1
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Mack AR, Kumar V, Taracila MA, Mojica MF, O'Shea M, Schinabeck W, Silver G, Hujer AM, Papp-Wallace KM, Chen S, Haider S, Caselli E, Prati F, van den Akker F, Bonomo RA. Natural protein engineering in the Ω-loop: the role of Y221 in ceftazidime and ceftolozane resistance in Pseudomonas-derived cephalosporinase. Antimicrob Agents Chemother 2023; 67:e0079123. [PMID: 37850746 PMCID: PMC10648885 DOI: 10.1128/aac.00791-23] [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: 06/19/2023] [Accepted: 08/07/2023] [Indexed: 10/19/2023] Open
Abstract
A wide variety of clinically observed single amino acid substitutions in the Ω-loop region have been associated with increased minimum inhibitory concentrations and resistance to ceftazidime (CAZ) and ceftolozane (TOL) in Pseudomonas-derived cephalosporinase and other class C β-lactamases. Herein, we demonstrate the naturally occurring tyrosine to histidine substitution of amino acid 221 (Y221H) in Pseudomonas-derived cephalosporinase (PDC) enables CAZ and TOL hydrolysis, leading to similar kinetic profiles (k cat = 2.3 ± 0.2 µM and 2.6 ± 0.1 µM, respectively). Mass spectrometry of PDC-3 establishes the formation of stable adducts consistent with the formation of an acyl enzyme complex, while spectra of E219K (a well-characterized, CAZ- and TOL-resistant comparator) and Y221H are consistent with more rapid turnover. Thermal denaturation experiments reveal decreased stability of the variants. Importantly, PDC-3, E219K, and Y221H are all inhibited by avibactam and the boronic acid transition state inhibitors (BATSIs) LP06 and S02030 with nanomolar IC50 values and the BATSIs stabilize all three enzymes. Crystal structures of PDC-3 and Y221H as apo enzymes and complexed with LP06 and S02030 (1.35-2.10 Å resolution) demonstrate ligand-induced conformational changes, including a significant shift in the position of the sidechain of residue 221 in Y221H (as predicted by enhanced sampling well-tempered metadynamics simulations) and extensive hydrogen bonding between the enzymes and BATSIs. The shift of residue 221 leads to the expansion of the active site pocket, and molecular docking suggests substrates orientate differently and make different intermolecular interactions in the enlarged active site compared to the wild-type enzyme.
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Affiliation(s)
- Andrew R. Mack
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Research Service, VA Northeast Ohio Healthcare System, Cleveland, Ohio, USA
| | - Vijay Kumar
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Magdalena A. Taracila
- Research Service, VA Northeast Ohio Healthcare System, Cleveland, Ohio, USA
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Maria F. Mojica
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Research Service, VA Northeast Ohio Healthcare System, Cleveland, Ohio, USA
- CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), Cleveland, Ohio, USA
| | - Margaret O'Shea
- Research Service, VA Northeast Ohio Healthcare System, Cleveland, Ohio, USA
| | - William Schinabeck
- Research Service, VA Northeast Ohio Healthcare System, Cleveland, Ohio, USA
| | - Galen Silver
- Research Service, VA Northeast Ohio Healthcare System, Cleveland, Ohio, USA
| | - Andrea M. Hujer
- Research Service, VA Northeast Ohio Healthcare System, Cleveland, Ohio, USA
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Krisztina M. Papp-Wallace
- Research Service, VA Northeast Ohio Healthcare System, Cleveland, Ohio, USA
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Shuang Chen
- Department of Pharmaceutical and Biological Chemistry, School of Pharmacy, University College London, London, England, United Kingdom
| | - Shozeb Haider
- Department of Pharmaceutical and Biological Chemistry, School of Pharmacy, University College London, London, England, United Kingdom
- UCL Centre for Advanced Research Computing, University College London, London, England, United Kingdom
| | - Emilia Caselli
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Fabio Prati
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Focco van den Akker
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Robert A. Bonomo
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), Cleveland, Ohio, USA
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Department of Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Clinician Scientist Investigator, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, USA
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2
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Bhattacharya S, Junghare V, Hazra M, Pandey NK, Mukherjee A, Dhankhar K, Das N, Roy P, Dubey RC, Hazra S. Characterization of a Class A β-Lactamase from Francisella tularensis (Ftu-1) Belonging to a Unique Subclass toward Understanding AMR. ACS BIO & MED CHEM AU 2023; 3:174-188. [PMID: 37101813 PMCID: PMC10125328 DOI: 10.1021/acsbiomedchemau.2c00044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 01/21/2023] [Accepted: 01/25/2023] [Indexed: 04/28/2023]
Abstract
β-lactamase production with vast catalytic divergence in the pathogenic strain limits the antibiotic spectrum in the clinical environment. Class A carbapenemase shares significant sequence similarities, structural features, and common catalytic mechanisms although their resistance spectrum differs from class A β-lactamase in carbapenem and monobactam hydrolysis. In other words, it limited the antibiotic treatment option against infection, causing carbapenemase-producing superbugs. Ftu-1 is a class A β-lactamase expressed by the Francisella tularensis strain, a potent causative organism of tularemia. The chromosomally encoded class A β-lactamase shares two conserved cysteine residues, a common characteristic of a carbapenemase, and a distinctive class in the phylogenetic tree. Complete biochemical and biophysical characterization of the enzyme was performed to understand the overall stability and environmental requirements to perform optimally. To comprehend the enzyme-drug interaction and its profile toward various chemistries of β-lactam and β-lactamase inhibitors, comprehensive kinetic and thermodynamic analyses were conducted using various β-lactam drugs. The dynamic property of Ftu-1 β-lactamase was also predicted using molecular dynamics (MD) simulation to compare its loop flexibility and ligand binding with other related class A β-lactamases. Overall, this study fosters a comprehensive understanding of Ftu-1, proposed to be an intermediate class by characterizing its kinetic profiling, stability by biochemical and biophysical methodologies, and susceptibility profiling. This understanding would be beneficial for the design of new-generation therapeutics.
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Affiliation(s)
- Sourya Bhattacharya
- Department
of Bioscience and Bioengineering, Indian
Institute of Technology Roorkee, Roorkee 247667, India
| | - Vivek Junghare
- Department
of Bioscience and Bioengineering, Indian
Institute of Technology Roorkee, Roorkee 247667, India
| | - Mousumi Hazra
- Department
of Botany and Microbiology, Gurukula Kangri
(Deemed to be University), Haridwar 249404, Uttarakhand, India
| | - Niteesh Kumar Pandey
- Department
of Bioscience and Bioengineering, Indian
Institute of Technology Roorkee, Roorkee 247667, India
| | - Abirlal Mukherjee
- Department
of Bioscience and Bioengineering, Indian
Institute of Technology Roorkee, Roorkee 247667, India
| | - Kunal Dhankhar
- Department
of Bioscience and Bioengineering, Indian
Institute of Technology Roorkee, Roorkee 247667, India
| | - Neeladrisingha Das
- Department
of Bioscience and Bioengineering, Indian
Institute of Technology Roorkee, Roorkee 247667, India
| | - Partha Roy
- Department
of Bioscience and Bioengineering, Indian
Institute of Technology Roorkee, Roorkee 247667, India
| | - Ramesh Chandra Dubey
- Department
of Botany and Microbiology, Gurukula Kangri
(Deemed to be University), Haridwar 249404, Uttarakhand, India
| | - Saugata Hazra
- Department
of Bioscience and Bioengineering, Indian
Institute of Technology Roorkee, Roorkee 247667, India
- Centre
of Nanotechnology, Indian Institute of Technology
Roorkee, Roorkee 247667, India
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3
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Junghare V, Alex R, Baidya A, Paul M, Alyethodi RR, Sengar GS, Kumar S, Singh U, Deb R, Hazra S. In silico modeling revealed new insights into the mechanism of action of enzyme 2'-5'-oligoadenylate synthetase in cattle. J Biomol Struct Dyn 2022; 40:14013-14026. [PMID: 34873989 DOI: 10.1080/07391102.2021.2001373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The innate immune system has an important role in developing the initial resistance to virus infection, and the ability of oligoadenylate synthetase to overcome viral evasion and enhance innate immunity is already established in humans. In the present study, we have tried to explore the molecular and structural variations present in Sahiwal (indigenous) and crossbred (Frieswal) cattle to identify the molecular mechanism of action of OAS1 gene in activation of innate immune response. The significant changes in structural alignment in terms of orientation of loops, shortening of β-sheets and formation of 3-10 α-helix was noticed in Sahiwal and Frieswal cattle. Further, it has been observed that OAS1 from Sahiwal had better binding with APC and DTP ligand than Frieswal OAS1. A remarkable change was seen in orientation at the nucleoside base region of both the ligands, which are bound with OAS1 protein from Frieswal and Sahiwal cattle. The Molecular Dynamic study of apo and ligand complex structures was provided more insight towards the stability of OAS1 from both cattle. This analysis displayed that the Sahiwal cattle protein has more steady nature throughout the simulation and has better binding towards Frieswal in terms of APC and DTP binding. Thus, OAS1 protein is the potential target for explaining the innate immune response in Sahiwal than Frieswal.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Vivek Junghare
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, India
| | - Rani Alex
- ICAR-Central Institute for Research on Cattle, Meerut Cantt, India
| | - Apoorva Baidya
- Department of Chemistry, Indian Intitute of Technology Bombay, Mumbai, India
| | - Manish Paul
- Department of Biotechnology, Maharaja Sriram Chandra Bhanja Deo University, Baripada, India
| | | | | | - Sushil Kumar
- ICAR-National Research Center on Pig, Guwahati, India
| | - Umesh Singh
- ICAR-National Research Center on Pig, Guwahati, India
| | - Rajib Deb
- ICAR-National Research Center on Pig, Guwahati, India
| | - Saugata Hazra
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, India.,Center of Nanotechnology, Indian Institute of Technology Roorkee, Roorkee, India
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4
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Poulton NC, Rock JM. Unraveling the mechanisms of intrinsic drug resistance in Mycobacterium tuberculosis. Front Cell Infect Microbiol 2022; 12:997283. [PMID: 36325467 PMCID: PMC9618640 DOI: 10.3389/fcimb.2022.997283] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 09/30/2022] [Indexed: 02/03/2023] Open
Abstract
Tuberculosis (TB) is among the most difficult infections to treat, requiring several months of multidrug therapy to produce a durable cure. The reasons necessitating long treatment times are complex and multifactorial. However, one major difficulty of treating TB is the resistance of the infecting bacterium, Mycobacterium tuberculosis (Mtb), to many distinct classes of antimicrobials. This review will focus on the major gaps in our understanding of intrinsic drug resistance in Mtb and how functional and chemical-genetics can help close those gaps. A better understanding of intrinsic drug resistance will help lay the foundation for strategies to disarm and circumvent these mechanisms to develop more potent antitubercular therapies.
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5
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Hazra M, Dubey RC. Interdisciplinary in silico studies to understand in-depth molecular level mechanism of drug resistance involving NS3-4A protease of HCV. J Biomol Struct Dyn 2022:1-20. [PMID: 35993498 DOI: 10.1080/07391102.2022.2113823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
Abstract
Hepatitis C virus (HCV) causes hepatitis, a life-threatening disease responsible for liver cirrhosis. Urgent measures have been taken to develop therapeutics against this deadly pathogen. NS3/4A protease is an extremely important target. A series of inhibitors have been developed against this viral protease including Faldaprevir. Unfortunately, the error-prone viral RNA polymerase causes the emergence of resistance, thereby causing reduced effectiveness of those peptidomimetic inhibitors. Among the drug resistant variants, three single amino acid residues (R155, A156 and D168) are notable for their presence in clinical isolates and also their effectivity against most of the known inhibitors in clinical development. Therefore, it is crucial to understand the mechanistic role of those drug resistant variants while designing potent novel inhibitors. In this communication, we have deeply analyzed through using in silico studies to understand the molecular mechanism of alteration of inhibitor binding between wild type and its R155K, A156V and D168V variants. Principal component analysis was carried to identify the backbone fluctuations of important residues in HCV NS3/4A responsible for the inhibitor binding and maintaining drug resistance. Free energy landscape as a function of the principal components has been used to identify the stability and conformation of the key residues that regulate inhibitor binding and their impact in developing drug resistance. Our findings are consistent with the trend of experimental results. The observations are also true in case of other Faldaprevir-like peptidomimetic inhibitors. Understanding this binding mechanism would be significant for the development of novel inhibitors with less susceptibility towards drug resistance.
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Affiliation(s)
- Mousumi Hazra
- Department of Botany and Microbiology, Gurukula Kangri (Deemed to be University), Haridwar, Uttarakhand, India
| | - Ramesh Chandra Dubey
- Department of Botany and Microbiology, Gurukula Kangri (Deemed to be University), Haridwar, Uttarakhand, India
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6
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Guy CS, Tomás RMF, Tang Q, Gibson MI, Fullam E. Imaging of antitubercular dimeric boronic acids at the mycobacterial cell surface by click-probe capture. Chem Commun (Camb) 2022; 58:9361-9364. [PMID: 35917119 PMCID: PMC9387567 DOI: 10.1039/d2cc02407a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Dimeric boronic acids kill Mycobacterium tuberculosis (Mtb) by targeting mycobacterial specific extracellular glycans, removing the requirement for a therapeutic agent to permeate the complex cell envelope. Here we report the successful development and use of new ‘clickable’ boronic acid probes as a powerful method to enable the direct detection and visualisation of this unique class of cell-surface targeting antitubercular agents. Antitubercular ‘clickable’ diboronic acid agents are directly incorporated into the mycobacterial cell envelope through glycan-targeting.![]()
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Affiliation(s)
- Collette S Guy
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK.
| | - Ruben M F Tomás
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK.,Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
| | - Qiao Tang
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK
| | - Matthew I Gibson
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK.,Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
| | - Elizabeth Fullam
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK.
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7
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Nowak MG, Skwarecki AS, Milewska MJ. Amino Acid Based Antimicrobial Agents - Synthesis and Properties. ChemMedChem 2021; 16:3513-3544. [PMID: 34596961 PMCID: PMC9293202 DOI: 10.1002/cmdc.202100503] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 09/02/2021] [Indexed: 12/20/2022]
Abstract
Structures of several dozen of known antibacterial, antifungal or antiprotozoal agents are based on the amino acid scaffold. In most of them, the amino acid skeleton is of a crucial importance for their antimicrobial activity, since very often they are structural analogs of amino acid intermediates of different microbial biosynthetic pathways. Particularly, some aminophosphonate or aminoboronate analogs of protein amino acids are effective enzyme inhibitors, as structural mimics of tetrahedral transition state intermediates. Synthesis of amino acid antimicrobials is a particular challenge, especially in terms of the need for enantioselective methods, including the asymmetric synthesis. All these issues are addressed in this review, summing up the current state‐of‐the‐art and presenting perspectives fur further progress.
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Affiliation(s)
- Michał G Nowak
- Department of Organic Chemistry and BioTechMed Center, Gdańsk University of Technology, 11/12 Gabriela Narutowicza Street, 80-233, Gdańsk, Poland
| | - Andrzej S Skwarecki
- Department of Pharmaceutical Technology and Biochemistry and BioTechMed Center, Gdańsk University of Technology, 11/12 Gabriela Narutowicza Street, 80-233, Gdańsk, Poland
| | - Maria J Milewska
- Department of Organic Chemistry and BioTechMed Center, Gdańsk University of Technology, 11/12 Gabriela Narutowicza Street, 80-233, Gdańsk, Poland
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8
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Manenti M, Gazzotti S, Lo Presti L, Molteni G, Silvani A. Highly diastereoselective entry to chiral oxindole-based β-amino boronic acids and spiro derivatives. Org Biomol Chem 2021; 19:7211-7216. [PMID: 34612343 DOI: 10.1039/d1ob01303c] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We here describe the first Cu-catalysed, diastereoselective 1,2-addition of 1,1-diborylmethane to chiral ketimines for the synthesis of quaternary stereocenters and spiro compounds. The method provides easy access to a range of chiral, highly functionalized compounds, namely oxindole-based β,β'-disubstituted β-amino boronates, boron-containing peptidomimetics and six-, seven-membered spirocyclic hemiboronic esters. Such unprecedented compounds are mostly obtained in high yields and easily isolated as single diastereoisomers, paving the way to a more intense exploitation of boron-containing compounds in diversity-oriented chemistry and drug-discovery programs. Concerning stereochemistry, the application of Ellman's auxiliary strategy allows in principle to access both steric series of target compounds.
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Affiliation(s)
- Marco Manenti
- Dipartimento di Chimica, Università degli Studi di Milano, Via Golgi 19, Milano, 20133, Italy.
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9
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Evaluating the covalent binding of carbapenems on BlaC using noncovalent interactions. J Mol Model 2021; 27:161. [PMID: 33966119 DOI: 10.1007/s00894-021-04760-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 04/18/2021] [Indexed: 10/21/2022]
Abstract
Carbapenems, as irreversible covalent binders and slow substrates to the class A β-lactamase (BlaC) of Mycobacterium tuberculosis, can inhibit BlaC to hydrolyze the β-lactam drugs which are used to control tuberculosis. Their binding on BlaC involves covalent bonding and noncovalent interaction. We introduce a hypothesis that the noncovalent interactions dominate the difference of binding free energies for covalent ligands based on the assumption that their covalent bonding energies are the same. MM/GBSA binding free energies calculated from the noncovalent interactions provided a threshold with respect to the experimental kinetic data, to select slow carbapenem substrates which were either constructed using the structural units of experimentally identified carbapenems or obtained from the similarity search over the ZINC15 database. Combining molecular docking with consensus scoring and molecular dynamics simulation with MM/GBSA binding free energy calculations, a computational protocol was developed from which several new tight-binding carbapenems were theoretically identified.
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10
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Understanding the molecular interactions of inhibitors against Bla1 beta-lactamase towards unraveling the mechanism of antimicrobial resistance. Int J Biol Macromol 2021; 177:337-350. [PMID: 33582216 DOI: 10.1016/j.ijbiomac.2021.02.069] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 02/07/2021] [Accepted: 02/08/2021] [Indexed: 11/24/2022]
Abstract
This study evaluated the inhibitory potential of various beta-lactamase inhibitors such as mechanism-based inhibitors (MBIs), carbapenems, monobactam, and non-beta-lactam inhibitors against Bla1, a class-A beta-lactamase encoded by Bacillus anthracis. The binding potential of different inhibitors was estimated using competitive kinetic assay, isothermal titration calorimetry, and Biolayer interferometry. We observed that tazobactam has better inhibition among other MBIs with a characteristics inhibition dissociation constant of 0.51 ± 0.13 μM. Avibactam was also identified as good inhibitor with an inhibition efficiency of 0.6 ± 0.04 μM. All the MBIs (KD = 1.90E-04 M, 2.05E-05 M, 3.55E-04 M for clavulanate, sulbactam and tazobactam) showed significantly better binding potential than carbapenems (KD = 1.02E-03 M, 2.74E-03 M, 1.24E-03 M for ertapenem, imipenem and biapenem respectively). Molecular dynamics simulations were carried out using Bla1-inhibitor complexes to understand the dynamics and stability. The minimum inhibitory concentration (MIC) was carried out by taking various substrates and inhibitors, and later it was followed by cell viability assay. Together, our study helps develop a proper understanding of Bla1 beta-lactamase and its interaction with inhibitory molecules. This study would facilitate comprehending the catalytic divergence of beta-lactamases and the newly emergent resistant strains, focusing on the new generation of therapeutics being less prone to antimicrobial resistance.
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11
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Lu LN, Liu C, Yang ZZ. Systematic Parameterization and Simulation of Boronic Acid-β-Lactamase Aqueous Solution in Developing the ABEEMσπ Polarizable Force Field. J Phys Chem A 2020; 124:8614-8632. [PMID: 32910648 DOI: 10.1021/acs.jpca.0c06806] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Boronic acid, an inhibitor of β-lactamase, has begun to be applied to the treatment of biological infections and tumors. Scientists are working to develop new and more effective boronic acid. Molecular dynamics (MD) simulation provides a powerful auxiliary tool for drug design. However, the current force fields have no boron-related parameters. In this work, an atom-bond electronegativity equalization method at the σπ level (ABEEMσπ) polarizable force field (ABEEMσπ PFF) of boronic acid and β-lactamase has been developed to determine the potential functions and parameters. The interaction between boron and serine in β-lactamase is regarded as a bonded mode. The interaction between them is simulated by the Morse potential energy function, which is close to the experimental change of the stretching potential energy in a large range. The potential energy surfaces of the bond length, bond angle, and dihedral angle of boronic acid-β-lactamase have the same stability point and change trend as M06-2X/6-311G**. For 47 boronic acid-β-lactamase training molecules, the linear correlation coefficient (R) of the charge distribution between the ABEEMσπ PFF and HF/STO-3G is greater than 0.96. Attributed to the fact that the charge distribution of the ABEEMσπ PFF can fluctuate with the change of geometry and environment, the polarization effect and charge-transfer effect are well reflected. The binding ability of different boronic acids with the same β-lactamase is different. A total of 10 boronic acid-β-lactamase model molecules and 10 boronic acid-β-lactamase and water complexes are simulated. The order of binding energy of five large model molecules calculated by the ABEEMσπ PFF is consistent with that of the MP2 method. The binding energies of boronic acid-β-lactamase and water complexes are close to those of the MP2 method. The results of MD simulation of five aqueous boronic acid-β-lactamase complexes in the NVT ensemble verify the rationality of boron-related parameters of the ABEEMσπ PFF, which have a good application prospect. This study lays a solid theoretical foundation for further study of the inhibition of boronic acid on β-lactamase.
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Affiliation(s)
- Li-Nan Lu
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian 116029, People's Republic of China
| | - Cui Liu
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian 116029, People's Republic of China
| | - Zhong-Zhi Yang
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian 116029, People's Republic of China
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12
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Xia Q, Chang HR, Li J, Wang JY, Peng YQ, Song GH. Tunable Synthesis of α-Amino Boronic Esters from Available Aldehydes and Amines through Sequential One-Pot Dehydration and Copper-Catalyzed Borylacylation. J Org Chem 2020; 85:2716-2724. [PMID: 31886664 DOI: 10.1021/acs.joc.9b02887] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Copper-catalyzed multicomponent borylacylation of imines with acid chlorides and bis(pinacolato)diboron was developed for the preparation of synthetically useful and pharmacologically relevant α-amino boronic acid derivatives. Starting from a range of acid chlorides and imines with aryl, heteroaryl, and alkyl substituents, most of these ligand-free reactions proceeded smoothly at room temperature in moderate to good yields. Furthermore, a facile and convenient one-pot, multistep access to the direct synthesis of α-amino boronic acid derivatives from available aldehydes and amines was also developed.
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Affiliation(s)
- Qi Xia
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy , East China University of Science and Technology , Shanghai , 200237 , P. R. China
| | - Hua-Rong Chang
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy , East China University of Science and Technology , Shanghai , 200237 , P. R. China
| | - Juan Li
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy , East China University of Science and Technology , Shanghai , 200237 , P. R. China
| | - Jia-Yi Wang
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy , East China University of Science and Technology , Shanghai , 200237 , P. R. China
| | - Yan-Qing Peng
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy , East China University of Science and Technology , Shanghai , 200237 , P. R. China
| | - Gong-Hua Song
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy , East China University of Science and Technology , Shanghai , 200237 , P. R. China
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13
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An insight into the complete biophysical and biochemical characterization of novel class A beta-lactamase (Bla1) from Bacillus anthracis. Int J Biol Macromol 2020; 145:510-526. [DOI: 10.1016/j.ijbiomac.2019.12.136] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Revised: 12/11/2019] [Accepted: 12/15/2019] [Indexed: 11/22/2022]
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14
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Guy CS, Murray K, Gibson MI, Fullam E. Dimeric benzoboroxoles for targeted activity against Mycobacterium tuberculosis. Org Biomol Chem 2019; 17:9524-9528. [PMID: 31659363 DOI: 10.1039/c9ob02222h] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Dimeric benzoboroxoles that are covalently linked by a short scaffold enhance selective anti-tubercular activity. These multimeric benzoboroxole compounds are capable of engaging the specific extracellular Mycobacterium tuberculosis glycans, do not lead to the evolution of resistance and bypass the need to cross the impermeable mycobacterial cell envelope barrier.
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Affiliation(s)
- Collette S Guy
- School of Life Sciences, University of Warwick, CV4 7AL, UK.
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15
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White DS, Choy CJ, Moural TW, Martin SE, Wang J, Gargaro S, Kang C, Berkman CE. Bis(benzoyl) phosphate inactivators of beta-lactamase C from Mtb. Bioorg Med Chem Lett 2019; 29:2116-2118. [PMID: 31281019 DOI: 10.1016/j.bmcl.2019.07.002] [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: 05/08/2019] [Revised: 06/27/2019] [Accepted: 07/01/2019] [Indexed: 11/26/2022]
Abstract
The class A β-lactamase BlaC is a cell surface expressed serine hydrolase of Mycobacterium tuberculosis (Mtb), one of the causative agents for Tuberculosis in humans. Mtb has demonstrated increased susceptibility to β-lactam antibiotics upon inactivation of BlaC; thus, making BlaC a rational enzyme target for therapeutic agents. Herein, we present the synthesis and structure-activity-relationship data for the 1st-generation library of bis(benzoyl) phosphates (1-10). Substituent effects ranged from σp = -0.27 to 0.78 for electronic and π = -0.41 to 1.98 for hydrophobic parameters. Compounds 1, 4 and 5 demonstrated the greatest inhibitory potency against BlaC in a time-dependent manner (kobs = 0.212, 0.324, and 0.450 mn-1 respectively). Combined crystal structure data and mass spectrometric analysis of a tryptic digest for BlaC inactivated with 4 provided evidence that the mechanism of inactivation by this bis(benzoyl) phosphate scaffold occurs via phosphorylation of the active-site Ser-70, ultimately leading to an aged form of the enzyme.
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Affiliation(s)
- Dawanna S White
- Washington State University, Department of Chemistry, Pullman, WA 99164-6340, United States
| | - Cindy J Choy
- Washington State University, Department of Chemistry, Pullman, WA 99164-6340, United States
| | - Timothy W Moural
- Washington State University, Department of Chemistry, Pullman, WA 99164-6340, United States
| | - Stacy E Martin
- Washington State University, Department of Chemistry, Pullman, WA 99164-6340, United States
| | - Jing Wang
- Washington State University, Tissue Imaging and Proteomics Laboratory, Pullman, WA 99164-4630, United States
| | - Samantha Gargaro
- Washington State University, Department of Chemistry, Pullman, WA 99164-6340, United States
| | - ChulHee Kang
- Washington State University, Department of Chemistry, Pullman, WA 99164-6340, United States
| | - Clifford E Berkman
- Washington State University, Department of Chemistry, Pullman, WA 99164-6340, United States.
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16
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Guy CS, Gibson MI, Fullam E. Targeting extracellular glycans: tuning multimeric boronic acids for pathogen-selective killing of Mycobacterium tuberculosis. Chem Sci 2019; 10:5935-5942. [PMID: 31360399 PMCID: PMC6566077 DOI: 10.1039/c9sc00415g] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 05/03/2019] [Indexed: 12/14/2022] Open
Abstract
Innovative chemotherapeutic agents that are active against Mycobacterium tuberculosis (Mtb) are urgently required to control the tuberculosis (TB) epidemic.
Innovative chemotherapeutic agents that are active against Mycobacterium tuberculosis (Mtb) are urgently required to control the tuberculosis (TB) epidemic. The Mtb cell envelope has distinct (lipo)polysaccharides and glycolipids that play a critical role in Mtb survival and pathogenesis and disruption of pathways involved in the assembly of the Mtb cell envelope are the primary target of anti-tubercular agents. Here we introduce a previously unexplored approach whereby chemical agents directly target the extracellular glycans within the unique Mtb cell envelope, rather than the intracellular biosynthetic machinery. We designed and synthesised multimeric boronic acids that are selectively lethal to Mtb and function by targeting these structurally unique and essential Mtb cell envelope glycans. By tuning the number of, and distance between, boronic acid units high selectivity to Mtb, low cytotoxicity against mammalian cells and no observable resistance was achieved. This non-conventional approach may prevent the development of drug-resistance and will act as a platform for the design of improved, pathogen-specific, next generation antibiotics.
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Affiliation(s)
- Collette S Guy
- School of Life Sciences , University of Warwick , CV4 7AL , UK . .,Department of Chemistry , University of Warwick , Coventry , CV4 7AL , UK .
| | - Matthew I Gibson
- Department of Chemistry , University of Warwick , Coventry , CV4 7AL , UK . .,Warwick Medical School , University of Warwick , Coventry , CV4 7AL , UK
| | - Elizabeth Fullam
- School of Life Sciences , University of Warwick , CV4 7AL , UK .
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17
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Tassoni R, Blok A, Pannu NS, Ubbink M. New Conformations of Acylation Adducts of Inhibitors of β-Lactamase from Mycobacterium tuberculosis. Biochemistry 2019; 58:997-1009. [PMID: 30632739 PMCID: PMC6383187 DOI: 10.1021/acs.biochem.8b01085] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
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Mycobacterium tuberculosis (Mtb), the main causative
agent of tuberculosis (TB), is naturally resistant to β-lactam
antibiotics due to the production of the extended spectrum β-lactamase
BlaC. β-Lactam/β-lactamase inhibitor combination therapies
can circumvent the BlaC-mediated resistance of Mtb and are promising
treatment options against TB. However, still little is known of the
exact mechanism of BlaC inhibition by the β-lactamase inhibitors
currently approved for clinical use, clavulanic acid, sulbactam, tazobactam,
and avibactam. Here, we present the X-ray diffraction crystal structures
of the acyl-enzyme adducts of wild-type BlaC with the four inhibitors.
The +70 Da adduct derived from clavulanate and the trans-enamine acylation adducts of sulbactam and tazobactam are reported.
BlaC in complex with avibactam revealed two inhibitor conformations.
Preacylation binding could not be observed because inhibitor binding
was not detected in BlaC variants carrying a substitution of the active
site serine 70 to either alanine or cysteine, by crystallography,
ITC or NMR. These results suggest that the catalytic serine 70 is
necessary not only for enzyme acylation but also for increasing BlaC
affinity for inhibitors in the preacylation state. The structure of
BlaC with the serine to cysteine mutation showed a covalent linkage
of the cysteine 70 Sγ atom to the nearby amino group of lysine
73. The differences of adduct conformations between BlaC and other
β-lactamases are discussed.
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Affiliation(s)
- Raffaella Tassoni
- Leiden Institute of Chemistry , Leiden University , Einsteinweg 55 , Leiden 2333CC , The Netherlands
| | - Anneloes Blok
- Leiden Institute of Chemistry , Leiden University , Einsteinweg 55 , Leiden 2333CC , The Netherlands
| | - Navraj S Pannu
- Leiden Institute of Chemistry , Leiden University , Einsteinweg 55 , Leiden 2333CC , The Netherlands
| | - Marcellus Ubbink
- Leiden Institute of Chemistry , Leiden University , Einsteinweg 55 , Leiden 2333CC , The Netherlands
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18
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Deciphering the Evolution of Cephalosporin Resistance to Ceftolozane-Tazobactam in Pseudomonas aeruginosa. mBio 2018; 9:mBio.02085-18. [PMID: 30538183 PMCID: PMC6299481 DOI: 10.1128/mbio.02085-18] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The presence of β-lactamases (e.g., PDC-3) that have naturally evolved and acquired the ability to break down β-lactam antibiotics (e.g., ceftazidime and ceftolozane) leads to highly resistant and potentially lethal Pseudomonas aeruginosa infections. We show that wild-type PDC-3 β-lactamase forms an acyl enzyme complex with ceftazidime, but it cannot accommodate the structurally similar ceftolozane that has a longer R2 side chain with increased basicity. A single amino acid substitution from a glutamate to a lysine at position 221 in PDC-3 (E221K) causes the tyrosine residue at 223 to adopt a new position poised for efficient hydrolysis of both cephalosporins. The importance of the mechanism of action of the E221K variant, in particular, is underscored by its evolutionary recurrences in multiple bacterial species. Understanding the biochemical and molecular basis for resistance is key to designing effective therapies and developing new β-lactam/β-lactamase inhibitor combinations. Pseudomonas aeruginosa produces a class C β-lactamase (e.g., PDC-3) that robustly hydrolyzes early generation cephalosporins often at the diffusion limit; therefore, bacteria possessing these β-lactamases are resistant to many β-lactam antibiotics. In response to this significant clinical threat, ceftolozane, a 3′ aminopyrazolium cephalosporin, was developed. Combined with tazobactam, ceftolozane promised to be effective against multidrug-resistant P. aeruginosa. Alarmingly, Ω-loop variants of the PDC β-lactamase (V213A, G216R, E221K, E221G, and Y223H) were identified in ceftolozane/tazobactam-resistant P. aeruginosa clinical isolates. Herein, we demonstrate that the Escherichia coli strain expressing the E221K variant of PDC-3 had the highest minimum inhibitory concentrations (MICs) against a panel of β-lactam antibiotics, including ceftolozane and ceftazidime, a cephalosporin that differs in structure largely in the R2 side chain. The kcat values of the E221K variant for both substrates were equivalent, whereas the Km for ceftolozane (341 ± 64 µM) was higher than that for ceftazidime (174 ± 20 µM). Timed mass spectrometry, thermal stability, and equilibrium unfolding studies revealed key mechanistic insights. Enhanced sampling molecular dynamics simulations identified conformational changes in the E221K variant Ω-loop, where a hidden pocket adjacent to the catalytic site opens and stabilizes ceftolozane for efficient hydrolysis. Encouragingly, the diazabicyclooctane β-lactamase inhibitor avibactam restored susceptibility to ceftolozane and ceftazidime in cells producing the E221K variant. In addition, a boronic acid transition state inhibitor, LP-06, lowered the ceftolozane and ceftazidime MICs by 8-fold for the E221K-expressing strain. Understanding these structural changes in evolutionarily selected variants is critical toward designing effective β-lactam/β-lactamase inhibitor therapies for P. aeruginosa infections.
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19
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Paul M, Kumar Panda M, Thatoi H. Developing Hispolon-based novel anticancer therapeutics against human (NF-κβ) using in silico approach of modelling, docking and protein dynamics. J Biomol Struct Dyn 2018; 37:3947-3967. [PMID: 30295165 DOI: 10.1080/07391102.2018.1532321] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Hispolon is a polyphenolic compound derived from black hoof mushroom (Phellinus linteus) or shaggy bracket mushroom (Inonotus hispidus) which induces the inhibition of cancer-promoting nuclear factor-kappa beta (NF-κβ) complex. To develop more potent lead molecules with enhanced anticancer efficiency, the mechanism of hispolon-mediated nuclear factor-κβ inhibition has been investigated by molecular modelling and docking. Ten derivatives of hispolon (DRG1-10) have been developed by pharmacophore-based design with a view to enhance the anticancer efficacy. Hispolon and its derivatives were further screened for different pharmacological parameters like binding free energy, drug likeliness, absorption-digestion-metabolism-excretion (ADME), permeability, mutagenicity, toxicity and inhibitory concentration 50 (IC50) to find a potent lead molecule. Based on pharmacological validation, comparative molecular dynamics (MD) simulations have been performed for three lead molecules: Hispolon, DRG2 and DRG7 complexed with human NF-κβ up to 50 ns. By analysing different factors like root mean square deviation (RMSD), root mean square fluctuation (RMSF), radius of gyration (Rg), solvent-accessible surface area (SASA) and principal component analysis (PCA), Gibb's free energy plots DRG2 have more binding efficiency compared to hispolon and DRG7. In RMSD plot, hispolon-bound NF-κβ has the most deviation within a range between 0.125 and 0.45 nm, and DRG2-bound complex showed the range between 0.125 and 0.25 nm. The residues of NF-κβ responsible for hydrophobic interactions with ligand, e.g. Met469, Leu522 and Cys533, have the lowest fluctuation values in DRG2-bound complex. The average Rg fluctuation for DRG2-bound NF-κβ has been recorded under 2.025 nm for most of the simulation time which is much less compared to hispolon and DRG7. Gibb's free energy plots also define the highest stability of DRG2-bound NF-κβ. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Manish Paul
- a Department of Biotechnology, North Orissa University , Baripada , Odisha , India
| | | | - Hrudayanath Thatoi
- a Department of Biotechnology, North Orissa University , Baripada , Odisha , India
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20
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Pal M, Bhattacharya S, Kalyan G, Hazra S. Cadherin profiling for therapeutic interventions in Epithelial Mesenchymal Transition (EMT) and tumorigenesis. Exp Cell Res 2018; 368:137-146. [DOI: 10.1016/j.yexcr.2018.04.014] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Revised: 03/15/2018] [Accepted: 04/13/2018] [Indexed: 12/14/2022]
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21
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Tan M, Li K, Yin J, You J. Manganese/cobalt-catalyzed oxidative C(sp3)–H/C(sp3)–H coupling: a route to α-tertiary β-arylethylamines. Chem Commun (Camb) 2018; 54:1221-1224. [DOI: 10.1039/c7cc08512e] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
An oxidative coupling reaction of an α-C(sp3)–H bond of amine with a benzylic C(sp3)–H bond provides diverse collections of α-tertiary β-arylethylamines.
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Affiliation(s)
- Meiling Tan
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University
- Chengdu 610064
- P. R. China
| | - Kaizhi Li
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University
- Chengdu 610064
- P. R. China
| | - Jiangliang Yin
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University
- Chengdu 610064
- P. R. China
| | - Jingsong You
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University
- Chengdu 610064
- P. R. China
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22
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Elings W, Tassoni R, van der Schoot SA, Luu W, Kynast JP, Dai L, Blok AJ, Timmer M, Florea BI, Pannu NS, Ubbink M. Phosphate Promotes the Recovery of Mycobacterium tuberculosis β-Lactamase from Clavulanic Acid Inhibition. Biochemistry 2017; 56:6257-6267. [PMID: 29087696 PMCID: PMC5707625 DOI: 10.1021/acs.biochem.7b00556] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
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The rise of multi-
and even totally antibiotic resistant forms
of Mycobacterium tuberculosis underlines the need
for new antibiotics. The pathogen is resistant to β-lactam compounds
due to its native serine β-lactamase, BlaC. This resistance
can be circumvented by administration of a β-lactamase inhibitor.
We studied the interaction between BlaC and the inhibitor clavulanic
acid. Our data show hydrolysis of clavulanic acid and recovery of
BlaC activity upon prolonged incubation. The rate of clavulanic acid
hydrolysis is much higher in the presence of phosphate ions. A specific
binding site for phosphate is identified in the active site pocket,
both in the crystalline state and in solution. NMR spectroscopy experiments
show that phosphate binds to this site with a dissociation constant
of 30 mM in the free enzyme. We conclude that inhibition of BlaC by
clavulanic acid is reversible and that phosphate ions can promote
the hydrolysis of the inhibitor.
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Affiliation(s)
- Wouter Elings
- Leiden Institute of Chemistry, Leiden University , Einsteinweg 55, Leiden, The Netherlands
| | - Raffaella Tassoni
- Leiden Institute of Chemistry, Leiden University , Einsteinweg 55, Leiden, The Netherlands
| | | | - Wendy Luu
- Leiden Institute of Chemistry, Leiden University , Einsteinweg 55, Leiden, The Netherlands
| | - Josef P Kynast
- Leiden Institute of Chemistry, Leiden University , Einsteinweg 55, Leiden, The Netherlands
| | - Lin Dai
- Leiden Institute of Chemistry, Leiden University , Einsteinweg 55, Leiden, The Netherlands
| | - Anneloes J Blok
- Leiden Institute of Chemistry, Leiden University , Einsteinweg 55, Leiden, The Netherlands
| | - Monika Timmer
- Leiden Institute of Chemistry, Leiden University , Einsteinweg 55, Leiden, The Netherlands
| | - Bogdan I Florea
- Leiden Institute of Chemistry, Leiden University , Einsteinweg 55, Leiden, The Netherlands
| | - Navraj S Pannu
- Leiden Institute of Chemistry, Leiden University , Einsteinweg 55, Leiden, The Netherlands
| | - Marcellus Ubbink
- Leiden Institute of Chemistry, Leiden University , Einsteinweg 55, Leiden, The Netherlands
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23
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Hazra G, Maity S, Bhowmick S, Ghorai P. Organocatalytic, enantioselective synthesis of benzoxaboroles via Wittig/oxa-Michael reaction Cascade of α-formyl boronic acids. Chem Sci 2017; 8:3026-3030. [PMID: 28451370 PMCID: PMC5380879 DOI: 10.1039/c6sc04522g] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 01/28/2017] [Indexed: 01/04/2023] Open
Abstract
An unprecedented enantioselective synthesis of 3-substituted benzoxaboroles has been developed. An in situ generated ortho-boronic acid containing chalcone provides the chiral benzoxaboroles via an asymmetric oxa-Michael addition of hydroxyl group attached to the boronic acid triggered by the cinchona alkaloid based chiral amino-squaramide catalysts. In general, good yields with good to excellent enantioselectivities (up to 99%) were obtained. The resulting benzoxaboroles were converted to the corresponding chiral β-hydroxy ketones without affecting the enantioselectivity.
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Affiliation(s)
- Gurupada Hazra
- Department of Chemistry , Indian Institute of Science Education and Research Bhopal , Bhopal By-pass Road, Bhauri , Bhopal-462066 , India .
| | - Sanjay Maity
- Department of Chemistry , Indian Institute of Science Education and Research Bhopal , Bhopal By-pass Road, Bhauri , Bhopal-462066 , India .
| | - Sudipto Bhowmick
- Department of Chemistry , Indian Institute of Science Education and Research Bhopal , Bhopal By-pass Road, Bhauri , Bhopal-462066 , India .
| | - Prasanta Ghorai
- Department of Chemistry , Indian Institute of Science Education and Research Bhopal , Bhopal By-pass Road, Bhauri , Bhopal-462066 , India .
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24
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Bharatiy S, Hazra M, Paul M, Mohapatra S, Samantaray D, Dubey R, Sanyal S, Datta S, Hazra S. In Silico Designing of an Industrially Sustainable Carbonic Anhydrase Using Molecular Dynamics Simulation. ACS OMEGA 2016; 1:1081-1103. [PMID: 30023502 PMCID: PMC6044688 DOI: 10.1021/acsomega.6b00041] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 09/15/2016] [Indexed: 06/08/2023]
Abstract
Carbonic anhydrase (CA) is a family of metalloenzymes that has the potential to sequestrate carbon dioxide (CO2) from the environment and reduce pollution. The goal of this study is to apply protein engineering to develop a modified CA enzyme that has both higher stability and activity and hence could be used for industrial purposes. In the current study, we have developed an in silico method to understand the molecular basis behind the stability of CA. We have performed comparative molecular dynamics simulation of two homologous α-CA, one of thermophilic origin (Sulfurihydrogenibium sp.) and its mesophilic counterpart (Neisseria gonorrhoeae), for 100 ns each at 300, 350, 400, and 500 K. Comparing the trajectories of two proteins using different stability-determining factors, we have designed a highly thermostable version of mesophilic α-CA by introducing three mutations (S44R, S139E, and K168R). The designed mutant α-CA maintains conformational stability at high temperatures. This study shows the potential to develop industrially stable variants of enzymes while maintaining high activity.
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Affiliation(s)
- Sachin
Kumar Bharatiy
- Department of Biotechnology and Centre for Nanotechnology, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India
| | - Mousumi Hazra
- Department
of Botany and Microbiology, Gurukula Kangri
University, Haridwar 249404, Uttarakhand, India
| | - Manish Paul
- Department
of Microbiology, Orissa University of Agriculture
and Technology, Bhubaneswar 751003, Odisha, India
| | - Swati Mohapatra
- Department of Biotechnology and Centre for Nanotechnology, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India
| | - Deviprasad Samantaray
- Department
of Microbiology, Orissa University of Agriculture
and Technology, Bhubaneswar 751003, Odisha, India
| | - Ramesh
Chandra Dubey
- Department
of Botany and Microbiology, Gurukula Kangri
University, Haridwar 249404, Uttarakhand, India
| | - Shourjya Sanyal
- Complex
and Adaptive System Laboratory, School of Physics, University College Dublin, Dublin 4, Ireland
| | - Saurav Datta
- Department of Biotechnology and Centre for Nanotechnology, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India
| | - Saugata Hazra
- Department of Biotechnology and Centre for Nanotechnology, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India
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25
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Abstract
This review describes available methods for the preparation of α-aminoboronic acids in their racemic or in their enantiopure form. Both, highly stereoselective syntheses and asymmetric procedures leading to the stereocontrolled generation of α-aminoboronic acid derivatives are included. The preparation of acyclic, carbocyclic and azacyclic α-aminoboronic acid derivatives is covered. Within each section, the different synthetic approaches have been classified according to the key bond which is formed to complete the α-aminoboronic acid skeleton.
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Affiliation(s)
- Patricia Andrés
- Departamento de Química Orgánica, Instituto de Síntesis Química y Catálisis Homogénea (ISQCH), CSIC-Universidad de Zaragoza, 50009 Zaragoza, Spain.
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