili
- GMCA@APS, X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, IL, USA
| | - Joanna Skiba
- Department of Organic Chemistry, Faculty of Chemistry, University of Lodz, Poland
| | - Konrad Kowalski
- Department of Organic Chemistry, Faculty of Chemistry, University of Lodz, Poland
| | - Yu Chen
- Department of Molecular Medicine, University of South Florida College of Medicine, Tampa, FL, USA
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High Pressure Spectroscopic Investigation on Proton Transfer in Squaric Acid and 4,4'-Bipyridine Co-crystal. Sci Rep 2017; 7:4677. [PMID: 28680044 PMCID: PMC5498627 DOI: 10.1038/s41598-017-04980-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 05/23/2017] [Indexed: 11/09/2022] Open
Abstract
In attempt to the obtain detailed geometric information of proton transfer compound (subsequently denote as SQBP) formed between squaric acid (SQ)and 4,4′-bipyridine(BP), and to investigate the mechanisms of pressure-induced double proton transfer and related structural phase transition, we carried out in-situ high pressure Raman spectroscopy of SQBP up to 20 GPa. A solid-solid phase transition together with double proton transfer phenomenon was confirmed by Raman spectroscopy at about 1.5 GPa, and the activation of C = O stretching mode in Raman spectra indicates a square-ring structure of SQ with four symmetric C = O bond formation. These results are further supported by first-principals calculations and in-situ high pressure infrared absorption spectroscopy. Additionally, Raman intensity analysis suggests that a higher-order phase transition with planar BP molecular structure occurred in the pressure range of 3~6 GPa. As a result, the π electron delocalization effect in BP dominated the intensity enhancement of C = O stretching mode in SQ. To the best of our knowledge, this is the first time observation of the intensity enhancement of proton donor’s normal modes induced by proton acceptor’s π electron delocalization.
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Abstract
The reaction between the antibiotic cefotaxime and the CTX-M-14 class A serine hydrolase is addressed from a theoretical point of view, by means of hybrid quantum mechanics/molecular mechanical (QM/MM) calculations, adopting a new approach that postulates that the residue Ser70 itself should play the role of the acid-base species required for the cefotaxime acylation. The proposed mechanism differs from earlier proposals existing in literature for other class A β-lactamases. The results confirm the hypothesis, and show that the reaction should occur via a concerted mechanism in which the acylation of the lactam carbonyl carbon, protonation of the N7 lactam atom, and opening of the β-lactam ring occurs simultaneously. Exploration of the potential energy surface shows three critical points, associated with reactants, transition state and product. The transition state is characterized by frequency, intrinsic reaction coordinate, atomic charge, and bond orders calculations. The calculated activation barrier is 20 kcal mol-1, and the reaction appears to be slightly endothermic by about 12 kcal mol-1. We conclude that this approach is feasible, and should be considered as an alternative mechanism or may exist in competition with others already published in the literature. This information should be useful for the design of novel antibiotics and β-lactamase inhibitors. Graphical abstract Three-dimensional view of the potential energy surface of cefotaxime.
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Affiliation(s)
- Ignacio Lizana
- Computational Chemistry Group, Faculty of Chemical Sciences, Universidad de Concepción, Concepción, Chile
| | - Eduardo J Delgado
- Computational Chemistry Group, Faculty of Chemical Sciences, Universidad de Concepción, Concepción, Chile.
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50
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Pemberton OA, Zhang X, Chen Y. Molecular Basis of Substrate Recognition and Product Release by the Klebsiella pneumoniae Carbapenemase (KPC-2). J Med Chem 2017; 60:3525-3530. [PMID: 28388065 DOI: 10.1021/acs.jmedchem.7b00158] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Carbapenem-resistant Enterobacteriaceae are resistant to most β-lactam antibiotics due to the production of the Klebsiella pneumoniae carbapenemase (KPC-2) class A β-lactamase. Here, we present the first product complex crystal structures of KPC-2 with β-lactam antibiotics containing hydrolyzed cefotaxime and faropenem. They provide experimental insights into substrate recognition by KPC-2 and its unique cephalosporinase/carbapenemase activity. These structures also represent the first product complexes for a wild-type serine β-lactamase, elucidating the product release mechanism of these enzymes in general.
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Affiliation(s)
- Orville A Pemberton
- Department of Molecular Medicine, University of South Florida , 12901 Bruce B. Downs Boulevard, Tampa, Florida 33612, United States
| | - Xiujun Zhang
- Department of Molecular Medicine, University of South Florida , 12901 Bruce B. Downs Boulevard, Tampa, Florida 33612, United States
| | - Yu Chen
- Department of Molecular Medicine, University of South Florida , 12901 Bruce B. Downs Boulevard, Tampa, Florida 33612, United States
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