1
|
Fröhlich C, Bunzel HA, Buda K, Mulholland AJ, van der Kamp MW, Johnsen PJ, Leiros HKS, Tokuriki N. Epistasis arises from shifting the rate-limiting step during enzyme evolution of a β-lactamase. Nat Catal 2024; 7:499-509. [PMID: 38828429 PMCID: PMC11136654 DOI: 10.1038/s41929-024-01117-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 01/25/2024] [Indexed: 06/05/2024]
Abstract
Epistasis, the non-additive effect of mutations, can provide combinatorial improvements to enzyme activity that substantially exceed the gains from individual mutations. Yet the molecular mechanisms of epistasis remain elusive, undermining our ability to predict pathogen evolution and engineer biocatalysts. Here we reveal how directed evolution of a β-lactamase yielded highly epistatic activity enhancements. Evolution selected four mutations that increase antibiotic resistance 40-fold, despite their marginal individual effects (≤2-fold). Synergistic improvements coincided with the introduction of super-stochiometric burst kinetics, indicating that epistasis is rooted in the enzyme's conformational dynamics. Our analysis reveals that epistasis stemmed from distinct effects of each mutation on the catalytic cycle. The initial mutation increased protein flexibility and accelerated substrate binding, which is rate-limiting in the wild-type enzyme. Subsequent mutations predominantly boosted the chemical steps by fine-tuning substrate interactions. Our work identifies an overlooked cause for epistasis: changing the rate-limiting step can result in substantial synergy that boosts enzyme activity.
Collapse
Affiliation(s)
| | - H. Adrian Bunzel
- Department of Biosystem Science and Engineering, ETH Zurich, Basel, Switzerland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, UK
- School of Biochemistry, University of Bristol, Bristol, UK
| | - Karol Buda
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia Canada
| | - Adrian J. Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, UK
| | - Marc W. van der Kamp
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, UK
- School of Biochemistry, University of Bristol, Bristol, UK
| | - Pål J. Johnsen
- Department of Pharmacy, UiT The Arctic University of Norway, Tromsø, Norway
| | | | - Nobuhiko Tokuriki
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia Canada
| |
Collapse
|
2
|
Park S, Fan J, Chamakuri S, Palaniappan M, Sharma K, Qin X, Wang J, Tan Z, Judge A, Hu L, Sankaran B, Li F, Prasad BVV, Matzuk MM, Palzkill T. Exploiting the Carboxylate-Binding Pocket of β-Lactamase Enzymes Using a Focused DNA-Encoded Chemical Library. J Med Chem 2024; 67:620-642. [PMID: 38117688 DOI: 10.1021/acs.jmedchem.3c01834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2023]
Abstract
β-Lactamase enzymes hydrolyze and thereby provide bacterial resistance to the important β-lactam class of antibiotics. The OXA-48 and NDM-1 β-lactamases cause resistance to the last-resort β-lactams, carbapenems, leading to a serious public health threat. Here, we utilized DNA-encoded chemical library (DECL) technology to discover novel β-lactamase inhibitors. We exploited the β-lactamase enzyme-substrate binding interactions and created a DECL targeting the carboxylate-binding pocket present in all β-lactamases. A library of 106 compounds, each containing a carboxylic acid or a tetrazole as an enzyme recognition element, was designed, constructed, and used to identify OXA-48 and NDM-1 inhibitors with micromolar to nanomolar potency. Further optimization led to NDM-1 inhibitors with increased potencies and biological activities. This work demonstrates that the carboxylate-binding pocket-targeting DECL, designed based on substrate binding information, aids in inhibitor identification and led to the discovery of novel non-β-lactam pharmacophores for the development of β-lactamase inhibitors for enzymes of different structural and mechanistic classes.
Collapse
Affiliation(s)
- Suhyeorn Park
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Jiayi Fan
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Srinivas Chamakuri
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Murugesan Palaniappan
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Kiran Sharma
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Xuan Qin
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Jian Wang
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Zhi Tan
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Allison Judge
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Liya Hu
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Banumathi Sankaran
- Berkeley Center for Structural Biology, Advanced Light Source, Lawrence Berkeley National Lab, Berkeley, California 94720, United States
| | - Feng Li
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - B V Venkataram Prasad
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Martin M Matzuk
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Timothy Palzkill
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
| |
Collapse
|
3
|
Nafaee ZH, Egyed V, Jancsó A, Tóth A, Gerami AM, Dang TT, Heiniger‐Schell J, Hemmingsen L, Hunyadi‐Gulyás É, Peintler G, Gyurcsik B. Revisiting the hydrolysis of ampicillin catalyzed by Temoneira-1 β-lactamase, and the effect of Ni(II), Cd(II) and Hg(II). Protein Sci 2023; 32:e4809. [PMID: 37853808 PMCID: PMC10661098 DOI: 10.1002/pro.4809] [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: 04/21/2023] [Revised: 09/18/2023] [Accepted: 10/15/2023] [Indexed: 10/20/2023]
Abstract
β-Lactamases grant resistance to bacteria against β-lactam antibiotics. The active center of TEM-1 β-lactamase accommodates a Ser-Xaa-Xaa-Lys motif. TEM-1 β-lactamase is not a metalloenzyme but it possesses several putative metal ion binding sites. The sites composed of His residue pairs chelate borderline transition metal ions such as Ni(II). In addition, there are many sulfur-containing donor groups that can coordinate soft metal ions such as Hg(II). Cd(II) may bind to both types of the above listed donor groups. No significant change was observed in the circular dichroism spectra of TEM-1 β-lactamase on increasing the metal ion content of the samples, with the exception of Hg(II) inducing a small change in the secondary structure of the protein. A weak nonspecific binding of Hg(II) was proven by mass spectrometry and 119m Hg perturbed angular correlation spectroscopy. The hydrolytic process of ampicillin catalyzed by TEM-1 β-lactamase was described by the kinetic analysis of the set of full catalytic progress curves, where the slow, yet observable conversion of the primary reaction product into a second one, identified as ampilloic acid by mass spectrometry, needed also to be considered in the applied model. Ni(II) and Cd(II) slightly promoted the catalytic activity of the enzyme while Hg(II) exerted a noticeable inhibitory effect. Hg(II) and Ni(II), applied at 10 μM concentration, inhibited the growth of E. coli BL21(DE3) in M9 minimal medium in the absence of ampicillin, but addition of the antibiotic could neutralize this toxic effect by complexing the metal ions.
Collapse
Affiliation(s)
- Zeyad H. Nafaee
- Department of Molecular and Analytical ChemistryUniversity of SzegedSzegedHungary
- College of PharmacyUniversity of BabylonBabelIraq
| | - Viktória Egyed
- Department of Molecular and Analytical ChemistryUniversity of SzegedSzegedHungary
| | - Attila Jancsó
- Department of Molecular and Analytical ChemistryUniversity of SzegedSzegedHungary
| | - Annamária Tóth
- Department of Molecular and Analytical ChemistryUniversity of SzegedSzegedHungary
| | - Adeleh Mokhles Gerami
- School of Particles and AcceleratorsInstitute for Research in Fundamental Sciences (IPM)TehranIran
- European Organization for Nuclear Research (CERN)GenevaSwitzerland
| | - Thanh Thien Dang
- Institute for Materials Science and Center for Nanointegration Duisburg‐Essen (CENIDE)University of Duisburg‐EssenEssenGermany
| | - Juliana Heiniger‐Schell
- European Organization for Nuclear Research (CERN)GenevaSwitzerland
- Institute for Materials Science and Center for Nanointegration Duisburg‐Essen (CENIDE)University of Duisburg‐EssenEssenGermany
| | - Lars Hemmingsen
- Department of ChemistryUniversity of CopenhagenCopenhagenDenmark
| | - Éva Hunyadi‐Gulyás
- Laboratory of Proteomics Research, Biological Research CentreHungarian Research Network (HUN‐REN)SzegedHungary
| | - Gábor Peintler
- Department of Physical Chemistry and Material SciencesUniversity of SzegedSzegedHungary
| | - Béla Gyurcsik
- Department of Molecular and Analytical ChemistryUniversity of SzegedSzegedHungary
| |
Collapse
|
4
|
Shang FF, Lu Q, Lin T, Pu M, Xiao R, Liu W, Deng H, Guo H, Quan ZS, Ding C, Shen QK. Discovery of Triazolyl Derivatives of Cucurbitacin B Targeting IGF2BP1 against Non-Small Cell Lung Cancer. J Med Chem 2023; 66:12931-12949. [PMID: 37681508 DOI: 10.1021/acs.jmedchem.3c00872] [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: 09/09/2023]
Abstract
Cucurbitacin B (CuB) is a potent but toxic anticancer natural product. Herein, we designed and synthesized 2-OH- and 16-OH-modified CuB derivatives to improve their antitumor efficacy and reduce toxicity. Among them, derivative A11 had the most potent antiproliferative activity against A549 lung cancer cells (IC50 = 0.009 μM) and was approximately 10-fold more potent than CuB, while the cytotoxicity of A11 toward normal L02 cells was about 10-fold less potent, indicating a much wider therapeutic window than CuB. Derivative A11 directly binds to the insulin-like growth factor 2 mRNA-binding protein 1 (IGF2BP1) protein with a KD value of 2.88 nM, which is about 23-fold more potent than CuB, leading to the decreased expression of downstream apoptosis- and cell cycle-related proteins. More importantly, A11 exhibited much more potent anticancer efficacy in an A549 xenograft mouse model with a TGI rate of 80% and a superior in vivo safety profile than that of CuB.
Collapse
Affiliation(s)
- Fan-Fan Shang
- Key Laboratory of Natural Medicines of the Changbai Mountain, Ministry of Education, College of Pharmacy, Yanbian University, Yanji 133002, China
- Shanghai Frontiers Science Center of Drug Target Identification and Delivery, National Key Laboratory of Innovative Immunotherapy, School of Pharmaceutical Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Qing Lu
- Shanghai Frontiers Science Center of Drug Target Identification and Delivery, National Key Laboratory of Innovative Immunotherapy, School of Pharmaceutical Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Tailiang Lin
- Shanghai Frontiers Science Center of Drug Target Identification and Delivery, National Key Laboratory of Innovative Immunotherapy, School of Pharmaceutical Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Miaoxia Pu
- Key Laboratory of Natural Medicines of the Changbai Mountain, Ministry of Education, College of Pharmacy, Yanbian University, Yanji 133002, China
- Key Laboratory of Natural Medicines of the Changbai Mountain, Ministry of Education, College of Integration Science, Yanbian University, Yanji 133002, China
| | - Ruoxuan Xiao
- Shanghai Frontiers Science Center of Drug Target Identification and Delivery, National Key Laboratory of Innovative Immunotherapy, School of Pharmaceutical Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Wanmei Liu
- Shanghai Frontiers Science Center of Drug Target Identification and Delivery, National Key Laboratory of Innovative Immunotherapy, School of Pharmaceutical Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hao Deng
- Key Laboratory of Natural Medicines of the Changbai Mountain, Ministry of Education, College of Pharmacy, Yanbian University, Yanji 133002, China
| | - Hongyan Guo
- Key Laboratory of Natural Medicines of the Changbai Mountain, Ministry of Education, College of Pharmacy, Yanbian University, Yanji 133002, China
| | - Zhe-Shan Quan
- Key Laboratory of Natural Medicines of the Changbai Mountain, Ministry of Education, College of Pharmacy, Yanbian University, Yanji 133002, China
| | - Chunyong Ding
- Shanghai Frontiers Science Center of Drug Target Identification and Delivery, National Key Laboratory of Innovative Immunotherapy, School of Pharmaceutical Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Qing-Kun Shen
- Key Laboratory of Natural Medicines of the Changbai Mountain, Ministry of Education, College of Pharmacy, Yanbian University, Yanji 133002, China
| |
Collapse
|
5
|
Takebayashi Y, Henderson SR, Chirgadze DY, Warburton PJ, Evans BA. OXA-66 structure and oligomerisation of OXA Ab enzymes. Access Microbiol 2022; 4:acmi000412. [PMID: 36415731 PMCID: PMC9675178 DOI: 10.1099/acmi.0.000412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 08/04/2022] [Indexed: 06/16/2023] Open
Abstract
The OXA β-lactamases are responsible for hydrolysing β-lactam antibiotics and contribute to the multidrug-resistant phenotype of several major human pathogens. The OXAAb enzymes are intrinsic to Acinetobacter baumannii and can confer resistance to carbapenem antibiotics. Here we determined the structure of the most prevalent OXAAb enzyme, OXA-66. The structure of OXA-66 was solved at a resolution of 2.1 Å and found to be very similar to the structure of OXA-51, the only other OXAAb enzyme that has had its structure solved. Our data contained one molecule per asymmetric unit, and analysis of positions responsible for dimer formation in other OXA enzymes suggest that OXA-66 likely exists as a monomer.
Collapse
Affiliation(s)
- Yuiko Takebayashi
- Department of Biomedical and Forensic Science, Anglia Ruskin University, Cambridge, UK
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
| | - Sara R. Henderson
- Norwich Medical School, University of East Anglia, Norwich, UK
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | | | - Philip J. Warburton
- Department of Biomedical and Forensic Science, Anglia Ruskin University, Cambridge, UK
- School of Biomedical Sciences, Faculty of Health, University of Plymouth, Plymouth, UK
| | - Benjamin A. Evans
- Department of Biomedical and Forensic Science, Anglia Ruskin University, Cambridge, UK
- Norwich Medical School, University of East Anglia, Norwich, UK
| |
Collapse
|
6
|
Wang X, Wang R, Zhang ZS, Zhang GY, Jin Z, Shen R, Du D, Tang YZ. Semisynthetic pleuromutilin antimicrobials with therapeutic potential against methicillin-resistant Staphylococcus aureus by targeting 50S ribosomal subunit. Eur J Med Chem 2022; 237:114341. [PMID: 35430480 DOI: 10.1016/j.ejmech.2022.114341] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 03/17/2022] [Accepted: 03/31/2022] [Indexed: 11/04/2022]
Abstract
A series of pleuromutilin analogs with a substituted 1,2,4-triazole were designed, synthesized and assessed for their in vitro and in vivo antibacterial activity. Initially, the MIC of the synthesized derivatives against five strains of Staphylococcus aureus (MRSA ATCC 43300, S. aureus ATCC 29213, clinical isolation of S. aureus AD3, S. aureus 144 and S. aureus SA17) were tested by the broth dilution method. Compounds 30a, 31b and 32a were the most active antibacterial agents in vitro against MRSA (MIC = 0.0625 μg/mL). The results of the time-kill curves showed that compounds 30a and 32a could reduce the amount of MRSA in vitro quickly (-7.70 log10 CFU/mL and -7.10 log10 CFU/mL reduction). In the experiment to further evaluate the in vivo antibacterial activity of compound 30a against MRSA, compound 30a (-1.71 log10 CFU/g) was effective in reducing MRSA load in thigh infected mice. Compound 30a (survival rate was 50%) displayed superior in vivo efficacy to that of tiamulin (survival rate was 30%) in the mouse systemic model. The results of further pharmacokinetic studies on compound 30a showed that the half-life (t1/2), clearance rate (Cl) and the area under the plasma concentration time curve (AUC0→∞) of compound 30a were 0.37 h, 5.43 L/h/kg and 1.84 μg h/mL, respectively. After affinity measurement by surface plasmon resonance (SPR), compound 30a exhibited high affinity with the 50S ribosome, with KD value of 1.95 × 10-6 M. Furthermore, the results of molecular docking studies revealed that compound 30a was successfully localized inside the binding pocket of 50S ribosomal subunit (ΔGb = -9.40 kcal/mol). Meanwhile, most of these compounds had no significant inhibitory effect on RAW 264.7 cells and 16HBE cells at the concentration of 8 μg/mL. The obtained outcomes showed that compound 30a could be utilized as an encouraging perspective in the development of a new therapeutic candidate for bacterial infection.
Collapse
Affiliation(s)
- Xiao Wang
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China; Cancer Research Center, Department of Stomatology, School of Medicine, Xiamen University, Xiamen, Fujian, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Rui Wang
- Cancer Research Center, Department of Stomatology, School of Medicine, Xiamen University, Xiamen, Fujian, China; Fujian Provincial Key Laboratory of Reproductive Health Research, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Zhao-Sheng Zhang
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China
| | - Guang-Yu Zhang
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China
| | - Zhen Jin
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Rong Shen
- Cancer Research Center, Department of Stomatology, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Dan Du
- Cancer Research Center, Department of Stomatology, School of Medicine, Xiamen University, Xiamen, Fujian, China; Fujian Provincial Key Laboratory of Reproductive Health Research, School of Medicine, Xiamen University, Xiamen, Fujian, China.
| | - You-Zhi Tang
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China.
| |
Collapse
|
7
|
Avci FG, Tastekil I, Jaisi A, Ozbek Sarica P, Sariyar Akbulut B. A review on the mechanistic details of OXA enzymes of ESKAPE pathogens. Pathog Glob Health 2022; 117:219-234. [PMID: 35758005 PMCID: PMC10081068 DOI: 10.1080/20477724.2022.2088496] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
Abstract
The production of β-lactamases is a prevalent mechanism that poses serious pressure on the control of bacterial resistance. Furthermore, the unavoidable and alarming increase in the transmission of bacteria producing extended-spectrum β-lactamases complicates treatment alternatives with existing drugs and/or approaches. Class D β-lactamases, designated as OXA enzymes, are characterized by their activity specifically towards oxacillins. They are widely distributed among the ESKAPE bugs that are associated with antibiotic resistance and life-threatening hospital infections. The inadequacy of current β-lactamase inhibitors for conventional treatments of 'OXA' mediated infections confirms the necessity of new approaches. Here, the focus is on the mechanistic details of OXA-10, OXA-23, and OXA-48, commonly found in highly virulent and antibiotic-resistant pathogens Acinetobacter baumannii, Klebsiella pneumoniae, Pseudomonas aeruginosa, and Enterobacter spp. to describe their similarities and differences. Furthermore, this review contains a specific emphasis on structural and computational perspectives, which will be valuable to guide efforts in the design/discovery of a common single-molecule drug against ESKAPE pathogens.
Collapse
Affiliation(s)
- Fatma Gizem Avci
- Bioengineering Department, Uskudar University, Uskudar, 34662, Turkey
| | - Ilgaz Tastekil
- Bioengineering Department, Marmara University, Kadikoy, 34722, Turkey
| | - Amit Jaisi
- Drug and Cosmetics Excellence Center, School of Pharmacy, Walailak University, 80160, Nakhon Si Thammarat, Thailand
| | | | | |
Collapse
|
8
|
Taylor DM, Anglin J, Hu L, Wang L, Sankaran B, Wang J, Matzuk MM, Prasad BV, Palzkill T. Unique Diacidic Fragments Inhibit the OXA-48 Carbapenemase and Enhance the Killing of Escherichia coli Producing OXA-48. ACS Infect Dis 2021; 7:3345-3354. [PMID: 34817169 PMCID: PMC9677231 DOI: 10.1021/acsinfecdis.1c00501] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Despite the advances in β-lactamase inhibitor development, limited options exist for the class D carbapenemase known as OXA-48. OXA-48 is one of the most prevalent carbapenemases in carbapenem-resistant Enterobacteriaceae infections and is not susceptible to most available β-lactamase inhibitors. Here, we screened various low-molecular-weight compounds (fragments) against OXA-48 to identify functional scaffolds for inhibitor development. Several biphenyl-, naphthalene-, fluorene-, anthraquinone-, and azobenzene-based compounds were found to inhibit OXA-48 with low micromolar potency despite their small size. Co-crystal structures of OXA-48 with several of these compounds revealed key interactions with the carboxylate-binding pocket, Arg214, and various hydrophobic residues of β-lactamase that can be exploited in future inhibitor development. A number of the low-micromolar-potency inhibitors, across different scaffolds, synergize with ampicillin to kill Escherichia coli expressing OXA-48, albeit at high concentrations of the respective inhibitors. Additionally, several compounds demonstrated micromolar potency toward the OXA-24 and OXA-58 class D carbapenemases that are prevalent in Acinetobacter baumannii. This work provides foundational information on a variety of chemical scaffolds that can guide the design of effective OXA-48 inhibitors that maintain efficacy as well as potency toward other major class D carbapenemases.
Collapse
Affiliation(s)
- Doris Mia Taylor
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Justin Anglin
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Liya Hu
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Lingfei Wang
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Banumathi Sankaran
- Molecular Biophysics and Integrated Bioimaging, Berkeley Center for Structural Biology, Advanced Light Source, Lawrence Berkeley National Laboratory, CA, 94720, USA
| | - Jin Wang
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Martin M. Matzuk
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - B.V. Venkataram Prasad
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Timothy Palzkill
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| |
Collapse
|
9
|
Lund BA, Thomassen AM, Carlsen TJW, Leiros HKS. Biochemical and biophysical characterization of the OXA-48-like carbapenemase OXA-436. Acta Crystallogr F Struct Biol Commun 2021; 77:312-318. [PMID: 34473108 PMCID: PMC8411929 DOI: 10.1107/s2053230x21008645] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 08/18/2021] [Indexed: 11/08/2023] Open
Abstract
The crystal structure of the class D β-lactamase OXA-436 was solved to a resolution of 1.80 Å. Higher catalytic rates were found at higher temperatures for the clinically important antibiotic imipenem, indicating better adaptation of OXA-436 to its mesophilic host than OXA-48, which is believed to originate from an environmental source. Furthermore, based on the most populated conformations during 100 ns molecular-dynamics simulations, it is postulated that the modulation of activity involves conformational shifts of the α3-α4 and β5-β6 loops. While these changes overall do not cause clinically significant shifts in the resistance profile, they show that antibiotic-resistance enzymes exist in a continuum. It is believed that these seemingly neutral differences in the sequence exist on a path leading to significant changes in substrate selectivity.
Collapse
Affiliation(s)
- Bjarte Aarmo Lund
- The Norwegian Structural Biology Centre (NorStruct), Department of Chemistry, UiT The Arctic University of Norway, 9037 Tromsø, Norway
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, UiT The Arctic University of Norway, 9037 Tromsø, Norway
| | - Ane Molden Thomassen
- The Norwegian Structural Biology Centre (NorStruct), Department of Chemistry, UiT The Arctic University of Norway, 9037 Tromsø, Norway
| | - Trine Josefine Warg Carlsen
- The Norwegian Structural Biology Centre (NorStruct), Department of Chemistry, UiT The Arctic University of Norway, 9037 Tromsø, Norway
| | - Hanna-Kirsti Schrøder Leiros
- The Norwegian Structural Biology Centre (NorStruct), Department of Chemistry, UiT The Arctic University of Norway, 9037 Tromsø, Norway
| |
Collapse
|
10
|
Discovery of Novel Chemical Series of OXA-48 β-Lactamase Inhibitors by High-Throughput Screening. Pharmaceuticals (Basel) 2021; 14:ph14070612. [PMID: 34202402 PMCID: PMC8308845 DOI: 10.3390/ph14070612] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 06/21/2021] [Accepted: 06/23/2021] [Indexed: 11/17/2022] Open
Abstract
The major cause of bacterial resistance to β-lactams is the production of hydrolytic β-lactamase enzymes. Nowadays, the combination of β-lactam antibiotics with β-lactamase inhibitors (BLIs) is the main strategy for overcoming such issues. Nevertheless, particularly challenging β-lactamases, such as OXA-48, pose the need for novel and effective treatments. Herein, we describe the screening of a proprietary compound collection against Klebsiella pneumoniae OXA-48, leading to the identification of several chemotypes, like the 4-ideneamino-4H-1,2,4-triazole (SC_2) and pyrazolo[3,4-b]pyridine (SC_7) cores as potential inhibitors. Importantly, the most potent representative of the latter series (ID2, AC50 = 0.99 μM) inhibited OXA-48 via a reversible and competitive mechanism of action, as demonstrated by biochemical and X-ray studies; furthermore, it slightly improved imipenem’s activity in Escherichia coli ATCC BAA-2523 β-lactam resistant strain. Also, ID2 showed good solubility and no sign of toxicity up to the highest tested concentration, resulting in a promising starting point for further optimization programs toward novel and effective non-β-lactam BLIs.
Collapse
|
11
|
Abstract
Very low antibiotic concentrations have been shown to drive the evolution of antimicrobial resistance. While substantial progress has been made to understand the driving role of low concentrations during resistance development for different antimicrobial classes, the importance of β-lactams, the most commonly used antibiotics, is still poorly studied. Our current understanding of how low antibiotic concentrations shape the evolution of contemporary β-lactamases is limited. Using the widespread carbapenemase OXA-48, we tested the long-standing hypothesis that selective compartments with low antibiotic concentrations cause standing genetic diversity that could act as a gateway to developing clinical resistance. Here, we subjected Escherichia coli expressing blaOXA-48, on a clinical plasmid, to experimental evolution at sub-MICs of ceftazidime. We identified and characterized seven single variants of OXA-48. Susceptibility profiles and dose-response curves showed that they increased resistance only marginally. However, in competition experiments at sub-MICs of ceftazidime, they demonstrated strong selectable fitness benefits. Increased resistance was also reflected in elevated catalytic efficiencies toward ceftazidime. These changes are likely caused by enhanced flexibility of the Ω- and β5-β6 loops and fine-tuning of preexisting active site residues. In conclusion, low-level concentrations of β-lactams can drive the evolution of β-lactamases through cryptic phenotypes which may act as stepping-stones toward clinical resistance. IMPORTANCE Very low antibiotic concentrations have been shown to drive the evolution of antimicrobial resistance. While substantial progress has been made to understand the driving role of low concentrations during resistance development for different antimicrobial classes, the importance of β-lactams, the most commonly used antibiotics, is still poorly studied. Here, we shed light on the evolutionary impact of low β-lactam concentrations on the widespread β-lactamase OXA-48. Our data indicate that the exposure to β-lactams at very low concentrations enhances β-lactamase diversity and drives the evolution of β-lactamases by significantly influencing their substrate specificity. Thus, in contrast to high concentrations, low levels of these drugs may substantially contribute to the diversification and divergent evolution of these enzymes, providing a standing genetic diversity that can be selected and mobilized when antibiotic pressure increases.
Collapse
|
12
|
Ai Y, Hwang L, MacKerell AD, Melnick A, Xue F. Progress toward B-Cell Lymphoma 6 BTB Domain Inhibitors for the Treatment of Diffuse Large B-Cell Lymphoma and Beyond. J Med Chem 2021; 64:4333-4358. [PMID: 33844535 DOI: 10.1021/acs.jmedchem.0c01686] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
B-cell lymphoma 6 (BCL6) is a master regulator of germinal center formation that produce antibody-secreting plasma cells and memory B-cells for sustained immune responses. The BTB domain of BCL6 (BCL6BTB) forms a homodimer that mediates transcriptional repression by recruiting its corepressor proteins to form a biologically functional transcriptional complex. The protein-protein interaction (PPI) between the BCL6BTB and its corepressors has emerged as a therapeutic target for the treatment of DLBCL and a number of other human cancers. This Perspective provides an overview of recent advances in the development of BCL6BTB inhibitors from reversible inhibitors, irreversible inhibitors, to BCL6 degraders. Inhibitor design and medicinal chemistry strategies for the development of novel compounds will be provided. The binding mode of new inhibitors to BCL6BTB are highlighted. Also, the in vitro and in vivo assays used for the evaluation of new compounds will be discussed.
Collapse
Affiliation(s)
- Yong Ai
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 Penn Street, Baltimore, Maryland 21201, United States
| | - Lucia Hwang
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 Penn Street, Baltimore, Maryland 21201, United States
| | - Alexander D MacKerell
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 Penn Street, Baltimore, Maryland 21201, United States
| | - Ari Melnick
- Department of Hematology and Oncology, Weill Cornell Medical College, New York, New York 10021, United States.,Department of Pharmacology, Weill Cornell Medical College, New York, New York 10021, United States
| | - Fengtian Xue
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 Penn Street, Baltimore, Maryland 21201, United States
| |
Collapse
|
13
|
Taylor DM, Anglin J, Park S, Ucisik MN, Faver JC, Simmons N, Jin Z, Palaniappan M, Nyshadham P, Li F, Campbell J, Hu L, Sankaran B, Prasad BV, Huang H, Matzuk MM, Palzkill T. Identifying Oxacillinase-48 Carbapenemase Inhibitors Using DNA-Encoded Chemical Libraries. ACS Infect Dis 2020; 6:1214-1227. [PMID: 32182432 PMCID: PMC7673237 DOI: 10.1021/acsinfecdis.0c00015] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Bacterial resistance to β-lactam antibiotics is largely mediated by β-lactamases, which catalyze the hydrolysis of these drugs and continue to emerge in response to antibiotic use. β-Lactamases that hydrolyze the last resort carbapenem class of β-lactam antibiotics (carbapenemases) are a growing global health threat. Inhibitors have been developed to prevent β-lactamase-mediated hydrolysis and restore the efficacy of these antibiotics. However, there are few inhibitors available for problematic carbapenemases such as oxacillinase-48 (OXA-48). A DNA-encoded chemical library approach was used to rapidly screen for compounds that bind and potentially inhibit OXA-48. Using this approach, a hit compound, CDD-97, was identified with submicromolar potency (Ki = 0.53 ± 0.08 μM) against OXA-48. X-ray crystallography showed that CDD-97 binds noncovalently in the active site of OXA-48. Synthesis and testing of derivatives of CDD-97 revealed structure-activity relationships and informed the design of a compound with a 2-fold increase in potency. CDD-97, however, synergizes poorly with β-lactam antibiotics to inhibit the growth of bacteria expressing OXA-48 due to poor accumulation into E. coli. Despite the low in vivo activity, CDD-97 provides new insights into OXA-48 inhibition and demonstrates the potential of using DNA-encoded chemistry technology to rapidly identify β-lactamase binders and to study β-lactamase inhibition, leading to clinically useful inhibitors.
Collapse
Affiliation(s)
- Doris Mia Taylor
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Justin Anglin
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX, 77030 USA
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Suhyeorn Park
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Melek N. Ucisik
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX, 77030 USA
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - John C. Faver
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX, 77030 USA
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Nicholas Simmons
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX, 77030 USA
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Zhuang Jin
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX, 77030 USA
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Murugesan Palaniappan
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX, 77030 USA
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Pranavanand Nyshadham
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX, 77030 USA
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Feng Li
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX, 77030 USA
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - James Campbell
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX, 77030 USA
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Liya Hu
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Banumathi Sankaran
- Berkeley Center for Structural Biology, Advanced Light Source, Lawrence Berkeley National Lab, CA, 94720, USA
| | - B.V. Venkataram Prasad
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Hongbing Huang
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX, 77030 USA
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Martin M. Matzuk
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX, 77030 USA
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Timothy Palzkill
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| |
Collapse
|
14
|
Abstract
Infections due to carbapenemase-producing Gram-negative pathogens are associated with limited treatment options and consequently lead to increased mortality and morbidity. In response, combinations of existing β-lactams and novel β-lactamase inhibitors, such as ceftazidime-avibactam (CAZ-AVI), have been developed as alternative treatment options. To understand the development of resistance and evolutionary trajectories under CAZ-AVI exposure, we studied the effects of ceftazidime (CAZ) and CAZ-AVI on the carbapenemase OXA-48 and the epidemic OXA-48 plasmid in Escherichia coli Exposure of CAZ and CAZ-AVI resulted in single (P68A) and double (P68A,Y211S) amino acid substitutions in OXA-48, respectively. The antimicrobial susceptibility data and enzyme kinetics showed that the P68A substitution was responsible for an increased activity toward CAZ, whereas P68A,Y211S led to a decrease in the inhibitory activity of AVI. X-ray crystallography and molecular modeling of the mutants demonstrated increased flexibility within the active site, which could explain the elevated CAZ hydrolysis and reduced inhibitory activity of AVI. Interestingly, these substitutions resulted in collateral effects compromising the activity of OXA-48 toward carbapenems and penicillins. Moreover, exposure to CAZ-AVI selected for mutations within the OXA-48-encoding plasmid that severely reduced fitness in the absence of antimicrobial selection. These evolutionary trade-offs may contribute to limit the evolution of OXA-48-mediated CAZ and CAZ-AVI resistance, as well as potentially resensitize isolates toward other therapeutic alternatives.IMPORTANCE The recent introduction of novel β-lactam/β-lactamase inhibitor combinations like ceftazidime-avibactam has increased our ability to treat infections caused by multidrug-resistant Gram-negative bacteria, including carbapenemase-producing Enterobacterales However, the increasing number of cases of reported resistance to ceftazidime-avibactam is a concern. OXA-48 is a carbapenemase that has no significant effect on ceftazidime, but is inhibited by avibactam. Since isolates with OXA-48 frequently harbor extended-spectrum β-lactamases that are inhibited by avibactam, it is likely that ceftazidime-avibactam will be used to treat infections caused by OXA-48-producing Enterobacterales. Our data show that exposure to ceftazidime-avibactam can lead to changes in OXA-48, resulting in increased ability to hydrolyze ceftazidime and withstand the inhibitory effect of avibactam. Thus, resistance toward ceftazidime-avibactam among OXA-48-producing Enterobacterales should be monitored. Interestingly, the compromising effect of the amino acid substitutions in OXA-48 on other β-lactams and the effect of ceftazidime-avibactam exposure on the epidemic OXA-48 plasmid indicate that the evolution of ceftazidime-avibactam resistance comes with collateral effects.
Collapse
|
15
|
Zhang Y, Lei J, He Y, Yang J, Wang W, Wasey A, Xu J, Lin Y, Fan H, Jing G, Zhang C, Jin Y. Label‐Free Visualization of Carbapenemase Activity in Living Bacteria. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201810834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Ye Zhang
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education College of Chemistry and Materials Science Northwest University 1 Xue Fu Avenue Xi'an 710127 P. R. China
| | - Jin‐E Lei
- The First Affiliated Hospital of Xi'an Jiaotong University Xi'an Jiatong University Xi'an 710061 P. R. China
| | - Yuan He
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education College of Chemistry and Materials Science Northwest University 1 Xue Fu Avenue Xi'an 710127 P. R. China
| | - Jianhua Yang
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education College of Chemistry and Materials Science Northwest University 1 Xue Fu Avenue Xi'an 710127 P. R. China
| | - Wenjing Wang
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education College of Chemistry and Materials Science Northwest University 1 Xue Fu Avenue Xi'an 710127 P. R. China
| | - Abdul Wasey
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education College of Chemistry and Materials Science Northwest University 1 Xue Fu Avenue Xi'an 710127 P. R. China
| | - Jiru Xu
- The First Affiliated Hospital of Xi'an Jiaotong University Xi'an Jiatong University Xi'an 710061 P. R. China
| | - Yue Lin
- Scion New Zealand Forest Research Institute) Rotorua 3010 New Zealand
| | - Haiming Fan
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education College of Chemistry and Materials Science Northwest University 1 Xue Fu Avenue Xi'an 710127 P. R. China
| | - Guangyin Jing
- College of Physics Northwest University 1 Xue Fu Avenue Xi'an 710127 P. R. China
| | - Ce Zhang
- College of Physics Northwest University 1 Xue Fu Avenue Xi'an 710127 P. R. China
| | - Yi Jin
- School of Chemistry Cardiff University Cardiff CF10 3AT UK
| |
Collapse
|
16
|
Zhang Y, Lei J, He Y, Yang J, Wang W, Wasey A, Xu J, Lin Y, Fan H, Jing G, Zhang C, Jin Y. Label‐Free Visualization of Carbapenemase Activity in Living Bacteria. Angew Chem Int Ed Engl 2018; 57:17120-17124. [DOI: 10.1002/anie.201810834] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 10/19/2018] [Indexed: 12/28/2022]
Affiliation(s)
- Ye Zhang
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education College of Chemistry and Materials Science Northwest University 1 Xue Fu Avenue Xi'an 710127 P. R. China
| | - Jin‐E Lei
- The First Affiliated Hospital of Xi'an Jiaotong University Xi'an Jiatong University Xi'an 710061 P. R. China
| | - Yuan He
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education College of Chemistry and Materials Science Northwest University 1 Xue Fu Avenue Xi'an 710127 P. R. China
| | - Jianhua Yang
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education College of Chemistry and Materials Science Northwest University 1 Xue Fu Avenue Xi'an 710127 P. R. China
| | - Wenjing Wang
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education College of Chemistry and Materials Science Northwest University 1 Xue Fu Avenue Xi'an 710127 P. R. China
| | - Abdul Wasey
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education College of Chemistry and Materials Science Northwest University 1 Xue Fu Avenue Xi'an 710127 P. R. China
| | - Jiru Xu
- The First Affiliated Hospital of Xi'an Jiaotong University Xi'an Jiatong University Xi'an 710061 P. R. China
| | - Yue Lin
- Scion New Zealand Forest Research Institute) Rotorua 3010 New Zealand
| | - Haiming Fan
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education College of Chemistry and Materials Science Northwest University 1 Xue Fu Avenue Xi'an 710127 P. R. China
| | - Guangyin Jing
- College of Physics Northwest University 1 Xue Fu Avenue Xi'an 710127 P. R. China
| | - Ce Zhang
- College of Physics Northwest University 1 Xue Fu Avenue Xi'an 710127 P. R. China
| | - Yi Jin
- School of Chemistry Cardiff University Cardiff CF10 3AT UK
| |
Collapse
|
17
|
Lund BA, Thomassen AM, Nesheim BHB, Carlsen TJO, Isaksson J, Christopeit T, Leiros HKS. The biological assembly of OXA-48 reveals a dimer interface with high charge complementarity and very high affinity. FEBS J 2018; 285:4214-4228. [PMID: 30153368 DOI: 10.1111/febs.14643] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 08/07/2018] [Accepted: 08/22/2018] [Indexed: 12/16/2022]
Abstract
Many class D β-lactamases form dimers in solution. The functional basis of the dimerization of OXA-48-like class D β-lactamases is not known, but in order to understand the structural requirements for dimerization of OXA-48, we have characterized the dimer interface. Size exclusion chromatography, small angle X-ray scattering (SAXS), and nuclear magnetic resonance (NMR) were used to confirm the oligomeric state of OXA-48 in solution. X-ray crystallographic structures were used to elucidate the key interactions of dimerization. In silico residue scanning combined with site-directed mutagenesis was used to probe hot spots of dimerization. The affinity of dimerization was quantified using microscale thermophoresis, and the overall thermostability was investigated using differential scanning calorimetry. OXA-48 was consistently found to be a dimer in solution regardless of the method used, and the biological assembly found from the SAXS envelope is consistent with the dimer identified from the crystal structures. The buried chloride that interacts with Arg206 and Arg206' at the dimer interface was found to enhance the thermal stability by > 4 °C and crystal structures and mutations (R189A, R189A/R206A) identified several additional important ionic interactions. The affinity for OXA-48 R206A dimerization was in the picomolar range, thus revealing very high dimer affinity. In summary, OXA-48 has a very stable dimer interface, facilitated by noncovalent and predominantly charged interactions, which is stronger than the dimer interfaces previously described for other class D β-lactamases. PDB CODES: The oxacillinase-48 (OXA-48) R206A structure has PDB ID: 5OFT and OXA-48 R189A has PDB ID: 6GOA.
Collapse
Affiliation(s)
- Bjarte Aarmo Lund
- Department of Chemistry, Faculty of Science and Technology, The Norwegian Structural Biology Centre (NorStruct), UiT The Arctic University of Norway, Tromsø, Norway
| | - Ane Molden Thomassen
- Department of Chemistry, Faculty of Science and Technology, The Norwegian Structural Biology Centre (NorStruct), UiT The Arctic University of Norway, Tromsø, Norway
| | - Birgit Helene Berg Nesheim
- Department of Chemistry, Faculty of Science and Technology, The Norwegian Structural Biology Centre (NorStruct), UiT The Arctic University of Norway, Tromsø, Norway
| | - Trine Josefine Olsen Carlsen
- Department of Chemistry, Faculty of Science and Technology, The Norwegian Structural Biology Centre (NorStruct), UiT The Arctic University of Norway, Tromsø, Norway
| | - Johan Isaksson
- Department of Chemistry, Faculty of Science and Technology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Tony Christopeit
- Department of Chemistry, Faculty of Science and Technology, The Norwegian Structural Biology Centre (NorStruct), UiT The Arctic University of Norway, Tromsø, Norway
| | - Hanna-Kirsti S Leiros
- Department of Chemistry, Faculty of Science and Technology, The Norwegian Structural Biology Centre (NorStruct), UiT The Arctic University of Norway, Tromsø, Norway
| |
Collapse
|
18
|
Cain R, Brem J, Zollman D, McDonough MA, Johnson RM, Spencer J, Makena A, Abboud MI, Cahill S, Lee SY, McHugh PJ, Schofield CJ, Fishwick CWG. In Silico Fragment-Based Design Identifies Subfamily B1 Metallo-β-lactamase Inhibitors. J Med Chem 2018; 61:1255-1260. [PMID: 29271657 DOI: 10.1021/acs.jmedchem.7b01728] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Zinc ion-dependent β-lactamases (MBLs) catalyze the hydrolysis of almost all β-lactam antibiotics and resist the action of clinically available β-lactamase inhibitors. We report how application of in silico fragment-based molecular design employing thiol-mediated metal anchorage leads to potent MBL inhibitors. The new inhibitors manifest potent inhibition of clinically important B1 subfamily MBLs, including the widespread NDM-1, IMP-1, and VIM-2 enzymes; with lower potency, some of them also inhibit clinically relevant Class A and D serine-β-lactamases. The inhibitors show selectivity for bacterial MBL enzymes compared to that for human MBL fold nucleases. Cocrystallization of one inhibitor, which shows potentiation of Meropenem activity against MBL-expressing Enterobacteriaceae, with VIM-2 reveals an unexpected binding mode, involving interactions with residues from conserved active site bordering loops.
Collapse
Affiliation(s)
- Ricky Cain
- School of Chemistry, University of Leeds , Leeds LS2 9JT, United Kingdom
| | - Jürgen Brem
- Department of Chemistry, University of Oxford , 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - David Zollman
- Department of Chemistry, University of Oxford , 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Michael A McDonough
- Department of Chemistry, University of Oxford , 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Rachel M Johnson
- School of Chemistry, University of Leeds , Leeds LS2 9JT, United Kingdom
| | - James Spencer
- School of Cellular and Molecular Medicine, University of Bristol , Biomedical Sciences Building, Bristol BS8 1TD, United Kingdom
| | - Anne Makena
- Department of Chemistry, University of Oxford , 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Martine I Abboud
- Department of Chemistry, University of Oxford , 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Samuel Cahill
- Department of Chemistry, University of Oxford , 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Sook Y Lee
- Department of Chemistry, University of Oxford , 12 Mansfield Road, Oxford OX1 3TA, United Kingdom.,Department of Oncology, Weatherall Institute of Molecular Medicine, University of Oxford , John Radcliffe Hospital, Oxford OX3 9DS, United Kingdom
| | - Peter J McHugh
- Department of Oncology, Weatherall Institute of Molecular Medicine, University of Oxford , John Radcliffe Hospital, Oxford OX3 9DS, United Kingdom
| | - Christopher J Schofield
- Department of Chemistry, University of Oxford , 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Colin W G Fishwick
- School of Chemistry, University of Leeds , Leeds LS2 9JT, United Kingdom
| |
Collapse
|
19
|
Akhter S, Lund BA, Ismael A, Langer M, Isaksson J, Christopeit T, Leiros HKS, Bayer A. A focused fragment library targeting the antibiotic resistance enzyme - Oxacillinase-48: Synthesis, structural evaluation and inhibitor design. Eur J Med Chem 2017; 145:634-648. [PMID: 29348071 DOI: 10.1016/j.ejmech.2017.12.085] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 12/24/2017] [Accepted: 12/26/2017] [Indexed: 01/05/2023]
Abstract
β-Lactam antibiotics are of utmost importance when treating bacterial infections in the medical community. However, currently their utility is threatened by the emergence and spread of β-lactam resistance. The most prevalent resistance mechanism to β-lactam antibiotics is expression of β-lactamase enzymes. One way to overcome resistance caused by β-lactamases, is the development of β-lactamase inhibitors and today several β-lactamase inhibitors e.g. avibactam, are approved in the clinic. Our focus is the oxacillinase-48 (OXA-48), an enzyme reported to spread rapidly across the world and commonly identified in Escherichia coli and Klebsiella pneumoniae. To guide inhibitor design, we used diversely substituted 3-aryl and 3-heteroaryl benzoic acids to probe the active site of OXA-48 for useful enzyme-inhibitor interactions. In the presented study, a focused fragment library containing 49 3-substituted benzoic acid derivatives were synthesised and biochemically characterized. Based on crystallographic data from 33 fragment-enzyme complexes, the fragments could be classified into R1 or R2 binders by their overall binding conformation in relation to the binding of the R1 and R2 side groups of imipenem. Moreover, binding interactions attractive for future inhibitor design were found and their usefulness explored by the rational design and evaluation of merged inhibitors from orthogonally binding fragments. The best inhibitors among the resulting 3,5-disubstituted benzoic acids showed inhibitory potential in the low micromolar range (IC50 = 2.9 μM). For these inhibitors, the complex X-ray structures revealed non-covalent binding to Arg250, Arg214 and Tyr211 in the active site and the interactions observed with the mono-substituted fragments were also identified in the merged structures.
Collapse
Affiliation(s)
- Sundus Akhter
- Department of Chemistry, Faculty of Science and Technology, UiT- The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Bjarte Aarmo Lund
- The Norwegian Structural Biology Centre (NorStruct), Department of Chemistry, Faculty of Science and Technology, UiT-The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Aya Ismael
- Department of Chemistry, Faculty of Science and Technology, UiT- The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Manuel Langer
- Department of Chemistry, Faculty of Science and Technology, UiT- The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Johan Isaksson
- Department of Chemistry, Faculty of Science and Technology, UiT- The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Tony Christopeit
- The Norwegian Structural Biology Centre (NorStruct), Department of Chemistry, Faculty of Science and Technology, UiT-The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Hanna-Kirsti S Leiros
- The Norwegian Structural Biology Centre (NorStruct), Department of Chemistry, Faculty of Science and Technology, UiT-The Arctic University of Norway, N-9037 Tromsø, Norway.
| | - Annette Bayer
- Department of Chemistry, Faculty of Science and Technology, UiT- The Arctic University of Norway, N-9037 Tromsø, Norway.
| |
Collapse
|
20
|
Lund BA, Thomassen AM, Carlsen TJO, Leiros HKS. Structure, activity and thermostability investigations of OXA-163, OXA-181 and OXA-245 using biochemical analysis, crystal structures and differential scanning calorimetry analysis. Acta Crystallogr F Struct Biol Commun 2017; 73:579-587. [PMID: 28994407 PMCID: PMC5633926 DOI: 10.1107/s2053230x17013838] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 09/25/2017] [Indexed: 01/20/2023] Open
Abstract
The first crystal structures of the class D β-lactamases OXA-181 and OXA-245 were determined to 2.05 and 2.20 Å resolution, respectively; in addition, the structure of a new crystal form of OXA-163 was resolved to 2.07 Å resolution. All of these enzymes are OXA-48-like and have been isolated from different clinical Klebsiella pneumoniae strains and also from other human pathogens such as Pseudomonas aeruginosa and Escherichia coli. Here, enzyme kinetics and thermostability studies are presented, and the new crystal structures are used to explain the observed variations. OXA-245 had the highest melting point (Tm = 55.8°C), as determined by differential scanning calorimetry, compared with OXA-163 (Tm = 49.4°C) and OXA-181 (Tm = 52.6°C). The differences could be explained by the loss of two salt bridges in OXA-163, and an overall decrease in the polarity of the surface of OXA-181 compared with OXA-245.
Collapse
Affiliation(s)
- Bjarte Aarmo Lund
- Department of Chemistry, UiT The Arctic University of Norway, 9037 Tromsø, Norway
| | - Ane Molden Thomassen
- Department of Chemistry, UiT The Arctic University of Norway, 9037 Tromsø, Norway
| | | | | |
Collapse
|
21
|
Discovery of a B-Cell Lymphoma 6 Protein-Protein Interaction Inhibitor by a Biophysics-Driven Fragment-Based Approach. J Med Chem 2017; 60:4358-4368. [PMID: 28471657 DOI: 10.1021/acs.jmedchem.7b00313] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
B-cell lymphoma 6 (BCL6) is a transcriptional factor that expresses in lymphocytes and regulates the differentiation and proliferation of lymphocytes. Therefore, BCL6 is a therapeutic target for autoimmune diseases and cancer treatment. This report presents the discovery of BCL6-corepressor interaction inhibitors by using a biophysics-driven fragment-based approach. Using the surface plasmon resonance (SPR)-based fragment screening, we successfully identified fragment 1 (SPR KD = 1200 μM, ligand efficiency (LE) = 0.28), a competitive binder to the natural ligand BCoR peptide. Moreover, we elaborated 1 into the more potent compound 7 (SPR KD = 0.078 μM, LE = 0.37, cell-free protein-protein interaction (PPI) IC50 = 0.48 μM (ELISA), cellular PPI IC50 = 8.6 μM (M2H)) by a structure-based design and structural integration with a second high-throughput screening hit.
Collapse
|