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Wu Y, Liu F, Glenn I, Fonseca-Valencia K, Paris L, Xiong Y, Jerome SV, Brooks CL, Shoichet BK. Identifying Artifacts from Large Library Docking. J Med Chem 2024; 67:16796-16806. [PMID: 39255340 DOI: 10.1021/acs.jmedchem.4c01632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/12/2024]
Abstract
While large library docking has discovered potent ligands for multiple targets, as the libraries have grown the hit lists can become dominated by rare artifacts that cheat our scoring functions. Here, we investigate rescoring top-ranked docked molecules with orthogonal methods to identify these artifacts, exploring implicit solvent models and absolute binding free energy perturbation as cross-filters. In retrospective studies, this approach deprioritized high-ranking nonbinders for nine targets while leaving true ligands relatively unaffected. We tested the method prospectively against hits from docking against AmpC β-lactamase. We prioritized 128 high-ranking molecules for synthesis and testing, a mixture of 39 molecules flagged as likely cheaters and 89 that were plausible inhibitors. None of the predicted cheating compounds inhibited AmpC detectably, while 57% of the 89 plausible compounds did so. As our libraries continue to grow, deprioritizing docking artifacts by rescoring with orthogonal methods may find wide use.
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Affiliation(s)
- Yujin Wu
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States
| | - Fangyu Liu
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States
| | - Isabella Glenn
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States
| | - Karla Fonseca-Valencia
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States
| | - Lu Paris
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States
| | - Yuyue Xiong
- Schrödinger, Inc., 9868 Scranton Road, San Diego, California 92121, United States
| | - Steven V Jerome
- Schrödinger, Inc., 1540 Broadway, New York, New York 10036, United States
| | - Charles L Brooks
- Biophysics Program, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Brian K Shoichet
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States
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Wu Y, Liu F, Glenn I, Fonseca-Valencia K, Paris L, Xiong Y, Jerome SV, Brooks CL, Shoichet BK. Identifying Artifacts from Large Library Docking. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.17.603966. [PMID: 39071262 PMCID: PMC11275789 DOI: 10.1101/2024.07.17.603966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
While large library docking has discovered potent ligands for multiple targets, as the libraries have grown, the very top of the hit-lists can become populated with artifacts that cheat our scoring functions. Though these cheating molecules are rare, they become ever-more dominant with library growth. Here, we investigate rescoring top-ranked molecules from docking screens with orthogonal methods to identify these artifacts, exploring implicit solvent models and absolute binding free energy perturbation (AB-FEP) as cross-filters. In retrospective studies, this approach deprioritized high-ranking non-binders for nine targets while leaving true ligands relatively unaffected. We tested the method prospectively against results from large library docking AmpC β-lactamase. From the very top of the docking hit lists, we prioritized 128 molecules for synthesis and experimental testing, a mixture of 39 molecules that rescoring flagged as likely cheaters and another 89 that were plausible true actives. None of the 39 predicted cheating compounds inhibited AmpC up to 200 μ M in enzyme assays, while 57% of the 89 plausible true actives did do so, with 19 of them inhibiting the enzyme with apparentK i values better than 50 μ M . As our libraries continue to grow, a strategy of catching docking artifacts by rescoring with orthogonal methods may find wide use in the field.
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Affiliation(s)
- Yujin Wu
- Department of Pharmaceutical Chemistry, University of California, San Francisco, 94158, United States
| | - Fangyu Liu
- Department of Pharmaceutical Chemistry, University of California, San Francisco, 94158, United States
| | - Isabella Glenn
- Department of Pharmaceutical Chemistry, University of California, San Francisco, 94158, United States
| | - Karla Fonseca-Valencia
- Department of Pharmaceutical Chemistry, University of California, San Francisco, 94158, United States
| | - Lu Paris
- Department of Pharmaceutical Chemistry, University of California, San Francisco, 94158, United States
| | - Yuyue Xiong
- Schrödinger, Inc., 9868 Scranton Road, San Diego, California 92121, United States
| | - Steven V. Jerome
- Schrödinger, Inc., 1540 Broadway, New York, New York, 10036, United States
| | - Charles L. Brooks
- Biophysics Program, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Brian K. Shoichet
- Department of Pharmaceutical Chemistry, University of California, San Francisco, 94158, United States
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Chen S, Mack AR, Hujer AM, Bethel CR, Bonomo RA, Haider S. Ω-Loop mutations control the dynamics of the active site by modulating a network of hydrogen bonds in PDC-3 β-lactamase. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.04.578824. [PMID: 38370743 PMCID: PMC10871217 DOI: 10.1101/2024.02.04.578824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
The expression of antibiotic-inactivating enzymes, such as Pseudomonas-derived cephalosporinase-3 (PDC-3), is a major mechanism of intrinsic resistance in bacteria. To explore the relationships between structural dynamics and altered substrate specificity as a result of amino acid substitutions in PDC-3, innovative computational methods like machine learning driven adaptive bandit molecular dynamics simulations and markov state modeling of the wild-type PDC-3 and nine clinically identified variants were conducted. Our analysis reveals that structural changes in the Ω loop controls the dynamics of the active site. The E219K and Y221A substitutions have the most pronounced effects. The modulation of three key hydrogen bonds K67(sc)-G220(bb), Y150(bb)-A292(bb) and N287(sc)-N314(sc) were found to result in an expansion of the active site, which could have implications for the binding and inactivation of cephalosporins. Overall, the findings highlight the importance of understanding the structural dynamics of PDC-3 in the development of new treatments for antibiotic-resistant infections.
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Affiliation(s)
| | - Andrew R Mack
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH, USA
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Andrea M Hujer
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH, USA
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Christopher R Bethel
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH, USA
| | - Robert A Bonomo
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH, USA
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA
- Clinician Scientist Investigator, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH, USA
- Departments of Pharmacology, Biochemistry, and Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, Cleveland, OH, USA
- CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES) Cleveland, OH, USA
| | - Shozeb Haider
- UCL School of Pharmacy, London UK
- UCL Centre for Advanced Research Computing, London UK
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Chiacchio MA, Legnani L, Fassi EMA, Roda G, Grazioso G. Development of AMBER Parameters for Molecular Simulations of Selected Boron-Based Covalent Ligands. Molecules 2023; 28:molecules28062866. [PMID: 36985837 PMCID: PMC10057150 DOI: 10.3390/molecules28062866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 03/20/2023] [Accepted: 03/21/2023] [Indexed: 03/30/2023] Open
Abstract
Boron containing compounds (BCCs) aroused increasing interest in the scientific community due to their wide application as drugs in various fields. In order to design new compounds hopefully endowed with pharmacological activity and also investigate their conformational behavior, the support of computational studies is crucial. Nevertheless, the suitable molecular mechanics parameterization and the force fields needed to perform these simulations are not completely available for this class of molecules. In this paper, Amber force field parameters for phenyl-, benzyl-, benzylamino-, and methylamino-boronates, a group of boron-containing compounds involved in different branches of the medicinal chemistry, were created. The robustness of the obtained data was confirmed through molecular dynamics simulations on ligand/β-lactamases covalent complexes. The ligand torsional angles, populated over the trajectory frames, were confirmed by values found in the ligand geometries, located through optimizations at the DFT/B3LYP/6-31g(d) level, using water as a solvent. In summary, this study successfully provided a library of parameters, opening the possibility to perform molecular dynamics simulations of this class of boron-containing compounds.
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Affiliation(s)
- Maria Assunta Chiacchio
- Department of Drug and Health Sciences, University of Catania, Viale A. Doria 6, 95125 Catania, Italy
| | - Laura Legnani
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
| | | | - Gabriella Roda
- Department of Pharmaceutical Sciences, University of Milan, Via L. Mangiagalli 25, 20133 Milan, Italy
| | - Giovanni Grazioso
- Department of Pharmaceutical Sciences, University of Milan, Via L. Mangiagalli 25, 20133 Milan, Italy
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Biochemical Insights into Imipenem Collateral Susceptibility Driven by ampC Mutations Conferring Ceftolozane/Tazobactam Resistance in Pseudomonas aeruginosa. Antimicrob Agents Chemother 2023; 67:e0140922. [PMID: 36715512 PMCID: PMC9933714 DOI: 10.1128/aac.01409-22] [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: 01/31/2023] Open
Abstract
Several Pseudomonas aeruginosa AmpC mutants have emerged that exhibit enhanced activity against ceftazidime and ceftolozane, while also evading inhibition by avibactam. Interestingly, P. aeruginosa strains harboring these AmpC mutations fortuitously exhibit enhanced carbapenem susceptibility. This acquired susceptibility was investigated by comparing the degradation of imipenem by wild-type and cephalosporin-resistant AmpC. We show that cephalosporin-resistant AmpC enzymes lose their efficacy for hydrolyzing imipenem and suggest that this may be due to their increased flexibility and dynamics relative to the wild type.
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Abstract
Class C β-lactamases or cephalosporinases can be classified into two functional groups (1, 1e) with considerable molecular variability (≤20% sequence identity). These enzymes are mostly encoded by chromosomal and inducible genes and are widespread among bacteria, including Proteobacteria in particular. Molecular identification is based principally on three catalytic motifs (64SXSK, 150YXN, 315KTG), but more than 70 conserved amino-acid residues (≥90%) have been identified, many close to these catalytic motifs. Nevertheless, the identification of a tiny, phylogenetically distant cluster (including enzymes from the genera Legionella, Bradyrhizobium, and Parachlamydia) has raised questions about the possible existence of a C2 subclass of β-lactamases, previously identified as serine hydrolases. In a context of the clinical emergence of extended-spectrum AmpC β-lactamases (ESACs), the genetic modifications observed in vivo and in vitro (point mutations, insertions, or deletions) during the evolution of these enzymes have mostly involved the Ω- and H-10/R2-loops, which vary considerably between genera, and, in some cases, the conserved triplet 150YXN. Furthermore, the conserved deletion of several amino-acid residues in opportunistic pathogenic species of Acinetobacter, such as A. baumannii, A. calcoaceticus, A. pittii and A. nosocomialis (deletion of residues 304-306), and in Hafnia alvei and H. paralvei (deletion of residues 289-290), provides support for the notion of natural ESACs. The emergence of higher levels of resistance to β-lactams, including carbapenems, and to inhibitors such as avibactam is a reality, as the enzymes responsible are subject to complex regulation encompassing several other genes (ampR, ampD, ampG, etc.). Combinations of resistance mechanisms may therefore be at work, including overproduction or change in permeability, with the loss of porins and/or activation of efflux systems.
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Mora-Ochomogo M, Lohans CT. β-Lactam antibiotic targets and resistance mechanisms: from covalent inhibitors to substrates. RSC Med Chem 2021; 12:1623-1639. [PMID: 34778765 PMCID: PMC8528271 DOI: 10.1039/d1md00200g] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 07/25/2021] [Indexed: 12/24/2022] Open
Abstract
The β-lactams are the most widely used antibacterial agents worldwide. These antibiotics, a group that includes the penicillins and cephalosporins, are covalent inhibitors that target bacterial penicillin-binding proteins and disrupt peptidoglycan synthesis. Bacteria can achieve resistance to β-lactams in several ways, including the production of serine β-lactamase enzymes. While β-lactams also covalently interact with serine β-lactamases, these enzymes are capable of deacylating this complex, treating the antibiotic as a substrate. In this tutorial-style review, we provide an overview of the β-lactam antibiotics, focusing on their covalent interactions with their target proteins and resistance mechanisms. We begin by describing the structurally diverse range of β-lactam antibiotics and β-lactamase inhibitors that are currently used as therapeutics. Then, we introduce the penicillin-binding proteins, describing their functions and structures, and highlighting their interactions with β-lactam antibiotics. We next describe the classes of serine β-lactamases, exploring some of the mechanisms by which they achieve the ability to degrade β-lactams. Finally, we introduce the l,d-transpeptidases, a group of bacterial enzymes involved in peptidoglycan synthesis which are also targeted by β-lactam antibiotics. Although resistance mechanisms are now prevalent for all antibiotics in this class, past successes in antibiotic development have at least delayed this onset of resistance. The β-lactams continue to be an essential tool for the treatment of infectious disease, and recent advances (e.g., β-lactamase inhibitor development) will continue to support their future use.
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Affiliation(s)
| | - Christopher T Lohans
- Department of Biomedical and Molecular Sciences, Queen's University Kingston ON K7L 3N6 Canada
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Mushtaq S, Vickers A, Ellaby N, Woodford N, Livermore DM. Selection and characterization of mutational resistance to aztreonam/avibactam in β-lactamase-producing Enterobacterales. J Antimicrob Chemother 2021; 77:98-111. [PMID: 34568905 DOI: 10.1093/jac/dkab346] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Accepted: 08/23/2021] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Aztreonam/avibactam is being developed for its broad activity against carbapenemase-producing Enterobacterales, including those with metallo-β-lactamases (MBLs). Its potential to select resistance in target pathogens was explored. Findings are compared with previous data for ceftazidime/avibactam and ceftaroline/avibactam. METHODS Single-step mutants were sought from 52 Enterobacterales with AmpC, ESBL, KPC, MBL and OXA-48-like enzymes. Mutation frequencies were calculated. MICs were determined by CLSI agar dilution. Genomes were sequenced using Illumina methodology. RESULTS Irrespective of β-lactamase type and of whether avibactam was used at 1 or 4 mg/L, mutants could rarely be obtained at >4× the starting MIC, and most MIC rises were correspondingly small. Putative resistance (MIC >8 + 4 mg/L) associated with changes to β-lactamases was seen only for mutants of AmpC, where it was associated with Asn346Tyr and Tyr150Cys substitutions. Asn346Tyr led to broad resistance to avibactam combinations; Tyr150Cys significantly affected only aztreonam/avibactam. MIC rises up to 4 + 4 mg/L were seen for producers of mutant KPC-2 or -3 enzymes, and were associated with Trp105Arg, Ser106Pro and Ser109Pro substitutions, which all reduced the MICs of other β-lactams. For producers of other β-lactamase types, we largely found mutants with lesions in baeRS or envZ, putatively affecting drug accumulation. Single mutants had lesions in ampD, affecting AmpC expression or ftsI, encoding PBP3. CONCLUSIONS The risk of mutational resistance to aztreonam/avibactam appears smaller than for ceftazidime/avibactam, where Asp179Tyr arises readily in KPC enzymes, conferring frank resistance. Asn346 substitutions in AmpC enzymes may remain a risk, having been repeatedly selected with multiple avibactam combinations in vitro.
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Affiliation(s)
- Shazad Mushtaq
- Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, Public Health England National Infection Service, London, UK
| | - Anna Vickers
- Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, Public Health England National Infection Service, London, UK
| | - Nicholas Ellaby
- Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, Public Health England National Infection Service, London, UK
| | - Neil Woodford
- Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, Public Health England National Infection Service, London, UK
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Farrokhzadeh A, Modarresi-Alam AR, Akher FB, Kleinpeter E, Kelling A, Schilde U. Investigation of the unusually high rotational energy barrier about the C-N bond in 5-(2-x-phenyl)-N,N-dimethyl-2H-tetrazole-2-carboxamides: Insights from dynamic 1H-NMR and DFT calculations. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2020.129363] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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10
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Structural Insights into Inhibition of the Acinetobacter-Derived Cephalosporinase ADC-7 by Ceftazidime and Its Boronic Acid Transition State Analog. Antimicrob Agents Chemother 2020; 64:AAC.01183-20. [PMID: 32988830 DOI: 10.1128/aac.01183-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Accepted: 09/16/2020] [Indexed: 02/08/2023] Open
Abstract
Extended-spectrum class C β-lactamases have evolved to rapidly inactivate expanded-spectrum cephalosporins, a class of antibiotics designed to be resistant to hydrolysis by β-lactamase enzymes. To better understand the mechanism by which Acinetobacter-derived cephalosporinase-7 (ADC-7), a chromosomal AmpC enzyme, hydrolyzes these molecules, we determined the X-ray crystal structure of ADC-7 in an acyl-enzyme complex with the cephalosporin ceftazidime (2.40 Å) as well as in complex with a boronic acid transition state analog inhibitor that contains the R1 side chain of ceftazidime (1.67 Å). In the acyl-enzyme complex, the carbonyl oxygen is situated in the oxyanion hole where it makes key stabilizing interactions with the main chain nitrogens of Ser64 and Ser315. The boronic acid O1 hydroxyl group is similarly positioned in this area. Conserved residues Gln120 and Asn152 form hydrogen bonds with the amide group of the R1 side chain in both complexes. These complexes represent two steps in the hydrolysis of expanded-spectrum cephalosporins by ADC-7 and offer insight into the inhibition of ADC-7 by ceftazidime through displacement of the deacylating water molecule as well as blocking its trajectory to the acyl carbonyl carbon. In addition, the transition state analog inhibitor, LP06, was shown to bind with high affinity to ADC-7 (Ki , 50 nM) and was able to restore ceftazidime susceptibility, offering the potential for optimization efforts of this type of inhibitor.
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Gowda K, Swarup HA, Nagarakere SC, Rangappa S, Kanchugarkoppal RS, Kempegowda M. Structural studies of 2,5-disubstituted 1,3,4-thiadiazole derivatives from dithioesters under the mild condition: Studies on antioxidant, antimicrobial activities, and molecular docking. SYNTHETIC COMMUN 2020. [DOI: 10.1080/00397911.2020.1745843] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Kemparaje Gowda
- Department of Studies in Chemistry, University of Mysore, Mysuru, India
| | - Hassan A. Swarup
- Department of Studies in Chemistry, University of Mysore, Mysuru, India
| | | | - Shobith Rangappa
- Adichunchanagiri Institute for Molecular Medicine, Mandya, India
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Cao Z, Zhao C, Zhu J, Yan S, Tian L, Sun X, Meng X. Gold‐Catalyzed Reaction of 2
H
‐Tetrazoles with Alkynes: Efficient Route to N‐Alkenylated Tetrazoles. ChemistrySelect 2019. [DOI: 10.1002/slct.201902532] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Ziping Cao
- School of Chemistry and Chemical EngineeringQufu Normal University Qufu 273165, Shandong P. R. China
- Shandong Key Laboratory of Life-Organic AnalysisKey Laboratory of Pharmaceutical Intermediates and Analysis of Natural Medicine Qufu 273165, Shandong P. R. China
| | - Changyin Zhao
- School of Chemistry and Chemical EngineeringQufu Normal University Qufu 273165, Shandong P. R. China
| | - Jiekun Zhu
- School of Chemistry and Chemical EngineeringQufu Normal University Qufu 273165, Shandong P. R. China
| | - Shikun Yan
- School of Chemistry and Chemical EngineeringQufu Normal University Qufu 273165, Shandong P. R. China
| | - Laijin Tian
- School of Chemistry and Chemical EngineeringQufu Normal University Qufu 273165, Shandong P. R. China
- Shandong Key Laboratory of Life-Organic AnalysisKey Laboratory of Pharmaceutical Intermediates and Analysis of Natural Medicine Qufu 273165, Shandong P. R. China
| | - Xuejun Sun
- School of Chemistry and Chemical EngineeringQufu Normal University Qufu 273165, Shandong P. R. China
| | - Xin Meng
- School of Chemistry and Chemical EngineeringQufu Normal University Qufu 273165, Shandong P. R. China
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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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Awasthi S, Gupta S, Tripathi R, Nair NN. Mechanism and Kinetics of Aztreonam Hydrolysis Catalyzed by Class-C β-Lactamase: A Temperature-Accelerated Sliced Sampling Study. J Phys Chem B 2018; 122:4299-4308. [DOI: 10.1021/acs.jpcb.8b01287] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Shalini Awasthi
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Shalini Gupta
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Ravi Tripathi
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Nisanth N. Nair
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
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15
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McGivern T, Afsharpour S, Marmion C. Copper complexes as artificial DNA metallonucleases: From Sigman’s reagent to next generation anti-cancer agent? Inorganica Chim Acta 2018. [DOI: 10.1016/j.ica.2017.08.043] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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16
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Edwardraja S, Eichinger A, Theobald I, Sommer CA, Reichert AJ, Skerra A. Rational Design of an Anticalin-Type Sugar-Binding Protein Using a Genetically Encoded Boronate Side Chain. ACS Synth Biol 2017; 6:2241-2247. [PMID: 28937743 DOI: 10.1021/acssynbio.7b00199] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The molecular recognition of carbohydrates plays a fundamental role in many biological processes. However, the development of carbohydrate-binding reagents for biomedical research and use poses a challenge due to the generally poor affinity of proteins toward sugars in aqueous solution. Here, we describe the effective molecular recognition of pyranose monosaccharides (in particular, galactose and mannose) by a rationally designed protein receptor based on the human lipocalin scaffold (Anticalin). Complexation relies on reversible covalent cis-diol boronate diester formation with a genetically encoded l-boronophenylalanine (Bpa) residue which was incorporated as a non-natural amino acid at a sterically permissive position in the ligand pocket of the Anticalin, as confirmed by X-ray crystallography. Compared with the metal-ion and/or avidity-dependent oligovalent lectins that prevail in nature, our approach offers a novel and promising route to generate tight sugar-binding reagents both as research reagents and for biomedical applications.
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Affiliation(s)
- Selvakumar Edwardraja
- Munich Center for Integrated
Protein Science (CIPS-M) and Lehrstuhl für Biologische Chemie, Technische Universität München, Emil-Erlenmeyer-Forum 5, 85354 Freising (Weihenstephan), Germany
| | - Andreas Eichinger
- Munich Center for Integrated
Protein Science (CIPS-M) and Lehrstuhl für Biologische Chemie, Technische Universität München, Emil-Erlenmeyer-Forum 5, 85354 Freising (Weihenstephan), Germany
| | - Ina Theobald
- Munich Center for Integrated
Protein Science (CIPS-M) and Lehrstuhl für Biologische Chemie, Technische Universität München, Emil-Erlenmeyer-Forum 5, 85354 Freising (Weihenstephan), Germany
| | - Carina Andrea Sommer
- Munich Center for Integrated
Protein Science (CIPS-M) and Lehrstuhl für Biologische Chemie, Technische Universität München, Emil-Erlenmeyer-Forum 5, 85354 Freising (Weihenstephan), Germany
| | - Andreas J. Reichert
- Munich Center for Integrated
Protein Science (CIPS-M) and Lehrstuhl für Biologische Chemie, Technische Universität München, Emil-Erlenmeyer-Forum 5, 85354 Freising (Weihenstephan), Germany
| | - Arne Skerra
- Munich Center for Integrated
Protein Science (CIPS-M) and Lehrstuhl für Biologische Chemie, Technische Universität München, Emil-Erlenmeyer-Forum 5, 85354 Freising (Weihenstephan), Germany
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Barreto ADFS, Dos Santos VA, Andrade CKZ. Consecutive hydrazino-Ugi-azide reactions: synthesis of acylhydrazines bearing 1,5-disubstituted tetrazoles. Beilstein J Org Chem 2017; 13:2596-2602. [PMID: 29259669 PMCID: PMC5727845 DOI: 10.3762/bjoc.13.256] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Accepted: 11/14/2017] [Indexed: 12/17/2022] Open
Abstract
Isocyanide-based multicomponent reactions (IMCRs) allow the construction of relatively complex molecules through a one-pot synthesis. The combination of IMCRs in a consecutive or sequential fashion further extends the complexity of the molecules obtained. Herein, we report the efficient application of this approach to the synthesis of acylhydrazines bearing 1,5-disubstituted tetrazoles. Our strategy was accomplished in only three steps: first, a one-pot hydrazino-Ugi-azide four-component reaction; second a hydrazinolysis and finally an additional hydrazino-Ugi-azide reaction. This sequence provides the title compounds in moderate to excellent yields. The products synthesized herein contain functional groups within their structures that can be easily modified to obtain new acylhydrazino 1,5-disubstituted tetrazoles.
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Affiliation(s)
- Angélica de Fátima S Barreto
- Laboratório de Química Metodológica e Orgânica Sintética, Instituto de Química, Universidade de Brasília, 70910-970, Brasília-DF, Brazil
| | - Veronica Alves Dos Santos
- Laboratório de Química Metodológica e Orgânica Sintética, Instituto de Química, Universidade de Brasília, 70910-970, Brasília-DF, Brazil
| | - Carlos Kleber Z Andrade
- Laboratório de Química Metodológica e Orgânica Sintética, Instituto de Química, Universidade de Brasília, 70910-970, Brasília-DF, Brazil
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18
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Ichinari D, Nagaki A, Yoshida JI. Generation of hazardous methyl azide and its application to synthesis of a key-intermediate of picarbutrazox, a new potent pesticide in flow. Bioorg Med Chem 2017; 25:6224-6228. [DOI: 10.1016/j.bmc.2017.07.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 07/01/2017] [Accepted: 07/04/2017] [Indexed: 11/26/2022]
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19
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Ezeokonkwo MA, Ogbonna ON, Okafor SN, Godwin-Nwakwasi EU, Ibeanu FN, Okoro UC. Angular Phenozaxine Ethers as Potent Multi-microbial Targets Inhibitors: Design, Synthesis, and Molecular Docking Studies. Front Chem 2017; 5:107. [PMID: 29238706 PMCID: PMC5712349 DOI: 10.3389/fchem.2017.00107] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 11/13/2017] [Indexed: 01/25/2023] Open
Abstract
The reaction of diaza-5H-benzo[a]phenoxazin-5-one and 5H-benzo[a]phenoxazin-5-one with various phenols catalyzed by Pd/t-BuXPhos/K3PO4 system gave previously unknown ether derivatives (7a-f and 8a-f) in good yields. UV-visible, FTIR, and 1H NMR data were used to confirm structures of the synthesized compounds. The parent compounds and the derivatives were screened in-silico for their drug-likeness and binding affinities to the microbial targets through molecular docking. Molinspiration software and AutoDock were used for the drug-likeness and docking studies, respectively. All the synthesized compounds showed strong drug-likeness. They also showed excellent binding affinities with glucosamine-6-phosphate synthase (2VF5), AmpC beta-lactamase (1KE4), and Lanosterol-14α-demethylase (3JUV), with compound 7e having the highest binding energies -9.5, -9.3, and -9.3 kcal/mol, respectively. These were found to be higher than the binding energies of the standard drugs. The binding energies of ciprofloxacin with 2VF5 and 1KE4 were -7.8 and -7.5 kcal/mol, respectively, while that of ketoconazole with 3JUV was -8.6 kcal/mol. The study showed that the synthesized compounds have multi-target inhibitory effects and can be very useful in multi-drug resistance cases. A 2D quantitative structural activity relationship (QSAR) model against target Glucosamine-6-phosphate synthase (2VF5) was developed using partial least squares regression (PLS) with good internal prediction (R2 = 0.7400) and external prediction (R2_ predicted = 0.5475) via Molecular Operating Environment (2014).
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Affiliation(s)
- Mercy A. Ezeokonkwo
- Department of Pure and Industrial Chemistry, University of Nigeria, Nsukka, Nigeria
| | | | - Sunday N. Okafor
- Department of Pharmaceutical and Medicinal Chemistry, University of Nigeria, Nsukka, Nigeria
| | | | | | - Uchechukwu C. Okoro
- Department of Pure and Industrial Chemistry, University of Nigeria, Nsukka, Nigeria
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20
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Zuppolini S, Quero G, Consales M, Diodato L, Vaiano P, Venturelli A, Santucci M, Spyrakis F, Costi MP, Giordano M, Cutolo A, Cusano A, Borriello A. Label-free fiber optic optrode for the detection of class C β-lactamases expressed by drug resistant bacteria. BIOMEDICAL OPTICS EXPRESS 2017; 8:5191-5205. [PMID: 29188113 PMCID: PMC5695963 DOI: 10.1364/boe.8.005191] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 08/24/2017] [Accepted: 08/24/2017] [Indexed: 06/01/2023]
Abstract
This paper reports the experimental assessment of an automated optical assay based on label free optical fiber optrodes for the fast detection of class C β-lactamases (AmpC BLs), actually considered as one of the most important sources of resistance to β-lactams antibiotics expressed by resistant bacteria. Reflection-type long period fiber gratings (RT-LPG) have been used as highly sensitive label free optrodes, while a higher affine boronic acid-based ligand was here selected to enhance the overall assay performances compared to those obtained in our first demonstration. In order to prove the feasibility analysis towards a fully automated optical assay, an engineered system was developed to simultaneously manipulate and interrogate multiple fiber optic optrodes in the different phases of the assay. The automated system tested in AmpC solutions at increasing concentrations demonstrated a limit of detection (LOD) of 6 nM, three times better when compared with the results obtained in our previous work. Moreover, the real effectiveness of the proposed optical assay has been also confirmed in complex matrices as the case of lysates of Escherichia coli overexpressing AmpC.
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Affiliation(s)
- Simona Zuppolini
- Institute for Polymers, Composites and Biomaterials - National Council of Research, Portici, Italy
- These authors contributed equally to this work
| | - Giuseppe Quero
- Optoelectronics Group, Dept. of Engineering, University of Sannio, Benevento, Italy
- These authors contributed equally to this work
| | - Marco Consales
- Optoelectronics Group, Dept. of Engineering, University of Sannio, Benevento, Italy
| | - Laura Diodato
- Institute for Polymers, Composites and Biomaterials - National Council of Research, Portici, Italy
| | - Patrizio Vaiano
- Optoelectronics Group, Dept. of Engineering, University of Sannio, Benevento, Italy
| | | | - Matteo Santucci
- Dept. of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Francesca Spyrakis
- Dept. of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
- Current Address: Dept. of Drug Science and Technology, University of Torino, Torino, Italy
| | - Maria P Costi
- Dept. of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | | | - Antonello Cutolo
- Optoelectronics Group, Dept. of Engineering, University of Sannio, Benevento, Italy
| | - Andrea Cusano
- Optoelectronics Group, Dept. of Engineering, University of Sannio, Benevento, Italy
| | - Anna Borriello
- Institute for Polymers, Composites and Biomaterials - National Council of Research, Portici, Italy
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Dandia A, Khan S, Sharma R, Parihar S, Parewa V. “On Water” Sustainable Synthesis of 1,5-Disubstituted Tetrazoles via Ugi-Azide Reaction through Perturbation of Kosmotropes Using Nacl. ChemistrySelect 2017. [DOI: 10.1002/slct.201702234] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Anshu Dandia
- Centre of Advanced Studies, Department of Chemistry; University of Rajasthan; Jaipur India
| | - Shahnawaz Khan
- Centre of Advanced Studies, Department of Chemistry; University of Rajasthan; Jaipur India
| | - Ruchi Sharma
- Centre of Advanced Studies, Department of Chemistry; University of Rajasthan; Jaipur India
| | - Sonam Parihar
- Centre of Advanced Studies, Department of Chemistry; University of Rajasthan; Jaipur India
| | - Vijay Parewa
- Centre of Advanced Studies, Department of Chemistry; University of Rajasthan; Jaipur India
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22
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Tokunaga H, Maeda J, Arakawa T, Tokunaga M. Reversible Activation of Halophilic β-lactamase from Methanol-Induced Inactive Form: Contrast to Irreversible Inactivation of Non-Halophilic Counterpart. Protein J 2017; 36:228-237. [DOI: 10.1007/s10930-017-9715-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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23
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Movahedifar F, Modarresi-Alam AR, Kleinpeter E, Schilde U. Dynamic 1H-NMR study of unusually high barrier to rotation about the partial C N double bond in N,N-dimethyl carbamoyl 5-aryloxytetrazoles. J Mol Struct 2017. [DOI: 10.1016/j.molstruc.2016.12.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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24
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Surendra Babu M, Rao BU, Krishna V, Mustafa S, Rao GN. Synthesis, characterization and DNA cleavage studies of isomeric pyridyl-tetrazole ligands and their Ni(II) and Zn(II) complexes. JOURNAL OF SAUDI CHEMICAL SOCIETY 2017. [DOI: 10.1016/j.jscs.2015.07.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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25
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Werner JP, Mitchell JM, Taracila MA, Bonomo RA, Powers RA. Exploring the potential of boronic acids as inhibitors of OXA-24/40 β-lactamase. Protein Sci 2017; 26:515-526. [PMID: 27997706 DOI: 10.1002/pro.3100] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 12/08/2016] [Accepted: 12/08/2016] [Indexed: 01/01/2023]
Abstract
β-lactam antibiotics are crucial to the management of bacterial infections in the medical community. Due to overuse and misuse, clinically significant bacteria are now resistant to many commercially available antibiotics. The most widespread resistance mechanism to β-lactams is the expression of β-lactamase enzymes. To overcome β-lactamase mediated resistance, inhibitors were designed to inactivate these enzymes. However, current inhibitors (clavulanic acid, tazobactam, and sulbactam) for β-lactamases also contain the characteristic β-lactam ring, making them susceptible to resistance mechanisms employed by bacteria. This presents a critical need for novel, non-β-lactam inhibitors that can circumvent these resistance mechanisms. The carbapenem-hydrolyzing class D β-lactamases (CHDLs) are of particular concern, given that they efficiently hydrolyze potent carbapenem antibiotics. Unfortunately, these enzymes are not inhibited by clinically available β-lactamase inhibitors, nor are they effectively inhibited by the newest, non-β-lactam inhibitor, avibactam. Boronic acids are known transition state analog inhibitors of class A and C β-lactamases, and are not extensively characterized as inhibitors of class D β-lactamases. Importantly, boronic acids provide a novel way to potentially inhibit class D β-lactamases. Sixteen boronic acids were selected and tested for inhibition of the CHDL OXA-24/40. Several compounds were identified as effective inhibitors of OXA-24/40, with Ki values as low as 5 μM. The X-ray crystal structures of OXA-24/40 in complex with BA3, BA4, BA8, and BA16 were determined and revealed the importance of interactions with hydrophobic residues Tyr112 and Trp115. These boronic acids serve as progenitors in optimization efforts of a novel series of inhibitors for class D β-lactamases.
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Affiliation(s)
- Josephine P Werner
- Department of Chemistry, Grand Valley State University, Allendale, Michigan, 49401
| | - Joshua M Mitchell
- Department of Chemistry, Grand Valley State University, Allendale, Michigan, 49401
| | - Magdalena A Taracila
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, 44106.,Departments of Medicine, Pharmacology, Biochemistry and Molecular Biology, and Microbiology, Case Western Reserve University, Cleveland, Ohio, 44106
| | - Robert A Bonomo
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, 44106.,Departments of Medicine, Pharmacology, Biochemistry and Molecular Biology, and Microbiology, Case Western Reserve University, Cleveland, Ohio, 44106
| | - Rachel A Powers
- Department of Chemistry, Grand Valley State University, Allendale, Michigan, 49401
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26
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Khatab TK, Mubarak AY, Soliman HA. Design and Synthesis Pairing Between Xanthene and Tetrazole in Pentacyclic System Using Tetrachlorosilane with Aurora Kinase Inhibitor Validation. J Heterocycl Chem 2017. [DOI: 10.1002/jhet.2846] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Tamer K. Khatab
- Organometallic and Organometalloid Chemistry Department; National Research Centre; 33 El-Behouth Street, Dokki 12622 Cairo Egypt
| | - Ahmed Y. Mubarak
- Chemistry Department, Faculty of Education and Languages; Amran University; Amran Yemen
| | - Hanan A. Soliman
- Photochemistry Department; National Research Centre; 33 El-Behouth Street, Dokki 12622 Cairo Egypt
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27
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Structure-based approach for identification of novel phenylboronic acids as serine-β-lactamase inhibitors. J Comput Aided Mol Des 2016; 30:851-861. [DOI: 10.1007/s10822-016-9962-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 09/02/2016] [Indexed: 11/25/2022]
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28
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Gold catalyzed double condensation reaction: Synthesis, antimicrobial and cytotoxicity of spirooxindole derivatives. Bioorg Med Chem Lett 2016; 26:4310-7. [DOI: 10.1016/j.bmcl.2016.07.036] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 07/07/2016] [Accepted: 07/18/2016] [Indexed: 12/13/2022]
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29
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Mustafa S, Rao BU, Surendrababu MS, Raju KK, Rao GN. Synthesis, Characterization, and Biological Activities of Pendant Arm-Pyridyltetrazole Copper(II) Complexes: DNA Binding/Cleavage Activity and Cytotoxic Studies. Chem Biodivers 2016; 12:1516-34. [PMID: 26460557 DOI: 10.1002/cbdv.201400369] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Indexed: 11/10/2022]
Abstract
2-(1H-Tetrazol-5-yl)pyridine (L) has been reacted separately with Me2NCH2CH2Cl⋅HCl and ClCH2CH2OH to yield two regioisomers in each case, N,N-dimethyl-2-[5-(pyridin-2-yl)-1H-tetrazol-1-yl]ethanamine (L1)/N,N-dimethyl-2-[5-(pyridin-2-yl)-2H-tetrazol-2-yl]ethanamine (L2) and 2-[5-(pyridin-2-yl)-1H-tetrazol-1-yl]ethanol (L3)/2-[5-(pyridin-2-yl)-2H-tetrazol-2-yl]ethanol (L4), respectively. These ligands, L1-L4, have been coordinated with CuCl2 ⋅H2O in 1 : 1 composition to furnish the corresponding complexes 1-4. EPR Spectra of Cu complexes 1 and 3 were characteristic of square planar geometry, with nuclear hyperfine spin 3/2. Single X-ray crystallographic studies of 3 revealed that the Cu center has a square planar structure. DNA binding studies were carried out by UV/VIS absorption; viscosity and thermal denaturation studies revealed that each of these complexes are avid binders of calf thymus DNA. Investigation of nucleolytic cleavage activities of the complexes was carried out on double-stranded pBR322 circular plasmid DNA by using a gel electrophoresis experiment under various conditions, where cleavage of DNA takes place by oxidative free-radical mechanism (OH(⋅)). In vitro anticancer activities of the complexes against MCF-7 (human breast adenocarcinoma) cells revealed that the complexes inhibit the growth of cancer cells. The IC50 values of the complexes showed that Cu complexes exhibit comparable cytotoxic activities compared to the standard drug cisplatin.
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Affiliation(s)
- Shaik Mustafa
- Department of Chemistry, GITAM University Hyderabad campus, Hyderabad 502329, India
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30
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Lacroix C, Fish I, Torosyan H, Parathaman P, Irwin JJ, Shoichet BK, Angers S. Identification of Novel Smoothened Ligands Using Structure-Based Docking. PLoS One 2016; 11:e0160365. [PMID: 27490099 PMCID: PMC4973902 DOI: 10.1371/journal.pone.0160365] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 07/18/2016] [Indexed: 12/21/2022] Open
Abstract
The seven transmembrane protein Smoothened is required for Hedgehog signaling during embryonic development and adult tissue homeostasis. Inappropriate activation of the Hedgehog signalling pathway leads to cancers such as basal cell carcinoma and medulloblastoma, and Smoothened inhibitors are now available clinically to treat these diseases. However, resistance to these inhibitors rapidly develops thereby limiting their efficacy. The determination of Smoothened crystal structures enables structure-based discovery of new ligands with new chemotypes that will be critical to combat resistance. In this study, we docked 3.2 million available, lead-like molecules against Smoothened, looking for those with high physical complementarity to its structure; this represents the first such campaign against the class Frizzled G-protein coupled receptor family. Twenty-one high-ranking compounds were selected for experimental testing, and four, representing three different chemotypes, were identified to antagonize Smoothened with IC50 values better than 50 μM. A screen for analogs revealed another six molecules, with IC50 values in the low micromolar range. Importantly, one of the most active of the new antagonists continued to be efficacious at the D473H mutant of Smoothened, which confers clinical resistance to the antagonist vismodegib in cancer treatment.
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Affiliation(s)
- Celine Lacroix
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada
| | - Inbar Fish
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, United States of America
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Ramat Aviv, Israel
| | - Hayarpi Torosyan
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, United States of America
| | - Pranavan Parathaman
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada
| | - John J. Irwin
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, United States of America
| | - Brian K. Shoichet
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, United States of America
- * E-mail: (BS); (SA)
| | - Stephane Angers
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada
- Department of Biochemistry, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
- * E-mail: (BS); (SA)
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31
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Parthasarathy K, Praveen C, Saranraj K, Balachandran C, Kumar PS. Synthesis, antimicrobial and cytotoxic evaluation of spirooxindole[pyrano-bis-2H-l-benzopyrans]. Med Chem Res 2016. [DOI: 10.1007/s00044-016-1645-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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32
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Avci FG, Altinisik FE, Vardar Ulu D, Ozkirimli Olmez E, Sariyar Akbulut B. An evolutionarily conserved allosteric site modulates beta-lactamase activity. J Enzyme Inhib Med Chem 2016; 31:33-40. [PMID: 27353461 DOI: 10.1080/14756366.2016.1201813] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Declining efficiency of antibiotic-inhibitor combinatorial therapies in treating beta-lactamase mediated resistance necessitates novel inhibitor development. Allosteric inhibition offers an alternative to conventional drugs that target the conserved active site. Here, we show that the evolutionarily conserved PWP triad located at the N-terminus of the H10 helix directly interacts with the allosteric site in TEM-1 beta-lactamase and regulates its activity. While point mutations in the PWP triad preserve the overall secondary structures around the allosteric site, they result in a more open and dynamic global structure with decreased chemical stability and increased aggregation propensity. These mutant enzymes with a less compact hydrophobic core around the allosteric site displayed significant activity loss. Detailed sequence and structure conservation analyses revealed that the PWP triad is an evolutionarily conserved motif unique to class A beta-lactamases aligning its allosteric site and hence is an effective potential target for enzyme regulation and selective drug design.
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Affiliation(s)
- Fatma Gizem Avci
- a Department of Bioengineering , Marmara University , İstanbul , Turkey
| | | | - Didem Vardar Ulu
- b Department of Chemistry , Boston University , Boston , MA , USA , and
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Tripathi R, Nair NN. Deacylation Mechanism and Kinetics of Acyl-Enzyme Complex of Class C β-Lactamase and Cephalothin. J Phys Chem B 2016; 120:2681-90. [PMID: 26918257 DOI: 10.1021/acs.jpcb.5b11623] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Understanding the molecular details of antibiotic resistance by the bacterial enzymes β-lactamases is vital for the development of novel antibiotics and inhibitors. In this spirit, the detailed mechanism of deacylation of the acyl-enzyme complex formed by cephalothin and class C β-lactamase is investigated here using hybrid quantum-mechanical/molecular-mechanical molecular dynamics methods. The roles of various active-site residues and substrate in the deacylation reaction are elucidated. We identify the base that activates the hydrolyzing water molecule and the residue that protonates the catalytic serine (Ser64). Conformational changes in the active sites and proton transfers that potentiate the efficiency of the deacylation reaction are presented. We have also characterized the oxyanion holes and other H-bonding interactions that stabilize the reaction intermediates. Together with the kinetic and mechanistic details of the acylation reaction, we analyze the complete mechanism and the overall kinetics of the drug hydrolysis. Finally, the apparent rate-determining step in the drug hydrolysis is scrutinized.
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Affiliation(s)
- Ravi Tripathi
- Department of Chemistry, Indian Institute of Technology Kanpur , Kanpur 208016, India
| | - Nisanth N Nair
- Department of Chemistry, Indian Institute of Technology Kanpur , Kanpur 208016, India
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34
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Li Y, Zhao Z, Liu Z, Su M, Wang R. AutoT&T v.2: An Efficient and Versatile Tool for Lead Structure Generation and Optimization. J Chem Inf Model 2016; 56:435-53. [DOI: 10.1021/acs.jcim.5b00691] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Yan Li
- State
Key Laboratory of Bioorganic and Natural Products Chemistry, Collaborative
Innovation Center of Chemistry for Life Sciences, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, People’s Republic of China
| | - Zhixiong Zhao
- State
Key Laboratory of Bioorganic and Natural Products Chemistry, Collaborative
Innovation Center of Chemistry for Life Sciences, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, People’s Republic of China
| | - Zhihai Liu
- State
Key Laboratory of Bioorganic and Natural Products Chemistry, Collaborative
Innovation Center of Chemistry for Life Sciences, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, People’s Republic of China
| | - Minyi Su
- State
Key Laboratory of Bioorganic and Natural Products Chemistry, Collaborative
Innovation Center of Chemistry for Life Sciences, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, People’s Republic of China
| | - Renxiao Wang
- State
Key Laboratory of Bioorganic and Natural Products Chemistry, Collaborative
Innovation Center of Chemistry for Life Sciences, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, People’s Republic of China
- State
Key Laboratory of Quality Research in Chinese Medicine, Macau Institute
for Applied Research in Medicine and Health, Macau University of Science and Technology, Macau, People’s Republic of China
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35
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H2O-mediated isatin spiro-epoxide ring opening with NaCN: Synthesis of novel 3-tetrazolylmethyl-3-hydroxy-oxindole hybrids and their anticancer evaluation. Eur J Med Chem 2015; 104:11-24. [DOI: 10.1016/j.ejmech.2015.09.025] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Revised: 09/14/2015] [Accepted: 09/15/2015] [Indexed: 01/11/2023]
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36
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Efficient and stereoselective synthesis of α-hydrazino tetrazoles through a pseudo five-component domino reaction. Tetrahedron 2015. [DOI: 10.1016/j.tet.2015.07.037] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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37
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McKinney DC, Zhou F, Eyermann CJ, Ferguson AD, Prince DB, Breen J, Giacobbe RA, Lahiri S, Verheijen JC. 4,5-Disubstituted 6-Aryloxy-1,3-dihydrobenzo[c][1,2]oxaboroles Are Broad-Spectrum Serine β-Lactamase Inhibitors. ACS Infect Dis 2015; 1:310-6. [PMID: 27622821 DOI: 10.1021/acsinfecdis.5b00031] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Bacterially expressed β-lactamases are rapidly eroding the clinical utility of the important β-lactam class of antibacterials, significantly impairing our ability to fight serious bacterial infections. This paper describes a study of oxaborole-derived β-lactamase inhibitors in which crystal structures and computational modeling aided in the rational design of analogues with improved spectrum of activity against class A, C, and D enzymes. Crystal structures of two of these inhibitors covalently bound to two different serine β-lactamases, class C Pseudomonas aeruginosa AmpC and class D OXA-10, are described herein. Improved physicochemical properties as well as increased activity against an array of β-lactamases resulted in substantial restoration of susceptibility to ceftazidime in Escherichia coli and Klebsiella pneumoniae.
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Affiliation(s)
- David C. McKinney
- Infection Innovative Medicines, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham Massachusetts 02451, United States
| | - Fei Zhou
- Infection Innovative Medicines, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham Massachusetts 02451, United States
| | - Charles J. Eyermann
- Infection Innovative Medicines, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham Massachusetts 02451, United States
| | | | | | | | - Robert A. Giacobbe
- Infection Innovative Medicines, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham Massachusetts 02451, United States
| | - Sushmita Lahiri
- Infection Innovative Medicines, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham Massachusetts 02451, United States
| | - Jeroen C. Verheijen
- Infection Innovative Medicines, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham Massachusetts 02451, United States
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38
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Conformational Change Observed in the Active Site of Class C β-Lactamase MOX-1 upon Binding to Aztreonam. Antimicrob Agents Chemother 2015; 59:5069-72. [PMID: 26055361 DOI: 10.1128/aac.04428-14] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 05/30/2015] [Indexed: 11/20/2022] Open
Abstract
We solved the crystal structure of the class C β-lactamase MOX-1 complexed with the inhibitor aztreonam at 1.9Å resolution. The main-chain oxygen of Ser315 interacts with the amide nitrogen of aztreonam. Surprisingly, compared to that in the structure of free MOX-1, this main-chain carboxyl changes its position significantly upon binding to aztreonam. This result indicates that the interaction between MOX-1 and β-lactams can be accompanied by conformational changes in the B3 β-strand main chain.
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Arai S, Yonezawa Y, Okazaki N, Matsumoto F, Shibazaki C, Shimizu R, Yamada M, Adachi M, Tamada T, Kawamoto M, Tokunaga H, Ishibashi M, Blaber M, Tokunaga M, Kuroki R. Structure of a highly acidic β-lactamase from the moderate halophile Chromohalobacter sp. 560 and the discovery of a Cs(+)-selective binding site. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2015; 71:541-54. [PMID: 25760604 PMCID: PMC4356365 DOI: 10.1107/s1399004714027734] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Accepted: 12/19/2014] [Indexed: 11/17/2022]
Abstract
Environmentally friendly absorbents are needed for Sr(2+) and Cs(+), as the removal of the radioactive Sr(2+) and Cs(+) that has leaked from the Fukushima Nuclear Power Plant is one of the most important problems in Japan. Halophilic proteins are known to have many acidic residues on their surface that can provide specific binding sites for metal ions such as Cs(+) or Sr(2+). The crystal structure of a halophilic β-lactamase from Chromohalobacter sp. 560 (HaBLA) was determined to resolutions of between 1.8 and 2.9 Å in space group P31 using X-ray crystallography. Moreover, the locations of bound Sr(2+) and Cs(+) ions were identified by anomalous X-ray diffraction. The location of one Cs(+)-specific binding site was identified in HaBLA even in the presence of a ninefold molar excess of Na(+) (90 mM Na(+)/10 mM Cs(+)). From an activity assay using isothermal titration calorimetry, the bound Sr(2+) and Cs(+) ions do not significantly affect the enzymatic function of HaBLA. The observation of a selective and high-affinity Cs(+)-binding site provides important information that is useful for the design of artificial Cs(+)-binding sites that may be useful in the bioremediation of radioactive isotopes.
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Affiliation(s)
- Shigeki Arai
- Quantum Beam Science Directorate, Japan Atomic Energy Agency, 2-4 Shirakata-shirane, Tokai, Ibaraki 319-1195, Japan
| | - Yasushi Yonezawa
- Quantum Beam Science Directorate, Japan Atomic Energy Agency, 2-4 Shirakata-shirane, Tokai, Ibaraki 319-1195, Japan
| | - Nobuo Okazaki
- Quantum Beam Science Directorate, Japan Atomic Energy Agency, 2-4 Shirakata-shirane, Tokai, Ibaraki 319-1195, Japan
| | - Fumiko Matsumoto
- Quantum Beam Science Directorate, Japan Atomic Energy Agency, 2-4 Shirakata-shirane, Tokai, Ibaraki 319-1195, Japan
| | - Chie Shibazaki
- Quantum Beam Science Directorate, Japan Atomic Energy Agency, 2-4 Shirakata-shirane, Tokai, Ibaraki 319-1195, Japan
| | - Rumi Shimizu
- Quantum Beam Science Directorate, Japan Atomic Energy Agency, 2-4 Shirakata-shirane, Tokai, Ibaraki 319-1195, Japan
| | - Mitsugu Yamada
- Quantum Beam Science Directorate, Japan Atomic Energy Agency, 2-4 Shirakata-shirane, Tokai, Ibaraki 319-1195, Japan
| | - Motoyasu Adachi
- Quantum Beam Science Directorate, Japan Atomic Energy Agency, 2-4 Shirakata-shirane, Tokai, Ibaraki 319-1195, Japan
| | - Taro Tamada
- Quantum Beam Science Directorate, Japan Atomic Energy Agency, 2-4 Shirakata-shirane, Tokai, Ibaraki 319-1195, Japan
| | - Masahide Kawamoto
- Saga Prefectural Regional Industry Support Center, Kyushu Synchrotron Light Research Center, 8-7 Yayoigaoka, Tosu, Saga 841-0005, Japan
| | - Hiroko Tokunaga
- Applied and Molecular Microbiology, Faculty of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
| | - Matsujiro Ishibashi
- Applied and Molecular Microbiology, Faculty of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
| | - Michael Blaber
- Quantum Beam Science Directorate, Japan Atomic Energy Agency, 2-4 Shirakata-shirane, Tokai, Ibaraki 319-1195, Japan
- College of Medicine, Florida State University, 1115 West Call Street, Tallahassee, FL 32306-4300, USA
| | - Masao Tokunaga
- Applied and Molecular Microbiology, Faculty of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
| | - Ryota Kuroki
- Quantum Beam Science Directorate, Japan Atomic Energy Agency, 2-4 Shirakata-shirane, Tokai, Ibaraki 319-1195, Japan
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Sgrignani J, Novati B, Colombo G, Grazioso G. Covalent docking of selected boron-based serine beta-lactamase inhibitors. J Comput Aided Mol Des 2015; 29:441-50. [DOI: 10.1007/s10822-015-9834-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 02/02/2015] [Indexed: 10/24/2022]
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Powers RA, Swanson HC, Taracila MA, Florek NW, Romagnoli C, Caselli E, Prati F, Bonomo RA, Wallar BJ. Biochemical and structural analysis of inhibitors targeting the ADC-7 cephalosporinase of Acinetobacter baumannii. Biochemistry 2014; 53:7670-9. [PMID: 25380506 PMCID: PMC4263437 DOI: 10.1021/bi500887n] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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β-Lactam
resistance in Acinetobacter baumannii presents one
of the greatest challenges to contemporary antimicrobial chemotherapy.
Much of this resistance to cephalosporins derives from the expression
of the class C β-lactamase enzymes, known as Acinetobacter-derived cephalosporinases (ADCs). Currently, β-lactamase inhibitors
are structurally similar to β-lactam substrates and are not
effective inactivators of this class C cephalosporinase. Herein, two boronic acid transition state inhibitors
(BATSIs S02030 and SM23) that are chemically distinct from β-lactams
were designed and tested for inhibition of ADC enzymes. BATSIs SM23
and S02030 bind with high affinity to ADC-7, a chromosomal cephalosporinase
from Acinetobacter baumannii (Ki = 21.1 ± 1.9 nM and 44.5 ± 2.2 nM, respectively).
The X-ray crystal structures of ADC-7 were determined in both the
apo form (1.73 Å resolution) and in complex with S02030 (2.0
Å resolution). In the complex, S02030 makes several canonical
interactions: the O1 oxygen of S02030 is bound in the oxyanion hole,
and the R1 amide group makes key interactions with conserved residues
Asn152 and Gln120. In addition, the carboxylate group of the inhibitor
is meant to mimic the C3/C4 carboxylate found
in β-lactams. The C3/C4 carboxylate recognition
site in class C enzymes is comprised of Asn346 and Arg349 (AmpC numbering),
and these residues are conserved in ADC-7. Interestingly, in the ADC-7/S02030
complex, the inhibitor carboxylate group is observed to interact with
Arg340, a residue that distinguishes ADC-7 from the related class
C enzyme AmpC. A thermodynamic analysis suggests that ΔH driven compounds may be optimized to generate
new lead agents. The ADC-7/BATSI complex provides insight into recognition
of non-β-lactam inhibitors by ADC enzymes and offers a starting
point for the structure-based optimization of this class of novel
β-lactamase inhibitors against a key resistance target.
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Affiliation(s)
- Rachel A Powers
- Department of Chemistry, Grand Valley State University , 1 Campus Drive, Allendale, Michigan 49401, United States
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42
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Sarvary A, Maleki A. A review of syntheses of 1,5-disubstituted tetrazole derivatives. Mol Divers 2014; 19:189-212. [PMID: 25273563 DOI: 10.1007/s11030-014-9553-3] [Citation(s) in RCA: 117] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Accepted: 09/12/2014] [Indexed: 11/26/2022]
Abstract
This report provides a brief overview of the various representative literature procedures for the synthesis of 1,5-disubstituted tetrazoles (1,5-DSTs) and fused 1,5-disubstituted tetrazoles with more than 120 references. Most of the published methods for the synthesis of 1,5-DSTs include the use of nitriles, amides, thioamides, imidoyl chlorides, heterocumulenes, isocyanates, isothiocyanates, carbodiimides, ketenimines, ketones, amines, and alkenes as the starting materials. The transformation of 1- and 5-substituted tetrazoles into 1,5-DSTs is also covered in this report.
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Affiliation(s)
- Afshin Sarvary
- Department of Science, Babol University of Technology, Babol, Iran
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43
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Hendershot JM, Mishra UJ, Smart RP, Schroeder W, Powers RA. Structure-based efforts to optimize a non-β-lactam inhibitor of AmpC β-lactamase. Bioorg Med Chem 2014; 22:3351-9. [PMID: 24835785 DOI: 10.1016/j.bmc.2014.04.051] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Revised: 04/16/2014] [Accepted: 04/25/2014] [Indexed: 11/26/2022]
Abstract
β-Lactams are the most widely prescribed class of antibiotics, yet their efficacy is threatened by expression of β-lactamase enzymes, which hydrolyze the defining lactam ring of these antibiotics. To overcome resistance due to β-lactamases, inhibitors that do not resemble β-lactams are needed. A novel, non-β-lactam inhibitor for the class C β-lactamase AmpC (3-[(4-chloroanilino)sulfonyl]thiophene-2-carboxylic acid; Ki 26μM) was previously identified. Based on this lead, a series of compounds with the potential to interact with residues at the edge of the active site were synthesized and tested for inhibition of AmpC. The length of the carbon chain spacer was extended by 1, 2, 3, and 4 carbons between the integral thiophene ring and the benzene ring (compounds 4, 5, 6, and 7). Compounds 4 and 6 showed minimal improvement over the lead compound (Ki 18 and 19μM, respectively), and compound 5 inhibited to the same extent as the lead. The X-ray crystal structures of AmpC in complexes with compounds 4, 5, and 6 were determined. The complexes provide insight into the structural reasons for the observed inhibition, and inform future optimization efforts in this series.
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Affiliation(s)
- Jenna M Hendershot
- Cell and Molecular Biology Program, Grand Valley State University, Allendale, MI 49401, United States
| | - Uma J Mishra
- Department of Chemistry, Grand Valley State University, Allendale, MI 49401, United States
| | - Robert P Smart
- Department of Chemistry, Grand Valley State University, Allendale, MI 49401, United States
| | - William Schroeder
- Department of Chemistry, Grand Valley State University, Allendale, MI 49401, United States
| | - Rachel A Powers
- Cell and Molecular Biology Program, Grand Valley State University, Allendale, MI 49401, United States; Department of Chemistry, Grand Valley State University, Allendale, MI 49401, United States.
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44
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Kamiya K, Baba T, Boero M, Matsui T, Negoro S, Shigeta Y. Nylon-Oligomer Hydrolase Promoting Cleavage Reactions in Unnatural Amide Compounds. J Phys Chem Lett 2014; 5:1210-1216. [PMID: 26274473 DOI: 10.1021/jz500323y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The active site of 6-aminohexanoate-dimer hydrolase, a nylon-6 byproduct-degrading enzyme with a β-lactamase fold, possesses a Ser112/Lys115/Tyr215 catalytic triad similar to the one of penicillin-recognizing family of serine-reactive hydrolases but includes a unique Tyr170 residue. By using a reactive quantum mechanics/molecular mechanics (QM/MM) approach, we work out its catalytic mechanism and related functional/structural specificities. At variance with other peptidases, we show that the involvement of Tyr170 in the enzyme-substrate interactions is responsible for a structural variation in the substrate-binding state. The acylation via a tetrahedral intermediate is the rate-limiting step, with a free-energy barrier of ∼21 kcal/mol, driven by the catalytic triad Ser112, Lys115, and Tyr215, acting as a nucleophile, general base, and general acid, respectively. The functional interaction of Tyr170 with this triad leads to an efficient disruption of the tetrahedral intermediate, promoting a conformational change of the substrate favorable for proton donation from the general acid.
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Affiliation(s)
- Katsumasa Kamiya
- †Center for Basic Education and Integrated Learning, Kanagawa Institute of Technology, 1030 Shimo-Ogino, Atsugi, Kanagawa 243-0292, Japan
| | - Takeshi Baba
- ‡Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Mauro Boero
- §Institut de Physique et Chimie des Matériaux de Strasbourg, UMR 7504 CNRS and University of Strasbourg, 23 rue du Loess, 67034 Strasbourg, France
| | - Toru Matsui
- ∥RIKEN, Advanced Institute for Computational Science, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Seiji Negoro
- ⊥Graduate School of Engineering, University of Hyogo, Himeji, Hyogo 671-2280, Japan
| | - Yasuteru Shigeta
- ‡Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
- #CREST, Japan Science and Technology Agency (JST), Kawaguchi, Saitama 332-0012 Japan
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45
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Draganov A, Wang D, Wang B. The Future of Boron in Medicinal Chemistry: Therapeutic and Diagnostic Applications. TOPICS IN MEDICINAL CHEMISTRY 2014. [DOI: 10.1007/7355_2014_65] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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46
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Watkins RR, Papp-Wallace KM, Drawz SM, Bonomo RA. Novel β-lactamase inhibitors: a therapeutic hope against the scourge of multidrug resistance. Front Microbiol 2013; 4:392. [PMID: 24399995 PMCID: PMC3871716 DOI: 10.3389/fmicb.2013.00392] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Accepted: 12/02/2013] [Indexed: 11/25/2022] Open
Abstract
The increasing incidence and prevalence of multi-drug resistance (MDR) among contemporary Gram-negative bacteria represents a significant threat to human health. Since their discovery, β-lactam antibiotics have been a major component of the armamentarium against these serious pathogens. Unfortunately, a wide range of β-lactamase enzymes have emerged that are capable of inactivating these powerful drugs. In the past 30 years, a major advancement in the battle against microbes has been the development of β-lactamase inhibitors, which restore the efficacy of β-lactam antibiotics (e.g., ampicillin/sulbactam, amoxicillin/clavulanate, ticarcillin/clavulanate, and piperacillin/tazobactam). Unfortunately, many newly discovered β-lactamases are not inactivated by currently available inhibitors. Is there hope? For the first time in many years, we can anticipate the development and introduction into clinical practice of novel inhibitors. Although these inhibitors may still not be effective for all β-lactamases, their introduction is still welcome. This review focuses on the novel β-lactamase inhibitors that are closest to being introduced in the clinic.
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Affiliation(s)
- Richard R Watkins
- Department of Internal Medicine, Northeast Ohio Medical University Rootstown, OH, USA ; Division of Infectious Diseases, Akron General Medical Center Akron, OH, USA
| | - Krisztina M Papp-Wallace
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center Cleveland, OH, USA ; Department of Medicine, Case Western Reserve University Cleveland, OH, USA
| | - Sarah M Drawz
- Department of Lab Medicine and Pathology, University of Minnesota Minneapolis, MN, USA
| | - Robert A Bonomo
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center Cleveland, OH, USA ; Department of Medicine, Case Western Reserve University Cleveland, OH, USA ; Pharmacology, Case Western Reserve University Cleveland, OH, USA ; Molecular Biology and Microbiology, Case Western Reserve University Cleveland, OH, USA
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47
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Tripathi R, Nair NN. Mechanism of acyl-enzyme complex formation from the Henry-Michaelis complex of class C β-lactamases with β-lactam antibiotics. J Am Chem Soc 2013; 135:14679-90. [PMID: 24010547 DOI: 10.1021/ja405319n] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Bacteria that cause most of the hospital-acquired infections make use of class C β-lactamase (CBL) among other enzymes to resist a wide spectrum of modern antibiotics and pose a major public health concern. Other than the general features, details of the defensive mechanism by CBL, leading to the hydrolysis of drug molecules, remain a matter of debate, in particular the identification of the general base and role of the active site residues and substrate. In an attempt to unravel the detailed molecular mechanism, we carried out extensive hybrid quantum mechanical/molecular mechanical Car-Parrinello molecular dynamics simulation of the reaction with the aid of the metadynamics technique. On this basis, we report here the mechanism of the formation of the acyl-enzyme complex from the Henry-Michaelis complex formed by β-lactam antibiotics and CBL. We considered two β-lactam antibiotics, namely, cephalothin and aztreonam, belonging to two different subfamilies. A general mechanism for the formation of a β-lactam antibiotic-CBL acyl-enzyme complex is elicited, and the individual roles of the active site residues and substrate are probed. The general base in the acylation step has been identified as Lys67, while Tyr150 aids the protonation of the β-lactam nitrogen through either the substrate carboxylate group or a water molecule.
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Affiliation(s)
- Ravi Tripathi
- Department of Chemistry, Indian Institute of Technology Kanpur , 208016 Kanpur, India
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48
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Cha SS, An YJ, Jeong CS, Kim MK, Jeon JH, Lee CM, Lee HS, Kang SG, Lee JH. Structural basis for the β-lactamase activity of EstU1, a family VIII carboxylesterase. Proteins 2013; 81:2045-51. [PMID: 23737193 DOI: 10.1002/prot.24334] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Revised: 05/08/2013] [Indexed: 11/08/2022]
Abstract
EstU1 is a unique family VIII carboxylesterase that displays hydrolytic activity toward the amide bond of clinically used β-lactam antibiotics as well as the ester bond of p-nitrophenyl esters. EstU1 assumes a β-lactamase-like modular architecture and contains the residues Ser100, Lys103, and Tyr218, which correspond to the three catalytic residues (Ser64, Lys67, and Tyr150, respectively) of class C β-lactamases. The structure of the EstU1/cephalothin complex demonstrates that the active site of EstU1 is not ideally tailored to perform an efficient deacylation reaction during the hydrolysis of β-lactam antibiotics. This result explains the weak β-lactamase activity of EstU1 compared with class C β-lactamases. Finally, structural and sequential comparison of EstU1 with other family VIII carboxylesterases elucidates an operative molecular strategy used by family VIII carboxylesterases to extend their substrate spectrum.
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Affiliation(s)
- Sun-Shin Cha
- Marine Biotechnology Research Division, Korea Institute of Ocean Science and Technology, Ansan, 426-744, Republic of Korea; Ocean Science and Technology School, Korea Maritime University, Pusan, 606-791, Republic of Korea; Department of Marine Biotechnology, University of Science and Technology, Daejeon, 305-333, Republic of Korea
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49
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Saiprathima P, Srinivas K, Sridhar B, Rao MM. “On water” one-pot synthesis of quaternary centered 3-hydroxy-3-(1H-tetrazol-5-yl)indolin-2-ones. RSC Adv 2013. [DOI: 10.1039/c3ra00021d] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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50
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Ruble JF, Lefurgy ST, Cornish VW, Powers RA. Structural analysis of the Asn152Gly mutant of P99 cephalosporinase. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2012; 68:1189-93. [PMID: 22948919 DOI: 10.1107/s0907444912024080] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2012] [Accepted: 05/26/2012] [Indexed: 11/10/2022]
Abstract
P99 cephalosporinase is a class C β-lactamase that is responsible in part for the widespread bacterial resistance to β-lactam antibiotics. Mutations of the conserved active-site residue Asn152 of the enzyme have been shown to alter β-lactam substrate specificity in vivo. Mutation of Asn152 to a glycine is notable in that it exhibits in vivo substrate-selectivity switching. In order to better understand the structural basis for this observed switch, the X-ray crystal structure of the apo Asn152Gly mutant of P99 was determined to 1.95 Å resolution. Unexpectedly, the artificial C-terminal His(6) tag of a symmetrically-related molecule was observed bound in the active site. The His(6) tag makes several interactions with key active-site residues, as well as with several sulfate ions. Additionally, the overall C-terminus occupies the space left vacant upon the mutation of Asn152 to glycine.
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Affiliation(s)
- James F Ruble
- Department of Chemistry, Grand Valley State University, Allendale, MI 49401, USA
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