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Benin BM, Kharel R, Hillyer T, Sun C, Cmolik A, Kuebler T, Sham YY, Bonomo R, Mighion JD, Shin WS. Development of non-β-Lactam covalent allosteric inhibitors targeting PBP2a in Methicillin-Resistant Staphylococcus aureus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.29.596450. [PMID: 38853829 PMCID: PMC11160701 DOI: 10.1101/2024.05.29.596450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA), a Gram-positive bacterial pathogen, continues to pose a serious threat to the current public health system in our society. The high level of resistance to β-lactam antibiotics in MRSA is attributed to the expression of penicillin-binding protein 2a (PBP2a), which catalyzes cell wall cross-linking. According to numerous research reports, the activity of the PBP2a protein is known to be regulated by an allosteric site distinct from the active site where cell wall cross-linking occurs. Here, we conducted a screening of 113 compounds containing a 1,3,4-oxadiazole core to design new covalent inhibitors targeting the allosteric site of PBP2a and establish their structural-activity relationship. The stereochemically selective synthesis of sulfonyl oxadiazole compounds identified in the initial screening resulted in a maximum eightfold enhancement in cell inhibition activity. The sulfonyl oxadiazole-based compounds formulated as PEG-based ointments, with low toxicity test results on human cells (CC 50 : >78μM), demonstrated potent antimicrobial effects not only in a mouse skin wound infection model but also against oxacillin-resistant clinical isolate MRSA (IC 50 ≈ 1μM), as evidenced by the results. Furthermore, additional studies utilizing LC-MS/MS and in-silico approaches clearly support the allosteric site covalent binding mechanism through the nucleophilic aromatic substitution (S N Ar) reaction, as well as its association with the closure of the major active site of PBP2a.
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Nasser Binjawhar D, Abu Ali OA, Alqahtani AS, Fayad E, Abo-Bakr AM, Mekhael AM, Sadek FM. Powerful Approach for New Drugs as Antibacterial Agents via Molecular Docking and In Vitro Studies of Some New Cyclic Imides and Quinazoline-2,5-diones. ACS OMEGA 2024; 9:18566-18575. [PMID: 38680340 PMCID: PMC11044208 DOI: 10.1021/acsomega.4c01176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 03/19/2024] [Accepted: 03/27/2024] [Indexed: 05/01/2024]
Abstract
We generated novel elven 1,2,3,6-tetrahydrophthalimides and tetrahydroquinazoline derivatives from 1,2,3,6-tetrahydrophthalic anhydride (1) in response to our interest in using the anhydrides to produce heterocyclic nitrogen compounds. The elemental and spectral analyses of the produced compounds validated the recommended configurations and MOE 2014.09 (Molecular Operating Environment) computations were used to perform their in silico analysis. The synthesized compounds have been analyzed and put through various experiments, including in vitro and in silico methods to assess their biological activity against Escherichia coli Penicillin-Binding Protein 3 (PBP3) and Staphylococcus aureus Penicillin-Binding Protein 2 (PBP2), among these compounds showing promising data as antibacterial drugs.
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Affiliation(s)
- Dalal Nasser Binjawhar
- Department
of Chemistry, College of Science, Princess
Nourah Bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia
| | - Ola A. Abu Ali
- Department
of Chemistry, College of Science, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Arwa Sultan Alqahtani
- Department
of Chemistry, College of Science, Imam Mohammad
Ibn Saud Islamic University (IMSIU), P.O. Box 90950, Riyadh 11623, Saudi Arabia
| | - Eman Fayad
- Department
of Biotechnology, College of Sciences, Taif
University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Ahmed M. Abo-Bakr
- Chemistry
Department, Faculty of Science, South Valley
University, P.O. Box 83523, Qena 83523, Egypt
| | - Antonous. M. Mekhael
- Cotton Leaf
Worm Department, Plant Protection Research Institute, Agriculture Research Center, P.O. Box 12619, Giza 12611, Egypt
| | - Fayza M. Sadek
- Radiation
Sciences Department, Medical Research Institution, Alexandria University, P.O. Box 21500, Alexandria 5424041, Egypt
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Aribisala JO, S'thebe NW, Sabiu S. In silico exploration of phenolics as modulators of penicillin binding protein (PBP) 2× of Streptococcus pneumoniae. Sci Rep 2024; 14:8788. [PMID: 38627456 PMCID: PMC11021432 DOI: 10.1038/s41598-024-59489-3] [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: 02/03/2024] [Accepted: 04/11/2024] [Indexed: 04/19/2024] Open
Abstract
Infections caused by multidrug-resistant Streptococcus pneumoniae remain the leading cause of pneumonia-related deaths in children < 5 years globally, and mutations in penicillin-binding protein (PBP) 2 × have been identified as the major cause of resistance in the organism to beta-lactams. Thus, the development of new modulators with enhanced binding of PBP2x is highly encouraged. In this study, phenolics, due to their reported antibacterial activities, were screened against the active site of PBP2x using structure-based pharmacophore and molecular docking techniques, and the ability of the top-hit phenolics to inhibit the active and allosteric sites of PBP2x was refined through 120 ns molecular dynamic simulation. Except for gallocatechin gallate and lysidicichin, respectively, at the active and allosteric sites of PBP2x, the top-hit phenolics had higher negative binding free energy (ΔGbind) than amoxicillin [active site (- 19.23 kcal/mol), allosteric site (- 33.75 kcal/mol)]. Although silicristin had the best broad-spectrum effects at the active (- 38.41 kcal/mol) and allosteric (- 50.54 kcal/mol) sites of PBP2x, the high thermodynamic entropy (4.90 Å) of the resulting complex might suggest the need for its possible structural refinement for enhanced potency. Interestingly, silicristin had a predicted synthetic feasibility score of < 5 and quantum calculations using the DFT B3LYP/6-31G+ (dp) revealed that silicristin is less stable and more reactive than amoxicillin. These findings point to the possible benefits of the top-hit phenolics, and most especially silicristin, in the direct and synergistic treatment of infections caused by S. pneumoniae. Accordingly, silicristin is currently the subject of further confirmatory in vitro research.
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Affiliation(s)
- Jamiu Olaseni Aribisala
- Department of Biotechnology and Food Science, Faculty of Applied Sciences, Durban University of Technology, P.O. Box 1334, Durban, 4000, South Africa
| | - Nosipho Wendy S'thebe
- Department of Biotechnology and Food Science, Faculty of Applied Sciences, Durban University of Technology, P.O. Box 1334, Durban, 4000, South Africa
| | - Saheed Sabiu
- Department of Biotechnology and Food Science, Faculty of Applied Sciences, Durban University of Technology, P.O. Box 1334, Durban, 4000, South Africa.
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Jiao F, Cui W, Wang P, Tong HHY, Guo J, Tao J. Synergistic inhibition mechanism of quinazolinone and piperacillin on penicillin-binding protein 2a: a promising approach for combating methicillin-resistant Staphylococcus aureus. J Biomol Struct Dyn 2024:1-13. [PMID: 38497736 DOI: 10.1080/07391102.2024.2330708] [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: 01/21/2024] [Accepted: 03/09/2024] [Indexed: 03/19/2024]
Abstract
The production of penicillin-binding protein 2a (PBP2a), a cell wall synthesis protein, is primarily responsible for the high-level resistance observed in methicillin-resistant Staphylococcus aureus (MRSA). PBP2a exhibits a significantly reduced affinity for most β-lactam antibiotics owing to its tightly closed active site. Quinazolinones (QNE), a novel class of non-β-lactam antibiotics, could initiate the allosteric regulation of PBP2a, resulting in the opening of the initially closed active pocket. Based on our previous study, we have a basic understanding of the dual-site inhibitor ceftaroline (CFT) induced allosteric regulation of PBP2a. However, there are still limitations in the knowledge of how combining medicines, QNE and piperacillin (PIP), induce the allosteric response of PBP2a and inhibit its function. Herein, molecular dynamics (MD) simulations were performed to elucidate the intricate mechanisms underlying the combination mode of QNE and PIP. Our study successfully captured the opening process of the active pocket upon the binding of the QNE at the allosteric site, which alters the signaling pathways with a favorable transmission to the active site. Subsequent docking experiments with different conformational states of the active pocket indicated that all three inhibitors, PIP, QNE, and CFT, exhibited higher docking scores and more favorable docking poses to the open active pocket. These findings reveal the implied mechanism of QNE-mediated allostery underlying combination therapy and provide novel insights into developing innovative therapeutic modalities against MRSA.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Fangfang Jiao
- Centre in Artificial Intelligence Driven Drug Discovery, Faculty of Applied Sciences, Macao Polytechnic University, Macao, China
| | - Weirong Cui
- Centre in Artificial Intelligence Driven Drug Discovery, Faculty of Applied Sciences, Macao Polytechnic University, Macao, China
| | - Pinkai Wang
- Department of Orthopedics, Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Henry H Y Tong
- Centre in Artificial Intelligence Driven Drug Discovery, Faculty of Applied Sciences, Macao Polytechnic University, Macao, China
| | - Jingjing Guo
- Centre in Artificial Intelligence Driven Drug Discovery, Faculty of Applied Sciences, Macao Polytechnic University, Macao, China
- Engineering Research Centre of Applied Technology on Machine Translation and Artificial Intelligence, Macao Polytechnic University, Macao, China
| | - Jun Tao
- Department of Orthopedics, Second Affiliated Hospital of Nanchang University, Nanchang, China
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Jacobs LMC, Consol P, Chen Y. Drug Discovery in the Field of β-Lactams: An Academic Perspective. Antibiotics (Basel) 2024; 13:59. [PMID: 38247618 PMCID: PMC10812508 DOI: 10.3390/antibiotics13010059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 12/21/2023] [Accepted: 12/23/2023] [Indexed: 01/23/2024] Open
Abstract
β-Lactams are the most widely prescribed class of antibiotics that inhibit penicillin-binding proteins (PBPs), particularly transpeptidases that function in peptidoglycan synthesis. A major mechanism of antibiotic resistance is the production of β-lactamase enzymes, which are capable of hydrolyzing β-lactam antibiotics. There have been many efforts to counter increasing bacterial resistance against β-lactams. These studies have mainly focused on three areas: discovering novel inhibitors against β-lactamases, developing new β-lactams less susceptible to existing resistance mechanisms, and identifying non-β-lactam inhibitors against cell wall transpeptidases. Drug discovery in the β-lactam field has afforded a range of research opportunities for academia. In this review, we summarize the recent new findings on both β-lactamases and cell wall transpeptidases because these two groups of enzymes are evolutionarily and functionally connected. Many efforts to develop new β-lactams have aimed to inhibit both transpeptidases and β-lactamases, while several promising novel β-lactamase inhibitors have shown the potential to be further developed into transpeptidase inhibitors. In addition, the drug discovery progress against each group of enzymes is presented in three aspects: understanding the targets, screening methodology, and new inhibitor chemotypes. This is to offer insights into not only the advancement in this field but also the challenges, opportunities, and resources for future research. In particular, cyclic boronate compounds are now capable of inhibiting all classes of β-lactamases, while the diazabicyclooctane (DBO) series of small molecules has led to not only new β-lactamase inhibitors but potentially a new class of antibiotics by directly targeting PBPs. With the cautiously optimistic successes of a number of new β-lactamase inhibitor chemotypes and many questions remaining to be answered about the structure and function of cell wall transpeptidases, non-β-lactam transpeptidase inhibitors may usher in the next exciting phase of drug discovery in this field.
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Affiliation(s)
| | | | - Yu Chen
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA; (L.M.C.J.); (P.C.)
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Jiao F, Bao Y, Li M, Zhang Y, Zhang F, Wang P, Tao J, Tong HHY, Guo J. Unraveling the mechanism of ceftaroline-induced allosteric regulation in penicillin-binding protein 2a: insights for novel antibiotic development against methicillin-resistant Staphylococcus aureus. Antimicrob Agents Chemother 2023; 67:e0089523. [PMID: 37971241 PMCID: PMC10720500 DOI: 10.1128/aac.00895-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 10/11/2023] [Indexed: 11/19/2023] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) acquires high-level resistance against β-lactam antibiotics by expressing penicillin-binding protein 2a (PBP2a). PBP2a is a cell wall-synthesizing protein whose closed active site exhibits a reduced binding affinity toward β-lactam antibiotics. Ceftaroline (CFT), a fifth-generation cephalosporin, can effectively inhibit the PBP2a activity by binding to an allosteric site to trigger the active site opening, allowing a second CFT to access the active site. However, the essential mechanism behind the allosteric behavior of PBP2a remains unclear. Herein, computational simulations are employed to elucidate how CFT allosterically regulates the conformation and dynamics of the active site of PBP2a. While CFT stabilizes the allosteric domain surrounding it, it simultaneously enhances the dynamics of the catalytic domain. Specifically, the study successfully captured the opening process of the active pocket in the allosteric CFT-bound systems and discovered that CFT alters the potential signal-propagating pathways from the allosteric site to the active site. These findings reveal the implied mechanism of the CFT-mediated allostery in PBP2a and provide new insights into dual-site drug design or combination therapy against MRSA targeting PBP2a.
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Affiliation(s)
- Fangfang Jiao
- Centre in Artificial Intelligence Driven Drug Discovery, Faculty of Applied Sciences, Macao Polytechnic University, Macao, China
| | - Yiqiong Bao
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Mengrong Li
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Yan Zhang
- School of Pharmacy, Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Feng Zhang
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Pinkai Wang
- Department of Orthopedics, Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Jun Tao
- Department of Orthopedics, Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Henry H. Y. Tong
- Centre in Artificial Intelligence Driven Drug Discovery, Faculty of Applied Sciences, Macao Polytechnic University, Macao, China
| | - Jingjing Guo
- Centre in Artificial Intelligence Driven Drug Discovery, Faculty of Applied Sciences, Macao Polytechnic University, Macao, China
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7
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Witek K, Kaczor A, Żesławska E, Podlewska S, Marć MA, Czarnota-Łydka K, Nitek W, Latacz G, Tejchman W, Bischoff M, Jacob C, Handzlik J. Chalcogen-Varied Imidazolone Derivatives as Antibiotic Resistance Breakers in Staphylococcus aureus Strains. Antibiotics (Basel) 2023; 12:1618. [PMID: 37998820 PMCID: PMC10669504 DOI: 10.3390/antibiotics12111618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 09/25/2023] [Accepted: 11/06/2023] [Indexed: 11/25/2023] Open
Abstract
In this study, a search for new therapeutic agents that may improve the antibacterial activity of conventional antibiotics and help to successfully overcome methicillin-resistant Staphylococcus aureus (MRSA) infections has been conducted. The purpose of this work was to extend the scope of our preliminary studies and to evaluate the adjuvant potency of new derivatives in a set of S. aureus clinical isolates. The study confirmed the high efficacy of piperazine derivatives of 5-arylideneimidazol-4-one (7-9) tested previously, and it enabled the authors to identify even more efficient modulators of bacterial resistance among new analogs. The greatest capacity to enhance oxacillin activity was determined for 1-benzhydrylpiperazine 5-spirofluorenehydantoin derivative (13) which, at concentrations as low as 0.0625 mM, restores the effectiveness of β-lactam antibiotics against MRSA strains. In silico studies showed that the probable mechanism of action of 13 is related to the binding of the molecule with the allosteric site of PBP2a. Interestingly, thiazole derivatives tested were shown to act as both oxacillin and erythromycin conjugators in S. aureus isolates, suggesting a complex mode of action (i.e., influence on the Msr(A) efflux pump). This high enhancer activity indicates the high potential of imidazolones to become commercially available antibiotic adjuvants.
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Affiliation(s)
- Karolina Witek
- Department of Technology and Biotechnology of Drugs, Jagiellonian University Medical College, Medyczna 9, 30-688 Krakow, Poland; (K.W.); (A.K.); (S.P.); (M.A.M.); (K.C.-Ł.); (G.L.)
- Department of Pharmaceutical Microbiology, Jagiellonian University Medical College, Medyczna 9, 30-688 Krakow, Poland
- Bioorganic Chemistry, School of Pharmacy, University of Saarland, Campus B2.1, D-66123 Saarbrüecken, Germany;
- Institute of Medical Microbiology and Hygiene, Saarland University, D-66421 Homburg, Germany;
| | - Aneta Kaczor
- Department of Technology and Biotechnology of Drugs, Jagiellonian University Medical College, Medyczna 9, 30-688 Krakow, Poland; (K.W.); (A.K.); (S.P.); (M.A.M.); (K.C.-Ł.); (G.L.)
| | - Ewa Żesławska
- Institute of Biology and Earth Sciences, Pedagogical University of Krakow, Podchorążych 2, 30-084 Krakow, Poland; (E.Ż.); (W.T.)
| | - Sabina Podlewska
- Department of Technology and Biotechnology of Drugs, Jagiellonian University Medical College, Medyczna 9, 30-688 Krakow, Poland; (K.W.); (A.K.); (S.P.); (M.A.M.); (K.C.-Ł.); (G.L.)
- Maj Institute of Pharmacology, Polish Academy of Sciences, Smętna 12, 31-343 Krakow, Poland
| | - Małgorzata Anna Marć
- Department of Technology and Biotechnology of Drugs, Jagiellonian University Medical College, Medyczna 9, 30-688 Krakow, Poland; (K.W.); (A.K.); (S.P.); (M.A.M.); (K.C.-Ł.); (G.L.)
| | - Kinga Czarnota-Łydka
- Department of Technology and Biotechnology of Drugs, Jagiellonian University Medical College, Medyczna 9, 30-688 Krakow, Poland; (K.W.); (A.K.); (S.P.); (M.A.M.); (K.C.-Ł.); (G.L.)
- Doctoral School of Medical and Health Sciences, Jagiellonian University Medical College, Św. Łazarza 15, 31-530 Krakow, Poland
| | - Wojciech Nitek
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland;
| | - Gniewomir Latacz
- Department of Technology and Biotechnology of Drugs, Jagiellonian University Medical College, Medyczna 9, 30-688 Krakow, Poland; (K.W.); (A.K.); (S.P.); (M.A.M.); (K.C.-Ł.); (G.L.)
| | - Waldemar Tejchman
- Institute of Biology and Earth Sciences, Pedagogical University of Krakow, Podchorążych 2, 30-084 Krakow, Poland; (E.Ż.); (W.T.)
| | - Markus Bischoff
- Institute of Medical Microbiology and Hygiene, Saarland University, D-66421 Homburg, Germany;
| | - Claus Jacob
- Bioorganic Chemistry, School of Pharmacy, University of Saarland, Campus B2.1, D-66123 Saarbrüecken, Germany;
| | - Jadwiga Handzlik
- Department of Technology and Biotechnology of Drugs, Jagiellonian University Medical College, Medyczna 9, 30-688 Krakow, Poland; (K.W.); (A.K.); (S.P.); (M.A.M.); (K.C.-Ł.); (G.L.)
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Oliveira LPS, Lima LR, Silva LB, Cruz JN, Ramos RS, Lima LS, Cardoso FMN, Silva AV, Rodrigues DP, Rodrigues GS, Proietti-Junior AA, dos Santos GB, Campos JM, Santos CBR. Hierarchical Virtual Screening of Potential New Antibiotics from Polyoxygenated Dibenzofurans against Staphylococcus aureus Strains. Pharmaceuticals (Basel) 2023; 16:1430. [PMID: 37895901 PMCID: PMC10610096 DOI: 10.3390/ph16101430] [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: 08/16/2023] [Revised: 09/25/2023] [Accepted: 10/01/2023] [Indexed: 10/29/2023] Open
Abstract
Staphylococcus aureus is a microorganism with high morbidity and mortality due to antibiotic-resistant strains, making the search for new therapeutic options urgent. In this context, computational drug design can facilitate the drug discovery process, optimizing time and resources. In this work, computational methods involving ligand- and structure-based virtual screening were employed to identify potential antibacterial agents against the S. aureus MRSA and VRSA strains. To achieve this goal, tetrahydroxybenzofuran, a promising antibacterial agent according to in vitro tests described in the literature, was adopted as the pivotal molecule and derivative molecules were considered to generate a pharmacophore model, which was used to perform virtual screening on the Pharmit platform. Through this result, twenty-four molecules were selected from the MolPort® database. Using the Tanimoto Index on the BindingDB web server, it was possible to select eighteen molecules with greater structural similarity in relation to commercial antibiotics (methicillin and oxacillin). Predictions of toxicological and pharmacokinetic properties (ADME/Tox) using the eighteen most similar molecules, showed that only three exhibited desired properties (LB255, LB320 and LB415). In the molecular docking study, the promising molecules LB255, LB320 and LB415 showed significant values in both molecular targets. LB320 presented better binding affinity to MRSA (-8.18 kcal/mol) and VRSA (-8.01 kcal/mol) targets. Through PASS web server, the three molecules, specially LB320, showed potential for antibacterial activity. Synthetic accessibility (SA) analysis performed on AMBIT and SwissADME web servers showed that LB255 and LB415 can be considered difficult to synthesize and LB320 is considered easy. In conclusion, the results suggest that these ligands, particularly LB320, may bind strongly to the studied targets and may have appropriate ADME/Tox properties in experimental studies.
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Affiliation(s)
- Lana P. S. Oliveira
- Graduate Program in Biotechnology and Biodiversity-Network BIONORTE, Federal University of Amapá, Macapá 68903-419, Brazil; (L.P.S.O.); (R.S.R.); (F.M.N.C.); (A.V.S.); (A.A.P.-J.)
- Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapá 68902-280, Brazil; (L.R.L.); (L.B.S.); (J.N.C.)
| | - Lúcio R. Lima
- Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapá 68902-280, Brazil; (L.R.L.); (L.B.S.); (J.N.C.)
- Graduate Program in Network in Pharmaceutical Innovation, Federal University of Amapá, Macapá 68902-280, Brazil
- Graduate Program in Medicinal Chemistry and Molecular Modeling, Health Science Institute, Federal Univesity of Pará, Belém 66075-110, Brazil
| | - Luciane B. Silva
- Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapá 68902-280, Brazil; (L.R.L.); (L.B.S.); (J.N.C.)
- Graduate Program in Medicinal Chemistry and Molecular Modeling, Health Science Institute, Federal Univesity of Pará, Belém 66075-110, Brazil
| | - Jorddy N. Cruz
- Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapá 68902-280, Brazil; (L.R.L.); (L.B.S.); (J.N.C.)
| | - Ryan S. Ramos
- Graduate Program in Biotechnology and Biodiversity-Network BIONORTE, Federal University of Amapá, Macapá 68903-419, Brazil; (L.P.S.O.); (R.S.R.); (F.M.N.C.); (A.V.S.); (A.A.P.-J.)
- Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapá 68902-280, Brazil; (L.R.L.); (L.B.S.); (J.N.C.)
| | - Luciana S. Lima
- Special Laboratory of Applied Microbiology, Department of Biological and Health Sciences, Federal University of Amapá, Macapá 68902-280, Brazil;
| | - Francy M. N. Cardoso
- Graduate Program in Biotechnology and Biodiversity-Network BIONORTE, Federal University of Amapá, Macapá 68903-419, Brazil; (L.P.S.O.); (R.S.R.); (F.M.N.C.); (A.V.S.); (A.A.P.-J.)
- Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapá 68902-280, Brazil; (L.R.L.); (L.B.S.); (J.N.C.)
- Special Laboratory of Applied Microbiology, Department of Biological and Health Sciences, Federal University of Amapá, Macapá 68902-280, Brazil;
| | - Aderaldo V. Silva
- Graduate Program in Biotechnology and Biodiversity-Network BIONORTE, Federal University of Amapá, Macapá 68903-419, Brazil; (L.P.S.O.); (R.S.R.); (F.M.N.C.); (A.V.S.); (A.A.P.-J.)
- Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapá 68902-280, Brazil; (L.R.L.); (L.B.S.); (J.N.C.)
| | - Dália P. Rodrigues
- Laboratory of Bacterial Enteric Pathogens, Oswaldo Cruz Foundation, FIOCRUZ, Rio de Janeiro 21045-900, Brazil;
| | - Gabriela S. Rodrigues
- Graduate Program in Health Sciences, Institute of Collective Health, Federal University of Western Pará, Santarém 68270-000, Brazil; (G.S.R.); (G.B.d.S.)
| | - Aldo A. Proietti-Junior
- Graduate Program in Biotechnology and Biodiversity-Network BIONORTE, Federal University of Amapá, Macapá 68903-419, Brazil; (L.P.S.O.); (R.S.R.); (F.M.N.C.); (A.V.S.); (A.A.P.-J.)
- Special Laboratory of Applied Microbiology, Department of Biological and Health Sciences, Federal University of Amapá, Macapá 68902-280, Brazil;
| | - Gabriela B. dos Santos
- Graduate Program in Health Sciences, Institute of Collective Health, Federal University of Western Pará, Santarém 68270-000, Brazil; (G.S.R.); (G.B.d.S.)
| | - Joaquín M. Campos
- Department of Pharmaceutical and Organic Chemistry, Faculty of Pharmacy, Institute of Biosanitary Research ibs. GRANADA, University of Granada, 18071 Granada, Spain;
| | - Cleydson B. R. Santos
- Graduate Program in Biotechnology and Biodiversity-Network BIONORTE, Federal University of Amapá, Macapá 68903-419, Brazil; (L.P.S.O.); (R.S.R.); (F.M.N.C.); (A.V.S.); (A.A.P.-J.)
- Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapá 68902-280, Brazil; (L.R.L.); (L.B.S.); (J.N.C.)
- Graduate Program in Network in Pharmaceutical Innovation, Federal University of Amapá, Macapá 68902-280, Brazil
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9
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Martínez-Caballero S, Freton C, Molina R, Bartual SG, Gueguen-Chaignon V, Mercy C, Gago F, Mahasenan KV, Muñoz IG, Lee M, Hesek D, Mobashery S, Hermoso JA, Grangeasse C. Molecular basis of the final step of cell division in Streptococcus pneumoniae. Cell Rep 2023; 42:112756. [PMID: 37418323 PMCID: PMC10434722 DOI: 10.1016/j.celrep.2023.112756] [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: 02/02/2023] [Revised: 05/13/2023] [Accepted: 06/21/2023] [Indexed: 07/09/2023] Open
Abstract
Bacterial cell-wall hydrolases must be tightly regulated during bacterial cell division to prevent aberrant cell lysis and to allow final separation of viable daughter cells. In a multidisciplinary work, we disclose the molecular dialogue between the cell-wall hydrolase LytB, wall teichoic acids, and the eukaryotic-like protein kinase StkP in Streptococcus pneumoniae. After characterizing the peptidoglycan recognition mode by the catalytic domain of LytB, we further demonstrate that LytB possesses a modular organization allowing the specific binding to wall teichoic acids and to the protein kinase StkP. Structural and cellular studies notably reveal that the temporal and spatial localization of LytB is governed by the interaction between specific modules of LytB and the final PASTA domain of StkP. Our data collectively provide a comprehensive understanding of how LytB performs final separation of daughter cells and highlights the regulatory role of eukaryotic-like kinases on lytic machineries in the last step of cell division in streptococci.
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Affiliation(s)
- Siseth Martínez-Caballero
- Department of Crystallography and Structural Biology, Instituto de Química-Física "Rocasolano," Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Céline Freton
- Molecular Microbiology and Structural Biochemistry, UMR 5086, Université de Lyon, CNRS, Lyon, France
| | - Rafael Molina
- Department of Crystallography and Structural Biology, Instituto de Química-Física "Rocasolano," Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Sergio G Bartual
- Department of Crystallography and Structural Biology, Instituto de Química-Física "Rocasolano," Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | | | - Chryslène Mercy
- Molecular Microbiology and Structural Biochemistry, UMR 5086, Université de Lyon, CNRS, Lyon, France
| | - Federico Gago
- Department of Biomedical Sciences & Instituto de Química Médica-CSIC Associated Unit, School of Medicine and Health Sciences, University of Alcalá, 28805 Alcalá de Henares, Spain
| | - Kiran V Mahasenan
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Inés G Muñoz
- Structural Biology Program, Spanish National Cancer Research Center (CNIO), 28029 Madrid, Spain
| | - Mijoon Lee
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Dusan Hesek
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Shahriar Mobashery
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Juan A Hermoso
- Department of Crystallography and Structural Biology, Instituto de Química-Física "Rocasolano," Consejo Superior de Investigaciones Científicas, Madrid, Spain.
| | - Christophe Grangeasse
- Molecular Microbiology and Structural Biochemistry, UMR 5086, Université de Lyon, CNRS, Lyon, France.
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10
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Farid N, Bux K, Ali K, Bashir A, Tahir R. Repurposing Amphotericin B: anti-microbial, molecular docking and molecular dynamics simulation studies suggest inhibition potential of Amphotericin B against MRSA. BMC Chem 2023; 17:67. [PMID: 37386581 DOI: 10.1186/s13065-023-00980-9] [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: 04/14/2023] [Accepted: 06/21/2023] [Indexed: 07/01/2023] Open
Abstract
Amphotericin B (AMPH) is an anti-fungal drug and this study, for the first time as best of our knowledge, reports the repurposing of the Amphotericin B. The drug was found to show significant antibacterial potential revealed by antimicrobial screening, molecular docking, and mode of action analysis targeting Penicillin Binding Protein 2a (PBP 2a protein) which is target of β-lactam drugs and is involved in cell wall synthesis. Mode of action analysis showed the drug to have hydrophobic and hydrophilic interactions with both C-terminal, trans-peptidase and non-penicillin binding domain of the protein. Additionally, to evaluate the impact of ligand binding on the protein's conformational dynamics, molecular dynamics (MD) simulations were used. Comparative Dynamical flexibility (RMSF) and Dynamics Cross Correlation (DCCM) followed by MD simulations revealed the complex formation significantly effecting structural dynamics of the enzyme significantly in the non-penicillin binding domain (327-668) and slightly in trans peptidase domain. Radius of gyration assessment further showed ligand binding also decreasing over all compactness of protein. Secondary structure analysis indicated the complex formation changing the conformational integrity in non-penicillin binding domain. Hydrogen bond analysis and MMPBSA, free energy of calculations followed by MD simulations, also complemented the antimicrobial and molecular docking revelations suggesting Amphotericin B to have substantial antibacterial potential.
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Affiliation(s)
- Neha Farid
- Department of Biosciences, Faculty of Life Sciences, Shaheed Zulfikar Ali Bhutto Institute of Science and Technology (SZABIST), Karachi, Pakistan.
| | - Khair Bux
- Department of Biosciences, Faculty of Life Sciences, Shaheed Zulfikar Ali Bhutto Institute of Science and Technology (SZABIST), Karachi, Pakistan.
| | - Kashif Ali
- Department of Biosciences, Faculty of Life Sciences, Shaheed Zulfikar Ali Bhutto Institute of Science and Technology (SZABIST), Karachi, Pakistan
| | - Asma Bashir
- Department of Biosciences, Faculty of Life Sciences, Shaheed Zulfikar Ali Bhutto Institute of Science and Technology (SZABIST), Karachi, Pakistan
| | - Rahima Tahir
- Department of Biosciences, Faculty of Life Sciences, Shaheed Zulfikar Ali Bhutto Institute of Science and Technology (SZABIST), Karachi, Pakistan
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11
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Harras MF, Sabour R, Farghaly TA, Ibrahim MH. Drug Repurposing Approach in Developing New Furosemide Analogs as Antimicrobial Candidates and Anti-PBP: Design, Synthesis, and Molecular Docking. Bioorg Chem 2023; 137:106585. [PMID: 37163813 DOI: 10.1016/j.bioorg.2023.106585] [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: 12/22/2022] [Revised: 04/09/2023] [Accepted: 05/01/2023] [Indexed: 05/12/2023]
Abstract
Multidrug-resistant microorganisms have become a global health problem, prompting research into new antimicrobials. Drug repurposing is a new technique in drug discovery used to improve drug development success. As a well-studied medication with a sulfonamide moiety, furosemide was chosen to study its antimicrobial effect on different microbial strains. In addition, a new family of furosemide analogs was investigated for their antimicrobial efficacy. According to the obtained results, the majority of the examined molecules exhibited potential antimicrobial activity. Compounds 3b and 4a had the best anti-MRSA results, with an MIC = 7.81 µg/mL. They also demonstrated potent anti-gram-negative activity against E. coli (MIC = 1.95 µg/mL and 3.91 µg/mL, respectively). A time-killing kinetics study against E. coli and MRSA showed bactericidal actions of 3b and 4a within 120-150 min. Moreover, an anti-PBP activity and an in vitro cytotoxicity evaluation were performed. Furosemide decreased the PBP2a levels in MRSA by 21.5% compared to the control. However, the furosemide analogs 3b and 4a demonstrated superior anti-PBP activity (55.9 and 57.1 % reduction in the expression of PBP2a, respectively). In addition, compound 4a was nearly nontoxic to normal WI-38 cells (IC50 = 248.60 μg /mL) indicating its high safety profile. Finally, the ability of furosemide and compounds 3b and 4a to bind to the target PBP2a enzyme has also been supported by molecular docking research.
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Affiliation(s)
- Marwa F Harras
- Department of Pharmaceutical Medicinal Chemistry and Drug Design, Faculty of Pharmacy (Girls), Al-Azhar University, Cairo, Egypt
| | - Rehab Sabour
- Department of Pharmaceutical Medicinal Chemistry and Drug Design, Faculty of Pharmacy (Girls), Al-Azhar University, Cairo, Egypt
| | - Thoraya A Farghaly
- Department of Chemistry, Faculty of Applied Science, Umm Al-Qura University, Makkah 24230, Saudi Arabia
| | - Mona H Ibrahim
- Department of Pharmaceutical Medicinal Chemistry and Drug Design, Faculty of Pharmacy (Girls), Al-Azhar University, Cairo, Egypt
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12
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Alhamwi AB, Atilgan C, Sensoy O. Nonlocal Effects of Antibiotic-Resistance-Causing Mutations Reveal an Alternative Region for Targeting on FtsW-Penicillin-Binding Protein 3 Complex of Haemophilus influenzae. J Chem Inf Model 2023; 63:3094-3104. [PMID: 37141552 DOI: 10.1021/acs.jcim.3c00127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Currently prescribed antibiotics target the catalytic sites of wild-type bacterial proteins; however, bacteria adopt mutations at this site, eventually leading to the emergence of resistance. Therefore, the identification of alternative drug binding sites is crucial, which requires knowledge of the dynamics of the mutant protein. Here, we set out to investigate the impact of a high-resistance-causing triple mutation (S385T + L389F + N526K) on the dynamics of a prioritized resistant pathogen, Haemophilus influenzae, using computational techniques. We studied penicillin-binding protein 3 (PBP3) and its complex with FtsW, which display resistance toward β-lactam antibiotics. We showed that mutations displayed local and nonlocal effects. In terms of the former, the orientation of the β-sheet, which surrounds the active site of PBP3, was impacted and the catalytic site was exposed to the periplasmic region. In addition, the flexibility of the β3-β4 loop, which modulates the catalysis of the enzyme, increased in the mutant FtsW-PBP3 complex. As for nonlocal effects, the dynamics of the pedestal domain (N-terminal periplasmic modulus (N-t)), i.e., the opening of the fork, was different between the wild-type and mutant enzymes. We showed the closed fork caused a greater number of residues to participate in the hypothesized allosteric communication network connecting N-t to the transpeptidase domain in the mutant enzyme. Finally, we demonstrated that the closed fork results in more favorable binding with β-lactam antibiotics, particularly cefixime, suggesting that small therapeutics that can stabilize the closed fork of mutant PBP3 may lead to the development of more effective molecules to combat resistant bacteria.
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Affiliation(s)
- Almotasem Belah Alhamwi
- Graduate School of Engineering and Natural Sciences, Istanbul Medipol University, 34810 Istanbul, Turkey
| | - Canan Atilgan
- Faculty of Engineering and Natural Sciences, Sabanci University, 34956 Istanbul, Turkey
| | - Ozge Sensoy
- Graduate School of Engineering and Natural Sciences, Istanbul Medipol University, 34810 Istanbul, Turkey
- Regenerative and Restorative Medicine Research Center (REMER), Research Institute for Health Sciences and Technologies (SABITA), Istanbul Medipol University, 34810 Istanbul, Turkey
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13
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Teixeira EH, Andrade AL, Pereira R, Farias LP, Monteiro GS, Marinho MM, Marinho ES, Santos HS, de Vasconcelos MA. Antimicrobial, Antibiofilm Activities and Synergic Effect of Triterpene 3β,6β,16β-trihydroxyilup-20(29)-ene Isolated from Combretum leprosum Leaves Against Staphylococcus Strains. Curr Microbiol 2023; 80:176. [PMID: 37029832 DOI: 10.1007/s00284-023-03284-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 03/23/2023] [Indexed: 04/09/2023]
Abstract
Antimicrobial resistance is a natural phenomenon and is becoming a huge global public health problem, since some microorganisms not respond to the treatment of several classes of antibiotics. The objective of the present study was to evaluate the antibacterial, antibiofilm, and synergistic effect of triterpene 3β,6β,16β-trihydroxyilup-20(29)-ene (CLF1) against Staphylococcus aureus and Staphylococcus epidermidis strains. Bacterial susceptibility to CLF1 was evaluated by minimum inhibitory concentration (MIC) and the minimum bactericidal concentration (MBC) assay. In addition, the effect combined with antibiotics (ampicillin and tetracycline) was verified by the checkerboard method. The biofilms susceptibility was assessed by enumeration of colony-forming units (CFUs) and quantification of total biomass by crystal violet staining. The compound showed bacteriostatic and bactericidal activity against all Staphylococcal strains tested. The synergistic effect with ampicillin was observed only for S. epidermidis strains. Moreover, CLF1 significantly inhibited the biofilm formation and disrupted preformed biofilm of the all strains. Scanning electron microscopy (SEM) images showed changes in the cell morphology and structure of S. aureus ATCC 700698 biofilms (a methicillin-resistant S. aureus strain). Molecular docking simulations showed that CLF1 has a more favorable interaction energy than the antibiotic ampicillin on penicillin-binding protein (PBP) 2a of MRSA, coupled in different regions of the protein. Based on the results obtained, CLF1 proved to be a promising antimicrobial compound against Staphylococcus biofilms.
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Affiliation(s)
- Edson Holanda Teixeira
- Laboratório Integrado de Biomoléculas, Departamento de Patologia e Medicina Legal, Universidade Federal do Ceará, Fortaleza, CE, Brazil.
| | - Alexandre Lopes Andrade
- Laboratório Integrado de Biomoléculas, Departamento de Patologia e Medicina Legal, Universidade Federal do Ceará, Fortaleza, CE, Brazil
| | - Rafael Pereira
- Laboratório Integrado de Biomoléculas, Departamento de Patologia e Medicina Legal, Universidade Federal do Ceará, Fortaleza, CE, Brazil
| | - Livia Pontes Farias
- Laboratório Integrado de Biomoléculas, Departamento de Patologia e Medicina Legal, Universidade Federal do Ceará, Fortaleza, CE, Brazil
| | - Gabrieli Sobral Monteiro
- Laboratório Integrado de Biomoléculas, Departamento de Patologia e Medicina Legal, Universidade Federal do Ceará, Fortaleza, CE, Brazil
| | - Marcia Machado Marinho
- Faculdade de Educação, Ciência e Letras de Iguatu, Universidade Estadual do Ceará, Iguatu, Ceará, Brazil
| | - Emmanuel Silva Marinho
- Faculdade de Filosofia Dom Aureliano Matos, Universidade Estadual do Ceará, Limoeiro do Norte, Ceará, Brazil
| | - Hélcio Silva Santos
- Centro de Ciências Exatas e Tecnologia, Universidade Estadual Vale do Acaraú, Sobral, Ceará, Brazil
| | - Mayron Alves de Vasconcelos
- Laboratório Integrado de Biomoléculas, Departamento de Patologia e Medicina Legal, Universidade Federal do Ceará, Fortaleza, CE, Brazil
- Universidade do Estado de Minas Gerais, Unidade de Divinopolis, Divinopolis, MG, 35501-179, Brazil
- Faculdade de Ciências Exatas e Naturais, Universidade do Estado do Rio Grande do Norte, Mossoró, RN, 59610-210, Brazil
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14
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Aribisala JO, Sabiu S. Cheminformatics Identification of Phenolics as Modulators of Penicillin-Binding Protein 2a of Staphylococcus aureus: A Structure–Activity-Relationship-Based Study. Pharmaceutics 2022; 14:pharmaceutics14091818. [PMID: 36145565 PMCID: PMC9503099 DOI: 10.3390/pharmaceutics14091818] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/24/2022] [Accepted: 08/26/2022] [Indexed: 01/16/2023] Open
Abstract
The acquisition of penicillin-binding protein (PBP) 2a in resistant strains of Staphylococcus aureus allows for the continuous production of cell walls even after the inactivation of intrinsic PBPs. Thus, the discovery of novel therapeutics with enhanced modulatory activity on PBP2a is crucial, and plant secondary metabolites, such as phenolics, have found relevance in this regard. In this study, using computational techniques, phenolics were screened against the active site of PBP2a, and the ability of the lead phenolics to modulate PBP2a’s active and allosteric sites was studied. The top-five phenolics (leads) identified through structure–activity-based screening, pharmacokinetics and synthetic feasibility evaluations were subjected to molecular dynamics simulations. Except for propan-2-one at the active site, the leads had a higher binding free energy at both the active and allosteric sites of PBP2a than amoxicillin. The leads, while promoting the thermodynamic stability of PBP2a, showed a more promising affinity at the allosteric site than the active site, with silicristin (−25.61 kcal/mol) and epicatechin gallate (−47.65 kcal/mol) having the best affinity at the active and allosteric sites, respectively. Interestingly, the modulation of Tyr446, the active site gatekeeper residue in PBP2a, was noted to correlate with the affinity of the leads at the allosteric site. Overall, these observations point to the leads’ ability to inhibit PBP2a, either directly or through allosteric modulation with conventional drugs. Further confirmatory in vitro studies on the leads are underway.
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15
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Lever J, Kreuder F, Henry J, Hung A, Allard PM, Brkljača R, Rix C, Taki AC, Gasser RB, Kaslin J, Wlodkowic D, Wolfender JL, Urban S. Targeted Isolation of Antibiotic Brominated Alkaloids from the Marine Sponge Pseudoceratina durissima Using Virtual Screening and Molecular Networking. Mar Drugs 2022; 20:md20090554. [PMID: 36135743 PMCID: PMC9503778 DOI: 10.3390/md20090554] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 08/22/2022] [Accepted: 08/25/2022] [Indexed: 11/23/2022] Open
Abstract
Many targeted natural product isolation approaches rely on the use of pre-existing bioactivity information to inform the strategy used for the isolation of new bioactive compounds. Bioactivity information can be available either in the form of prior assay data or via Structure Activity Relationship (SAR) information which can indicate a potential chemotype that exhibits a desired bioactivity. The work described herein utilizes a unique method of targeted isolation using structure-based virtual screening to identify potential antibacterial compounds active against MRSA within the marine sponge order Verongiida. This is coupled with molecular networking-guided, targeted isolation to provide a novel drug discovery procedure. A total of 12 previously reported bromotyrosine-derived alkaloids were isolated from the marine sponge species Pseudoceratina durissima, and the compound, (+)-aeroplysinin-1 (1) displayed activity against the MRSA pathogen (MIC: <32 µg/mL). The compounds (1−3, 6 and 9) were assessed for their central nervous system (CNS) interaction and behavioral toxicity to zebrafish (Danio rerio) larvae, whereby several of the compounds were shown to induce significant hyperactivity. Anthelmintic activity against the parasitic nematode Haemonchus contorutus was also evaluated (2−4, 6−8).
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Affiliation(s)
- James Lever
- School of Science (Applied Chemistry and Environmental Sciences), RMIT University, GPO Box 2476 Melbourne, VIC 3001, Australia
| | - Florian Kreuder
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia
| | - Jason Henry
- Neurotoxicology Lab., School of Science (Biosciences), RMIT University, Bundoora, VIC 3083, Australia
| | - Andrew Hung
- School of Science (Applied Chemistry and Environmental Sciences), RMIT University, GPO Box 2476 Melbourne, VIC 3001, Australia
| | | | - Robert Brkljača
- Monash Biomedical Imaging, Monash University, Clayton, VIC 3168, Australia
| | - Colin Rix
- School of Science (Applied Chemistry and Environmental Sciences), RMIT University, GPO Box 2476 Melbourne, VIC 3001, Australia
| | - Aya C. Taki
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agriculture Sciences, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Robin B. Gasser
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agriculture Sciences, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Jan Kaslin
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3800, Australia
| | - Donald Wlodkowic
- Neurotoxicology Lab., School of Science (Biosciences), RMIT University, Bundoora, VIC 3083, Australia
| | - Jean-Luc Wolfender
- School of Pharmaceutical Sciences of Western Switzerland, University of Geneva, CMU, Rue Michel-Servet 1, 1211 Geneva, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, CMU, 1211 Geneva, Switzerland
| | - Sylvia Urban
- School of Science (Applied Chemistry and Environmental Sciences), RMIT University, GPO Box 2476 Melbourne, VIC 3001, Australia
- Correspondence:
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16
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On the force field optimisation of [Formula: see text]-lactam cores using the force field Toolkit. J Comput Aided Mol Des 2022; 36:537-547. [PMID: 35819650 PMCID: PMC9399072 DOI: 10.1007/s10822-022-00464-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 06/21/2022] [Indexed: 11/29/2022]
Abstract
When employing molecular dynamics (MD) simulations for computer-aided drug design, the quality of the used force fields is highly important. Here we present reparametrisations of the force fields for the core molecules from 9 different \documentclass[12pt]{minimal}
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\begin{document}$$\beta$$\end{document}β-lactam classes, for which we utilized the force field Toolkit and Gaussian calculations. We focus on the parametrisation of the dihedral angles, with the goal of reproducing the optimised quantum geometry in MD simulations. Parameters taken from CGenFF turn out to be a good initial guess for the multiplicity of each dihedral angle, but the key to a successful parametrisation is found to lie in the phase shifts. Based on the optimised quantum geometry, we come up with a strategy for predicting the phase shifts prior to the dihedral potential fitting. This allows us to successfully parameterise 8 out of the 11 molecules studied here, while the remaining 3 molecules can also be parameterised with small adjustments. Our work highlights the importance of predicting the dihedral phase shifts in the ligand parametrisation protocol, and provides a simple yet valuable strategy for improving the process of parameterising force fields of drug-like molecules.
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17
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Li QQ, Chae HS, Kang OH, Kwon DY. Synergistic Antibacterial Activity with Conventional Antibiotics and Mechanism of Action of Shikonin against Methicillin-Resistant Staphylococcus aureus. Int J Mol Sci 2022; 23:ijms23147551. [PMID: 35886892 PMCID: PMC9322759 DOI: 10.3390/ijms23147551] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Revised: 07/01/2022] [Accepted: 07/06/2022] [Indexed: 12/11/2022] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) is a troublesome pathogen that poses a global threat to public health. Shikonin (SKN) isolated from Lithospermum erythrorhizon (L. erythrorhizon) possesses a variety of biological activities. This study aims to explore the effect of the combined application of SKN and traditional antibiotics on the vitality of MRSA and the inherent antibacterial mechanism of SKN. The synergies between SKN and antibiotics against MRSA and its clinical strain have been demonstrated by the checkerboard assay and the time-kill assay. The effect of SKN on disrupting the integrity and permeability of bacterial cell membranes was verified by a nucleotide and protein leakage assay and a bacteriolysis assay. As determined by crystal violet staining, SKN inhibited the biofilm formation of clinical MRSA strains. The results of Western blot and qRT-PCR showed that SKN could inhibit the expression of proteins and genes related to drug resistance and S. aureus exotoxins. SKN inhibited the ability of RAW264.7 cells to release the pro-inflammatory cytokines TNF-α and IL-6, as measured by ELISA. Our findings suggest that SKN has the potential to be developed as a promising alternative for the treatment of MRSA infections.
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Affiliation(s)
- Qian-Qian Li
- Department of Oriental Pharmacy, College of Pharmacy and Wonkwang Oriental Medicines Research Institute, Wonkwang University, Iksan 54538, Jeonbuk, Korea;
| | - Hee-Sung Chae
- National Center for Natural Products Research, School of Pharmacy, The University of Mississippi, Oxford, MS 38677, USA;
| | - Ok-Hwa Kang
- Department of Oriental Pharmacy, College of Pharmacy and Wonkwang Oriental Medicines Research Institute, Wonkwang University, Iksan 54538, Jeonbuk, Korea;
- Correspondence: (O.-H.K.); (D.-Y.K.); Tel.: +82-63-850-6802 (O.-H.K.)
| | - Dong-Yeul Kwon
- Department of Oriental Pharmacy, College of Pharmacy and Wonkwang Oriental Medicines Research Institute, Wonkwang University, Iksan 54538, Jeonbuk, Korea;
- Correspondence: (O.-H.K.); (D.-Y.K.); Tel.: +82-63-850-6802 (O.-H.K.)
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18
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The NaHCO 3-Responsive Phenotype in Methicillin-Resistant Staphylococcus aureus (MRSA) Is Influenced by mecA Genotype. Antimicrob Agents Chemother 2022; 66:e0025222. [PMID: 35575577 PMCID: PMC9211399 DOI: 10.1128/aac.00252-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) strains are a leading cause of many invasive clinical syndromes, and pose treatment difficulties due to their in vitro resistance to most β-lactams on standard laboratory testing. A novel phenotype frequently identified in MRSA strains, termed ‘NaHCO3-responsiveness’, is a property whereby strains are susceptible in vitro to many β-lactams in the presence of NaHCO3. Specific mecA genotypes, repression of mecA/PBP2a expression and perturbed maturation of PBP2a by NaHCO3 have all been associated with this phenotype. The aim of this study was to define the relationship between specific mecA genotypes and PBP2a substitutions, on the one hand, with NaHCO3-responsiveness in vitro. Mutations were made in the mecA ribosomal binding site (RBS -7) and at amino acid position 246 of its coding region in parental strains MW2 (NaHCO3-responsive) and C36 (NaHCO3- nonresponsive) to generate ‘swap’ variants, each harboring the other’s mecA-RBS/coding region genotypes. Successful swaps were confirmed by both sequencing, as well as predicted swap of in vitro penicillin-clavulanate susceptibility phenotypes. MW2 swap variants harboring the nonresponsive mecA genotypes became NaHCO3-nonresponsive (resistant to the β-lactam, oxacillin [OXA]), in the presence of NaHCO3. Moreover, these swap variants had lost NaHCO3-mediated repression of mecA/PBP2a expression. In contrast, C36 swap variants harboring the NaHCO3-responsive mecA genotypes remained NaHCO3-nonresponsive phenotypically, and still exhibited nonrepressible mecA/PBP2a expression. These data demonstrate that in addition to the mecA genotype, NaHCO3-responsiveness may also depend on strain-specific genetic backgrounds.
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19
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In Vitro and In Silico Antistaphylococcal Activity of Indole Alkaloids Isolated from Tabernaemontana cymosa Jacq (Apocynaceae). Sci Pharm 2022. [DOI: 10.3390/scipharm90020038] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The species of the genus Tabernaemontana have a long tradition of use in different pathologies of infectious origins; the antibacterial, antifungal, and antiviral effects related to the control of the pathologies where the species of this genus are used, have been attributed to the indole monoterpene alkaloids, mainly those of the iboga type. There are more than 1000 alkaloids isolated from different species of Tabernaemontana and other genera of the Apocynaceae family, several of which lack studies related to antibacterial activity. In the present study, four monoterpene indole alkaloids were isolated from the seeds of the species Tabernaemontana cymosa Jacq, namely voacangine (1), voacangine-7-hydroxyindolenine (2), 3-oxovoacangine (3), and rupicoline (4), which were tested in an in vitro antibacterial activity study against the bacteria S. aureus, sensitive and resistant to methicillin, and classified by the World Health Organization as critical for the investigation of new antibiotics. Of the four alkaloids tested, only voacangine was active against S. aureus, with an MIC of 50 µg/mL. In addition, an in silico study was carried out between the four isolated alkaloids and some proteins of this bacterium, finding that voacangine also showed binding to proteins involved in cell wall synthesis, mainly PBP2 and PBP2a.
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Choi Y, Park JS, Kim J, Min K, Mahasenan K, Kim C, Yoon HJ, Lim S, Cheon DH, Lee Y, Ryu S, Mobashery S, Kim BM, Lee HH. Structure-based inhibitor design for reshaping bacterial morphology. Commun Biol 2022; 5:395. [PMID: 35484224 PMCID: PMC9050674 DOI: 10.1038/s42003-022-03355-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 04/12/2022] [Indexed: 11/09/2022] Open
Abstract
The spiral shape of intestinal pathogen Campylobacter jejuni is critical for invasion of intestinal mucosa epithelial cells. Insofar as this cell morphology plays a role in the pathology of C. jejuni infection, its restructuring by pharmacological intervention could be an unexplored means to prevention of infection. We recently described that peptidoglycan hydrolase 3 (Pgp3) is involved in the spiral-shape formation of C. jejuni. We report herein the design and synthesis of the hydroxamate-based inhibitors targeting Pgp3. C. jejuni cells exposed to these inhibitors changed from the helical- to rod-shaped morphology, comparable to the case of the pgp3-deletion mutant. Evidence for the mechanism of action was provided by crystal structures of Pgp3 in complex with inhibitors, shedding light into the binding modes of inhibitors within the active site, supported by kinetics and molecular-dynamics simulations. C. jejuni exposed to these inhibitors underwent the morphological change from helical- to rod-shaped bacteria, an event that reduce the ability for invasion of the host cells. This proof of concept suggests that alteration of morphology affects the interference with the bacterial infection.
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Affiliation(s)
- Yuri Choi
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul, 08826, Korea
| | - Ji Su Park
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul, 08826, Korea
| | - Jinshil Kim
- Department of Food and Animal Biotechnology, Department of Agricultural Biotechnology, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Korea.,Center for Food and Bioconvergence, Seoul National University, Seoul, 08826, Korea
| | - Kyungjin Min
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul, 08826, Korea
| | - Kiran Mahasenan
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, 46556, United States
| | - Choon Kim
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, 46556, United States
| | - Hye-Jin Yoon
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul, 08826, Korea
| | - Sewon Lim
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul, 08826, Korea
| | - Dae Hee Cheon
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul, 08826, Korea
| | - Yan Lee
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul, 08826, Korea
| | - Sangryeol Ryu
- Department of Food and Animal Biotechnology, Department of Agricultural Biotechnology, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Korea.,Center for Food and Bioconvergence, Seoul National University, Seoul, 08826, Korea
| | - Shahriar Mobashery
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, 46556, United States.
| | - B Moon Kim
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul, 08826, Korea.
| | - Hyung Ho Lee
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul, 08826, Korea.
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21
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Ersoy SC, Chan LC, Yeaman MR, Chambers HF, Proctor RA, Ludwig KC, Schneider T, Manna AC, Cheung A, Bayer AS. Impacts of NaHCO3 on β-Lactam Binding to PBP2a Protein Variants Associated with the NaHCO3-Responsive versus NaHCO3-Non-Responsive Phenotypes. Antibiotics (Basel) 2022; 11:antibiotics11040462. [PMID: 35453214 PMCID: PMC9028190 DOI: 10.3390/antibiotics11040462] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/23/2022] [Accepted: 03/26/2022] [Indexed: 12/13/2022] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) regulates resistance to β-lactams via preferential production of an alternative penicillin-binding protein (PBP), PBP2a. PBP2a binds many β-lactam antibiotics with less affinity than PBPs which are predominant in methicillin-susceptible (MSSA) strains. A novel, rather frequent in vitro phenotype was recently identified among clinical MRSA bloodstream isolates, termed “NaHCO3-responsiveness”. This phenotype features β-lactam susceptibility of certain MRSA strains only in the presence of NaHCO3. Two distinct PBP2a variants, 246G and 246E, have been linked to the NaHCO3-responsive and NaHCO3-non-responsive MRSA phenotypes, respectively. To determine the mechanistic impact of PBP2a variants on β-lactam susceptibility, binding profiles of a fluorescent penicillin probe (Bocillin-FL) to each purified PBP2a variant were assessed and compared to whole-cell binding profiles characterized by flow cytometry in the presence vs. absence of NaHCO3. These investigations revealed that NaHCO3 differentially influenced the binding of the fluorescent penicillin, Bocillin-FL, to the PBP2a variants, with binding intensity and rate of binding significantly enhanced in the 246G compared to the 246E variant. Of note, the NaHCO3-β-lactam (oxacillin)-responsive JE2 strain, which natively harbors the 246G variant, had enhanced Bocillin-FL whole-cell binding following exposure to NaHCO3. This NaHCO3-mediated increase in whole-cell Bocillin-FL binding was not observed in the NaHCO3-non-responsive parental strain, COL, which contains the 246E PBP2a variant. Surprisingly, genetic swaps of the mecA coding sites between JE2 and COL did not alter the NaHCO3-enhanced binding seen in JE2 vs. COL. These data suggest that the non-coding regions of mecA may be involved in NaHCO3-responsiveness. This investigation also provides strong evidence that the NaHCO3-responsive phenotype in MRSA may involve NaHCO3-mediated increases in both initial cell surface β-lactam binding, as well as ultimate PBP2a binding of β-lactams.
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Affiliation(s)
- Selvi C. Ersoy
- The Lundquist Institute for Biomedical Innovation, Harbor-UCLA Medical Center, Torrance, CA 90502, USA; (S.C.E.); (L.C.C.); (M.R.Y.)
| | - Liana C. Chan
- The Lundquist Institute for Biomedical Innovation, Harbor-UCLA Medical Center, Torrance, CA 90502, USA; (S.C.E.); (L.C.C.); (M.R.Y.)
- David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
- Division of Infectious Diseases, Department of Medicine, Harbor-UCLA Medical Center, Torrance, CA 90502, USA
- Division of Molecular Medicine, Department of Medicine, Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Michael R. Yeaman
- The Lundquist Institute for Biomedical Innovation, Harbor-UCLA Medical Center, Torrance, CA 90502, USA; (S.C.E.); (L.C.C.); (M.R.Y.)
- David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
- Division of Infectious Diseases, Department of Medicine, Harbor-UCLA Medical Center, Torrance, CA 90502, USA
- Division of Molecular Medicine, Department of Medicine, Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Henry F. Chambers
- School of Medicine, University of California-San Francisco (UCSF), San Francisco, CA 94143, USA;
| | - Richard A. Proctor
- Departments of Medicine and Medical Microbiology/Immunology, School of Medicine and Public Health, University of Wisconsin, Madison, WI 53715, USA;
| | - Kevin C. Ludwig
- Institute for Pharmaceutical Microbiology, University Hospital Bonn, University of Bonn, D-53113 Bonn, Germany; (K.C.L.); (T.S.)
| | - Tanja Schneider
- Institute for Pharmaceutical Microbiology, University Hospital Bonn, University of Bonn, D-53113 Bonn, Germany; (K.C.L.); (T.S.)
| | - Adhar C. Manna
- Department of Microbiology & Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA; (A.C.M.); (A.C.)
| | - Ambrose Cheung
- Department of Microbiology & Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA; (A.C.M.); (A.C.)
| | - Arnold S. Bayer
- The Lundquist Institute for Biomedical Innovation, Harbor-UCLA Medical Center, Torrance, CA 90502, USA; (S.C.E.); (L.C.C.); (M.R.Y.)
- David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
- Division of Infectious Diseases, Department of Medicine, Harbor-UCLA Medical Center, Torrance, CA 90502, USA
- Correspondence: ; Tel.: +1-310-222-6422
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22
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Woroszyło M, Ciecholewska-Juśko D, Junka A, Drozd R, Wardach M, Migdał P, Szymczyk-Ziółkowska P, Styburski D, Fijałkowski K. Rotating Magnetic Field Increases β-Lactam Antibiotic Susceptibility of Methicillin-Resistant Staphylococcus aureus Strains. Int J Mol Sci 2021; 22:ijms222212397. [PMID: 34830278 PMCID: PMC8618647 DOI: 10.3390/ijms222212397] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 11/12/2021] [Accepted: 11/15/2021] [Indexed: 11/16/2022] Open
Abstract
Methicillin-resistant strains of Staphylococcus aureus (MRSA) have developed resistance to most β-lactam antibiotics and have become a global health issue. In this work, we analyzed the impact of a rotating magnetic field (RMF) of well-defined and strictly controlled characteristics coupled with β-lactam antibiotics against a total of 28 methicillin-resistant and sensitive S. aureus strains. The results indicate that the application of RMF combined with β-lactam antibiotics correlated with favorable changes in growth inhibition zones or in minimal inhibitory concentrations of the antibiotics compared to controls unexposed to RMF. Fluorescence microscopy indicated a drop in the relative number of cells with intact cell walls after exposure to RMF. These findings were additionally supported by the use of SEM and TEM microscopy, which revealed morphological alterations of RMF-exposed cells manifested by change of shape, drop in cell wall density and cytoplasm condensation. The obtained results indicate that the originally limited impact of β-lactam antibiotics in MRSA is boosted by the disturbances caused by RMF in the bacterial cell walls. Taking into account the high clinical need for new therapeutic options, effective against MRSA, the data presented in this study have high developmental potential and could serve as a basis for new treatment options for MRSA infections.
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Affiliation(s)
- Marta Woroszyło
- Department of Microbiology and Biotechnology, Faculty of Biotechnology and Animal Husbandry, West Pomeranian University of Technology in Szczecin, Piastów 45, 70-311 Szczecin, Poland; (M.W.); (D.C.-J.); (R.D.)
| | - Daria Ciecholewska-Juśko
- Department of Microbiology and Biotechnology, Faculty of Biotechnology and Animal Husbandry, West Pomeranian University of Technology in Szczecin, Piastów 45, 70-311 Szczecin, Poland; (M.W.); (D.C.-J.); (R.D.)
| | - Adam Junka
- Department of Pharmaceutical Microbiology and Parasitology, Faculty of Pharmacy, Medical University of Wroclaw, Borowska 211a, 50-534 Wrocław, Poland
- Laboratory of Microbiology, Łukasiewicz Research Network–PORT Polish Center for Technology Development, 54-066 Wrocław, Poland
- Correspondence: (A.J.); (K.F.); Tel.: +48-88-922-93-41 (A.J.); +48-91-449-6714 (K.F.)
| | - Radosław Drozd
- Department of Microbiology and Biotechnology, Faculty of Biotechnology and Animal Husbandry, West Pomeranian University of Technology in Szczecin, Piastów 45, 70-311 Szczecin, Poland; (M.W.); (D.C.-J.); (R.D.)
| | - Marcin Wardach
- Faculty of Electrical Engineering, West Pomeranian University of Technology in Szczecin, Sikorskiego 37, 70-313 Szczecin, Poland;
| | - Paweł Migdał
- Department of Environment, Hygiene and Animal Welfare, Faculty of Biology and Animal Science, Wroclaw University of Environmental and Life Sciences, Chełmońskiego 38C, 51-630 Wrocław, Poland;
| | - Patrycja Szymczyk-Ziółkowska
- Centre for Advanced Manufacturing Technologies (CAMT/FPC), Faculty of Mechanical Engineering, Wroclaw University of Science and Technology, Łukasiewicza 5, 50-371 Wrocław, Poland;
| | - Daniel Styburski
- Laboratory of Chromatography and Mass Spectroscopy, Faculty of Biotechnology and Animal Husbandry, West Pomeranian University of Technology in Szczecin, Klemensa Janickiego 29, 71-270 Szczecin, Poland;
| | - Karol Fijałkowski
- Department of Microbiology and Biotechnology, Faculty of Biotechnology and Animal Husbandry, West Pomeranian University of Technology in Szczecin, Piastów 45, 70-311 Szczecin, Poland; (M.W.); (D.C.-J.); (R.D.)
- Correspondence: (A.J.); (K.F.); Tel.: +48-88-922-93-41 (A.J.); +48-91-449-6714 (K.F.)
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23
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Martínez-Caballero S, Mahasenan KV, Kim C, Molina R, Feltzer R, Lee M, Bouley R, Hesek D, Fisher JF, Muñoz IG, Chang M, Mobashery S, Hermoso JA. Integrative structural biology of the penicillin-binding protein-1 from Staphylococcus aureus, an essential component of the divisome machinery. Comput Struct Biotechnol J 2021; 19:5392-5405. [PMID: 34667534 PMCID: PMC8493512 DOI: 10.1016/j.csbj.2021.09.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 09/13/2021] [Accepted: 09/15/2021] [Indexed: 12/18/2022] Open
Abstract
The penicillin-binding proteins are the enzyme catalysts of the critical transpeptidation crosslinking polymerization reaction of bacterial peptidoglycan synthesis and the molecular targets of the penicillin antibiotics. Here, we report a combined crystallographic, small-angle X-ray scattering (SAXS) in-solution structure, computational and biophysical analysis of PBP1 of Staphylococcus aureus (saPBP1), providing mechanistic clues about its function and regulation during cell division. The structure reveals the pedestal domain, the transpeptidase domain, and most of the linker connecting to the "penicillin-binding protein and serine/threonine kinase associated" (PASTA) domains, but not its two PASTA domains, despite their presence in the construct. To address this absence, the structure of the PASTA domains was determined at 1.5 Å resolution. Extensive molecular-dynamics simulations interpret the PASTA domains of saPBP1 as conformationally mobile and separated from the transpeptidase domain. This conclusion was confirmed by SAXS experiments on the full-length protein in solution. A series of crystallographic complexes with β-lactam antibiotics (as inhibitors) and penta-Gly (as a substrate mimetic) allowed the molecular characterization of both inhibition by antibiotics and binding for the donor and acceptor peptidoglycan strands. Mass-spectrometry experiments with synthetic peptidoglycan fragments revealed binding by PASTA domains in coordination with the remaining domains. The observed mobility of the PASTA domain in saPBP1 could play a crucial role for in vivo interaction with its glycosyltransferase partner in the membrane or with other components of the divisome machinery, as well as for coordination of transpeptidation and polymerization processes in the bacterial divisome.
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Affiliation(s)
- Siseth Martínez-Caballero
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry "Rocasolano", CSIC, 28006 Madrid, Spain
| | - Kiran V Mahasenan
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Choon Kim
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Rafael Molina
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry "Rocasolano", CSIC, 28006 Madrid, Spain
| | - Rhona Feltzer
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Mijoon Lee
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Renee Bouley
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Dusan Hesek
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Jed F Fisher
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Inés G Muñoz
- Structural Biology Programme, Spanish National Cancer Research Center (CNIO), 28029 Madrid, Spain
| | - Mayland Chang
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Shahriar Mobashery
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Juan A Hermoso
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry "Rocasolano", CSIC, 28006 Madrid, Spain
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24
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Ftsh Sensitizes Methicillin-Resistant Staphylococcus aureus to β-Lactam Antibiotics by Degrading YpfP, a Lipoteichoic Acid Synthesis Enzyme. Antibiotics (Basel) 2021; 10:antibiotics10101198. [PMID: 34680778 PMCID: PMC8532640 DOI: 10.3390/antibiotics10101198] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Revised: 09/17/2021] [Accepted: 09/27/2021] [Indexed: 12/20/2022] Open
Abstract
In the Gram-positive pathogen Staphylococcus aureus, FtsH, a membrane-bound metalloprotease, plays a critical role in bacterial virulence and stress resistance. This protease is also known to sensitize methicillin-resistant Staphylococcus aureus (MRSA) to β-lactam antibiotics; however, the molecular mechanism is not known. Here, by the analysis of FtsH substrate mutants, we found that FtsH sensitizes MRSA specifically to β-lactams by degrading YpfP, the enzyme synthesizing the anchor molecule for lipoteichoic acid (LTA). Both the overexpression of FtsH and the disruption of ypfP-sensitized MRSA to β-lactams were observed. The knockout mutation in ftsH and ypfP increased the thickness of the cell wall. The β-lactam sensitization coincided with the production of aberrantly large LTA molecules. The combination of three mutations in the rpoC, vraB, and SAUSA300_2133 genes blocked the β-lactam-sensitizing effect of FtsH. Murine infection with the ypfP mutant could be treated by oxacillin, a β-lactam antibiotic ineffective against MRSA; however, the effective concentration of oxacillin differed depending on the S. aureus strain. Our study demonstrated that the β-lactam sensitizing effect of FtsH is due to its digestion of YpfP. It also suggests that the larger LTA molecules are responsible for the β-lactam sensitization phenotype, and YpfP is a viable target for developing novel anti-MRSA drugs.
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Samotrueva MA, Ozerov AA, Starikova AA, Gabitova NM, Merezhkina DV, Tsibizova AA, Tyurenkov IN. ANTIMICROBIAL ACTIVITY STUDY OF NEW QUINAZOLIN-4(3H)-ONES AGAINST STAPHYLOCOCCUS AUREUS AND STREPTOCOCCUS PNEUMONIAE. PHARMACY & PHARMACOLOGY 2021. [DOI: 10.19163/2307-9266-2021-9-4-318-329] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Quinazolin-4(3H)-one derivatives exhibiting a wide spectrum of a pharmacological activity, represent a promising class of substances used to obtain antibacterial agents, which is especially important in the context of the emergence of pathogenic microorganisms’ resistance to drugs used in medicine. It has been proved that compounds having a naphthyl radical in the molecule, as well as an amide group bound to the benzene ring as quinazolinone substituents, are characterized by a pronounced antimicrobial activity against Staphylococcus aureus and Streptococcus pneumoniae.The aim of the research is a primary microbiological screening of the in vitro antimicrobial activity of new quinazolin-4(3H)-one derivatives against Staphylococcus aureus and Streptococcus pneumoniae, as well as the assessment of the relationship between the pharmacological effect and the structural transformation of the substance molecule, lipophilicity and the possibility of forming resistance to them.Materials and methods. The experimental studies have been carried out using well-known nosocomial pathogens of infectious and inflammatory diseases Staphylococcus aureus and Streptococcus pneumoniae by a serial dilution method.Results. A compound containing a naphthyl radical in its structure, which contributes to an increase in the hydrophobicity of the substance and its solubility in the membrane of a bacterial cell, has a bacteriostatic effect against both Staphylococcus aureus and Streptococcus pneumoniae. A similar pharmacological effect is exhibited by a derivative with an amide group as a substituent of the quinazolinone nucleus linked to a phenyl radical, which probably contributes to an increase in the degree of binding to active sites of enzymes involved in the DNA replication, and protein synthesis. Obviously, the increased lipophilicity, which promotes better binding to the efflux protein, cannot serve as objective characteristics of the emergence possibility of the pathogen’s resistance to this substance.Conclusion. Among the synthesized compounds, the leading substances that exhibit an antimicrobial activity against Staphylococcus aureus and Streptococcus pneumonia, have been identified. The assessment of the chemical structure made it possible to substantiate their pharmacological action and draw conclusions about the possibility of developing resistance to it in microbial cells.
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Affiliation(s)
- M. A. Samotrueva
- Аstrakhan State Medical University
121, Bakinskaya Str., Astrakhan, Russia, 414000
| | - A. A. Ozerov
- 1. Volgograd State Medical University
1, Pavshikh Bortsov Sq., Volgograd, Russia, 400131
2. Volgograd Medical Research Center
1, Pavshikh Bortsov Sq., Volgograd, Russia, 400131
| | - A. A. Starikova
- Аstrakhan State Medical University
121, Bakinskaya Str., Astrakhan, Russia, 414000
| | - N. M. Gabitova
- 1. Аstrakhan State Medical University
121, Bakinskaya Str., Astrakhan, Russia, 414000
2. Scientific Research Institute for the Study of Leprosy
3, Nikolay Ostrovsky Ave., Astrakhan, Russia, 414057
| | - D. V. Merezhkina
- Volgograd State Medical University
1, Pavshikh Bortsov Sq., Volgograd, Russia, 400131
| | - A. A. Tsibizova
- Аstrakhan State Medical University
121, Bakinskaya Str., Astrakhan, Russia, 414000
| | - I. N. Tyurenkov
- 1. Volgograd State Medical University
1, Pavshikh Bortsov Sq., Volgograd, Russia, 400131
2. Volgograd Medical Research Center
1, Pavshikh Bortsov Sq., Volgograd, Russia, 400131
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26
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Non- β-Lactam Allosteric Inhibitors Target Methicillin-Resistant Staphylococcus aureus: An In Silico Drug Discovery Study. Antibiotics (Basel) 2021; 10:antibiotics10080934. [PMID: 34438984 PMCID: PMC8388891 DOI: 10.3390/antibiotics10080934] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 07/18/2021] [Accepted: 07/29/2021] [Indexed: 11/17/2022] Open
Abstract
Penicillin-binding proteins (PBPs) catalyze the final stages for peptidoglycan cell-wall bio-synthesis. Mutations in the PBP2a subunit can attenuate β-lactam antibiotic activity, resulting in unimpeded cell-wall formation and methicillin-resistant Staphylococcus aureus (MRSA). A double mutation in PBP2a (i.e., N146K and E150K) is resistant to β-lactam inhibitors; however, (E)-3-(2-(4-cyanostyryl)-4-oxoquinazolin-3(4H)-yl) benzoic acid (QNZ), a heterocyclic antibiotic devoid of a β-lactam ring, interacts non-covalently with PBP2a allosteric site and inhibits PBP enzymatic activity. In the search for novel inhibitors that target this PBP2a allosteric site in acidic medium, an in silico screening was performed. Chemical databases including eMolecules, ChEMBL, and ChEBI were virtually screened for candidate inhibitors with a physicochemical similarity to QNZ. PBP2a binding affinities from the screening were calculated based on molecular docking with co-crystallized ligand QNZ serving as a reference. Molecular minimization calculations were performed for inhibitors with docking scores lower than QNZ (calc. −8.3 kcal/mol) followed by combined MD simulations and MM-GBSA binding energy calculations. Compounds eMol26313223 and eMol26314565 exhibited promising inhibitor activities based on binding affinities (ΔGbinding) that were twice that of QNZ (−38.5, −34.5, and −15.4 kcal/mol, respectively). Structural and energetic analyses over a 50 ns MD simulation revealed high stability for the inhibitors when complexed with the double mutated PBP2a. The pharmacokinetic properties of the two inhibitors were predicted using an in silico ADMET analysis. Calculated binding affinities hold promise for eMol26313223 and eMol26314565 as allosteric inhibitors of PBP2a in acidic medium and establish that further in vitro and in vivo inhibition experimentation is warranted.
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27
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Huang P, Wang Z, Cai K, Wei L, Chu Y, Guo M, Fan E. Targeting Bacterial Membrane Proteins to Explore the Beneficial Effects of Natural Products: New Antibiotics against Drug Resistance. Curr Med Chem 2021; 29:2109-2126. [PMID: 34126882 DOI: 10.2174/0929867328666210614121222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 04/27/2021] [Accepted: 04/30/2021] [Indexed: 11/22/2022]
Abstract
Antibiotic resistance is currently a world health crisis that urges the development of new antibacterial substances. To this end, natural products, including flavonoids, alkaloids, terpenoids, steroids, peptides and organic acids that play a vital role in the development of medicines and thus constitute a rich source in clinical practices, provide an important source of drugs directly or for the screen of lead compounds for new antibiotic development. Because membrane proteins, which comprise more than 60% of the current clinical drug targets, play crucial roles in signal transduction, transport, bacterial pathogenicity and drug resistance, as well as immunogenicity, it is our aim to summarize those natural products with different structures that target bacterial membrane proteins, such as efflux pumps and enzymes, to provide an overview for the development of new antibiotics to deal with antibiotic resistance.
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Affiliation(s)
- Piying Huang
- State Key Laboratory of Medical Molecular Biology, Department of Microbiology and Parasitology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Zhe Wang
- State Key Laboratory of Medical Molecular Biology, Department of Microbiology and Parasitology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Kun Cai
- State Key Laboratory of Medical Molecular Biology, Department of Microbiology and Parasitology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Liangwan Wei
- State Key Laboratory of Medical Molecular Biology, Department of Microbiology and Parasitology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Yindi Chu
- State Key Laboratory of Medical Molecular Biology, Department of Microbiology and Parasitology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Mingquan Guo
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
| | - Enguo Fan
- State Key Laboratory of Medical Molecular Biology, Department of Microbiology and Parasitology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
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28
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Beha MJ, Ryu JS, Kim YS, Chung HJ. Delivery of antisense oligonucleotides using multi-layer coated gold nanoparticles to methicillin-resistant S. aureus for combinatorial treatment. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2021; 126:112167. [PMID: 34082968 DOI: 10.1016/j.msec.2021.112167] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 04/19/2021] [Accepted: 04/30/2021] [Indexed: 11/27/2022]
Abstract
The spread of multidrug-resistant (MDR) bacterial infections has become a serious global threat. We introduce multi-layer coated gold nanoparticles (MLGNPs) delivering antisense oligonucleotides (ASOs) targeting the resistance gene of methicillin-resistant Staphylococcus aureus (MRSA), as a selective antimicrobial by restoring susceptibility. MLGNPs were prepared by multi-step surface immobilization of gold nanoparticles (GNPs) with polyethylenimine (PEI) and loaded with ASO targeting the mecA gene. The MLGNPs were shown to be efficiently internalized into various types of Gram-positive bacteria, including MRSA, Staphylococcus epidermidis, and Bacillus subtilis, which was superior to single-layer coated GNPs and free PEI polymer. The delivery of MLGNPs into MRSA resulted in up to 74% silencing of the mecA gene with high selectivity, in a dose-dependent manner. The treatment of MLGNPs to MRSA in the presence of oxacillin, a beta-lactam antibiotic, showed major suppression (~71%) of bacterial growth, due to the recovery of antibacterial sensitivity. Furthermore, the treatment of MLGNPs in a complex system showed preferential uptake into bacteria over mammalian cells, demonstrating the suitable characteristics of MLGNPs for selective delivery into bacteria. The current approach can be potentially applied for targeting various types of MDR bacterial infections by specific silencing of a resistance gene, as a combinatorial therapeutic used with conventional antibiotics.
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Affiliation(s)
- Marcel Janis Beha
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Jea Sung Ryu
- Graduate School of Nanoscience and Technology, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Yang Soo Kim
- Division of Infectious Diseases, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Hyun Jung Chung
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea; Graduate School of Nanoscience and Technology, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea.
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Mutation-Based Antibiotic Resistance Mechanism in Methicillin-Resistant Staphylococcus aureus Clinical Isolates. Pharmaceuticals (Basel) 2021; 14:ph14050420. [PMID: 34062812 PMCID: PMC8147353 DOI: 10.3390/ph14050420] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 04/15/2021] [Accepted: 04/25/2021] [Indexed: 12/18/2022] Open
Abstract
β-Lactam antibiotics target penicillin-binding proteins and inhibit the synthesis of peptidoglycan, a crucial step in cell wall biosynthesis. Staphylococcus aureus acquires resistance against β-lactam antibiotics by producing a penicillin-binding protein 2a (PBP2a), encoded by the mecA gene. PBP2a participates in peptidoglycan biosynthesis and exhibits a poor affinity towards β-lactam antibiotics. The current study was performed to determine the diversity and the role of missense mutations of PBP2a in the antibiotic resistance mechanism. The methicillin-resistant Staphylococcus aureus (MRSA) isolates from clinical samples were identified using phenotypic and genotypic techniques. The highest frequency (60%, 18 out of 30) of MRSA was observed in wound specimens. Sequence variation analysis of the mecA gene showed four amino acid substitutions (i.e., E239K, E239R, G246E, and E447K). The E239R mutation was found to be novel. The protein-ligand docking results showed that the E239R mutation in the allosteric site of PBP2a induces conformational changes in the active site and, thus, hinders its interaction with cefoxitin. Therefore, the present report indicates that mutation in the allosteric site of PBP2a provides a more closed active site conformation than wide-type PBP2a and then causes the high-level resistance to cefoxitin.
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Fisher JF, Mobashery S. β-Lactams against the Fortress of the Gram-Positive Staphylococcus aureus Bacterium. Chem Rev 2021; 121:3412-3463. [PMID: 33373523 PMCID: PMC8653850 DOI: 10.1021/acs.chemrev.0c01010] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The biological diversity of the unicellular bacteria-whether assessed by shape, food, metabolism, or ecological niche-surely rivals (if not exceeds) that of the multicellular eukaryotes. The relationship between bacteria whose ecological niche is the eukaryote, and the eukaryote, is often symbiosis or stasis. Some bacteria, however, seek advantage in this relationship. One of the most successful-to the disadvantage of the eukaryote-is the small (less than 1 μm diameter) and nearly spherical Staphylococcus aureus bacterium. For decades, successful clinical control of its infection has been accomplished using β-lactam antibiotics such as the penicillins and the cephalosporins. Over these same decades S. aureus has perfected resistance mechanisms against these antibiotics, which are then countered by new generations of β-lactam structure. This review addresses the current breadth of biochemical and microbiological efforts to preserve the future of the β-lactam antibiotics through a better understanding of how S. aureus protects the enzyme targets of the β-lactams, the penicillin-binding proteins. The penicillin-binding proteins are essential enzyme catalysts for the biosynthesis of the cell wall, and understanding how this cell wall is integrated into the protective cell envelope of the bacterium may identify new antibacterials and new adjuvants that preserve the efficacy of the β-lactams.
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Affiliation(s)
- Jed F Fisher
- Department of Chemistry and Biochemistry, McCourtney Hall, University of Notre Dame, Notre Dame Indiana 46556, United States
| | - Shahriar Mobashery
- Department of Chemistry and Biochemistry, McCourtney Hall, University of Notre Dame, Notre Dame Indiana 46556, United States
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Jia J, Luo Y, Zhong X, He L. Methicillin-resistance Staphylococcus aureus (MRSA) Pyruvate kinase (PK) inhibitors and Their Antimicrobial Activities. Curr Med Chem 2021; 29:908-923. [PMID: 33749550 DOI: 10.2174/0929867328666210322103340] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 02/10/2021] [Accepted: 02/14/2021] [Indexed: 11/22/2022]
Abstract
Resistance to antibiotics has been widely existed in the health care and community setting, thus developing a novel aspect of new antibiotics is urgently necessary. Methicillin-resistance Staphylococcus aureus (MRSA) Pyruvate kinase (PK) is crucial to the survive of bacterial, making it a novel antimicrobial target. In the past decade, most reported PK inhibitors including indole, flavonoid, phenazine derivative from natural product small molecules or their analogues, or virtual screening from small molecule compound library. This review covers the PK inhibitors and their antimicrobial activities reported from the beginning of 2011 through the middle of 2020. The Structure Activity Relationships (SARs) was discussed briefly as well.
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Affiliation(s)
- Jingjing Jia
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, Department of Medicinal Chemistry, West China School of Pharmacy, Sichuan University, Chengdu, Sichuan 610041. China
| | - Yang Luo
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, Department of Medicinal Chemistry, West China School of Pharmacy, Sichuan University, Chengdu, Sichuan 610041. China
| | - Xue Zhong
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, Department of Medicinal Chemistry, West China School of Pharmacy, Sichuan University, Chengdu, Sichuan 610041. China
| | - Ling He
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, Department of Medicinal Chemistry, West China School of Pharmacy, Sichuan University, Chengdu, Sichuan 610041. China
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Araújo AR, Araújo AC, Reis RL, Pires RA. Vescalagin and Castalagin Present Bactericidal Activity toward Methicillin-Resistant Bacteria. ACS Biomater Sci Eng 2021; 7:1022-1030. [PMID: 33596039 DOI: 10.1021/acsbiomaterials.0c01698] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Polyphenols have been extensively exploited in the biomedical field because of their wide range of bioactive properties and historical use as traditional medicines. They typically present antioxidant, antimicrobial, antiamyloidogenic, and/or antitumor activities. In particular, cork water extracts and their components, have been previously reported to present antioxidant and antiamyloidogenic properties. On the basis of this knowledge, we tested cork water extract (CWE), cork water enriched extract (CWE-E), vescalagin/castalagin (two of the main polyphenols present in CWE and CWE-E) for their antibacterial activity against four bacterial strains, namely, methicillin-resistant Staphylococcus epidermidis (MRSE), Staphylococcus aureus (SA), methicillin-resistant Staphylococcus aureus (MRSA), and Pseudomonas aeruginosa (PA). Vescalagin and castalagin presented bactericidal activity against all the tested bacterial strains, in particular toward the methicillin-resistant ones, i.e., MRSA and MRSE, as well as the ability to inhibit the formation of biofilms and to disrupt preformed ones. Moreover, vescalagin/castalagin seem to modulate the normal assembly of the peptidoglycans at the bacteria surface, promoting the disruption of their cell wall, leading to bacterial cell death. We also demonstrate that vescalagin/castalagin can be loaded into alginate hydrogels to generate antibacterial biomaterials that are not toxic to eukaryotic cells.
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Affiliation(s)
- Ana R Araújo
- 3B's Research Group, I3Bs-Research Institute on Biomaterials, Biodegradables and Biomimetics, University of Minho, Headquarters of the European Institute of Excellence on Tissue Engineering and Regenerative Medicine, Avepark, Parque de Ciência e Tecnologia, Zona Industrial da Gandra, 4805-017, Barco, Guimarães, Portugal.,ICVS/3B's-PT Government Associate Laboratory, Braga/Guimarães, Avepark, Zona Industrial da Gandra, 4805-017, Barco, Guimarães, Portugal
| | - Ana C Araújo
- 3B's Research Group, I3Bs-Research Institute on Biomaterials, Biodegradables and Biomimetics, University of Minho, Headquarters of the European Institute of Excellence on Tissue Engineering and Regenerative Medicine, Avepark, Parque de Ciência e Tecnologia, Zona Industrial da Gandra, 4805-017, Barco, Guimarães, Portugal.,ICVS/3B's-PT Government Associate Laboratory, Braga/Guimarães, Avepark, Zona Industrial da Gandra, 4805-017, Barco, Guimarães, Portugal
| | - Rui L Reis
- 3B's Research Group, I3Bs-Research Institute on Biomaterials, Biodegradables and Biomimetics, University of Minho, Headquarters of the European Institute of Excellence on Tissue Engineering and Regenerative Medicine, Avepark, Parque de Ciência e Tecnologia, Zona Industrial da Gandra, 4805-017, Barco, Guimarães, Portugal.,ICVS/3B's-PT Government Associate Laboratory, Braga/Guimarães, Avepark, Zona Industrial da Gandra, 4805-017, Barco, Guimarães, Portugal
| | - Ricardo A Pires
- 3B's Research Group, I3Bs-Research Institute on Biomaterials, Biodegradables and Biomimetics, University of Minho, Headquarters of the European Institute of Excellence on Tissue Engineering and Regenerative Medicine, Avepark, Parque de Ciência e Tecnologia, Zona Industrial da Gandra, 4805-017, Barco, Guimarães, Portugal.,ICVS/3B's-PT Government Associate Laboratory, Braga/Guimarães, Avepark, Zona Industrial da Gandra, 4805-017, Barco, Guimarães, Portugal
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Chang M, Mahasenan KV, Hermoso JA, Mobashery S. Unconventional Antibacterials and Adjuvants. Acc Chem Res 2021; 54:917-929. [PMID: 33512995 DOI: 10.1021/acs.accounts.0c00776] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The need for new classes of antibacterials is genuine in light of the dearth of clinical options for the treatment of bacterial infections. The prodigious discoveries of antibiotics during the 1940s to 1970s, a period wistfully referred to as the Golden Age of Antibiotics, have not kept up in the face of emergence of resistant bacteria in the past few decades. There has been a renewed interest in old drugs, the repurposing of the existing antibiotics and pairing of synergistic antibiotics or of an antibiotic with an adjuvant. Notwithstanding, discoveries of novel classes of these life-saving drugs have become increasingly difficult, calling for new paradigms. We describe, herein, three strategies from our laboratories toward discoveries of new antibacterials and adjuvants using computational and multidisciplinary experimental methods. One approach targets penicillin-binding proteins (PBPs), biosynthetic enzymes of cell-wall peptidoglycan, for discoveries of non-β-lactam inhibitors. Oxadiazoles and quinazolinones emerged as two structural classes out of these efforts. Several hundred analogs of these two classes of antibiotics have been synthesized and fully characterized in our laboratories. A second approach ventures into inhibition of allosteric regulation of cell-wall biosynthesis. The mechanistic details of allosteric regulation of PBP2a of Staphylococcus aureus, discovered in our laboratories, is outlined. The allosteric site in this protein is at 60 Å distance to the active site, whereby ligand binding at the former makes access to the latter by the substrate possible. We have documented that both quinazolinones and ceftaroline, a fifth-generation cephalosporin, bind to the allosteric site in manifestation of the antibacterial activity. Attempts at inhibition of the regulatory phosphorylation events identified three classes of antibacterial adjuvants and one class of antibacterials, the picolinamides. The chemical structures for these hits went through diversification by synthesis of hundreds of analogs. These analogs were characterized in various assays for identification of leads with adjuvant and antibacterial activities. Furthermore, we revisited the mechanism of bulgecins, a class of adjuvants discovered and abandoned in the 1980s. These compounds potentiate the activities of β-lactam antibiotics by the formation of bulges at the sites of septum formation during bacterial replication, which are points of structural weakness in the envelope. These bulges experience rupture, which leads to bacterial death. Bulgecin A inhibits the lytic transglycosylase Slt of Pseudomonas aeruginosa as a likely transition-state mimetic for its turnover of the cell-wall peptidoglycan. Once damage to cell wall is inflicted by a β-lactam antibiotic, the function of Slt is to repair the damage. When Slt is inhibited by bulgecin A, the organism cannot cope with it and would undergo rapid lysis. Bulgecin A is an effective adjuvant of β-lactam antibiotics. These discoveries of small-molecule classes of antibacterials or of adjuvants to antibacterials hold promise in strategies for treatment of bacterial infections.
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Affiliation(s)
- Mayland Chang
- Department of Chemistry and Biochemistry, University of Notre Dame, McCourtney Hall, Notre Dame Indiana 46556, United States
| | - Kiran V. Mahasenan
- Department of Chemistry and Biochemistry, University of Notre Dame, McCourtney Hall, Notre Dame Indiana 46556, United States
| | - Juan A. Hermoso
- Departamento de Cristalografía y Biología Estructural, Instituto de Química-Física “Rocasolano”, CSIC, Serrano 119, 28006-Madrid Spain
| | - Shahriar Mobashery
- Department of Chemistry and Biochemistry, University of Notre Dame, McCourtney Hall, Notre Dame Indiana 46556, United States
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Laser-Irradiated Chlorpromazine as a Potent Anti-Biofilm Agent for Coating of Biomedical Devices. COATINGS 2020. [DOI: 10.3390/coatings10121230] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Nowadays, antibiotic resistance has become increasingly common, triggering a global health crisis, immediately needing alternative, including repurposed drugs with potent bactericidal effects. We demonstrated that chlorpromazine aqueous solutions exposed to laser radiation exhibited visible activity against various microorganisms. The aim of this study was to investigate the quantitative antimicrobial activity of chlorpromazine in non-irradiated and 4-h laser irradiated form. Also, we examined the effect of both solutions impregnated on a cotton patch, cannula, and urinary catheter against Gram-positive Staphylococcus aureus and Gram-negative Pseudomonas aeruginosa and Escherichia coli. In all experimental versions, the chlorpromazine antimicrobial activity was enhanced by laser exposure. Besides the experimental results, the in silico analyses using molecular docking proved that the improved antimicrobial activity of the irradiated compound was a result of the combined action of the photoproducts on the biological target (s). Our results show that laser radiation could alter the molecular structure of various drugs and their effects, proving to be a promising strategy to halt antibiotic resistance, by repurposing current medicines for new antimicrobial strategies, thereby decreasing the costs and time for the development of more efficient drugs.
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Chakraborty K, Kizhakkekalam VK, Joy M. Chemical mining of heterotrophic Shewanella algae reveals anti-infective potential of macrocyclic polyketides against multidrug-resistant pathogens. Bioorg Chem 2020; 108:104533. [PMID: 33342567 DOI: 10.1016/j.bioorg.2020.104533] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Revised: 11/25/2020] [Accepted: 12/03/2020] [Indexed: 11/17/2022]
Abstract
Heterotrophic Gamma-proteobacterium Shewanella algae MTCC 12715, associated with an intertidal red algae Hypnea valentiae, presented broad-spectra of antibacterial activities against pathogenic bacteria bringing about nosocomial infection. Bioassay-guided fractionation of the bacterial crude extract resulted in two undescribed macrocyclic polyketide analogs, with anti-infective activities against methicillin-resistant Staphylococcus aureus and vancomycin-resistant Enterococcus faecalis (MIC 3.1-5.0 µg/mL). In order to identify the polyketide biosynthetic machinery termed type-I polyketide synthase (pks-I) encoding biologically active secondary metabolites in this strain, the ketosynthase-coding regions of DNA with ≈700 bp size, were amplified, and the partial sequence was submitted in the GenBank (accession number MH157093). The titled compounds were classified under macrocyclic polyketides bearing dodecahydropyrano-trioxacyclooctadecine-dione and trioxo-octadecahydro-1H-benzo[o]tetraoxacyclopentacosine-carboxylate functionalities. Structure-activity correlation analysis displayed that hydrophobic descriptor of the studied compounds could play a prominent role in its anti-infective property against the opportunistic pathogens. Further, in silico molecular docking studies were performed in the allosteric sites of penicillin-binding protein (PBP2a) coded by mecA genes of MRSA, and the best binding pose for each compound (docking score -8.47 kcal/mol and -9.58 kcal/mol, respectively) could be correlated with their in vitro antibacterial activities. The pks-I assisted biosynthetic pathway of macrocyclic polyketides through step-wise decarboxylative condensation initiated by malonate-acyl carrier protein corroborated their structural attributes. Chemical mining of the studied macroalgae-associated heterotrophic bacterium thus revealed the promising antagonistic properties of macrocyclic polyketides isolated from Shewanella algae MTCC 12715 against multidrug-resistant pathogens.
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Affiliation(s)
- Kajal Chakraborty
- Marine Bioprospecting Section of Marine Biotechnology Division, Central Marine Fisheries Research Institute, Ernakulam North, P.B. No. 1603, Cochin, India.
| | - Vinaya Kizhakkepatt Kizhakkekalam
- Marine Bioprospecting Section of Marine Biotechnology Division, Central Marine Fisheries Research Institute, Ernakulam North, P.B. No. 1603, Cochin, India; Faculty of Marine Sciences, Lakeside Campus, Cochin University of Science and Technology, Cochin, Kerala State, India
| | - Minju Joy
- Marine Bioprospecting Section of Marine Biotechnology Division, Central Marine Fisheries Research Institute, Ernakulam North, P.B. No. 1603, Cochin, India
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Chakraborty K, Kizhakkekalam VK, Joy M. Macrocyclic polyketides with siderophore mode of action from marine heterotrophic Shewanella algae: Prospective anti-infective leads attenuate drug-resistant pathogens. J Appl Microbiol 2020; 130:1552-1570. [PMID: 33006801 DOI: 10.1111/jam.14875] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 07/19/2020] [Accepted: 09/24/2020] [Indexed: 02/01/2023]
Abstract
AIMS Biotechnological and chemical characterization of previously undescribed homologous siderophore-type macrocyclic polyketides from heterotrophic Shewanella algae Microbial Type Culture Collection (MTCC) 12715 affiliated with Rhodophycean macroalga Hypnea valentiae of marine origin, with significant anti-infective potential against drug-resistant pathogens. METHODS AND RESULTS The heterotrophic bacterial strain in symbiotic association with intertidal macroalga H. valentiae was isolated to homogeneity in a culture-dependent method and screened for bioactivities by spot-over-lawn assay. The bacterial organic extract was purified and characterized by extensive chromatographic and spectroscopic methods, respectively, and was assessed for antibacterial activities with disc diffusion and microtube dilution methods. The macrocyclic polyketide compounds exhibited wide-spectrum of anti-infective potential against clinically significant vancomycin-resistant Enterococcus faecalis (VREfs), methicillin-resistant Staphylococcus aureus (MRSA), Pseudomonas aeruginosa and Klebsiella pneumonia with minimum inhibitory concentration of about 1-3 µg ml-1 , insomuch as the antibiotics chloramphenicol and ampicillin were active at ≥6·25 µg ml-1 . The studied compounds unveiled Fe3+ chelating activity, which designated that their prospective anti-infective activities against the pathogens could be due to their siderophore mechanism of action. In support of that, the bacterium exhibited siderophore production on bioassay involving the cast upon culture agar plate, and the presence of siderophore biosynthetic gene (≈1000 bp) (MF 981936) further corroborated the inference. In silico molecular modelling with penicillin-binding protein (PBP2a) coded by mecA genes of MRSA (docking score -11·68 to -12·69 kcal mol-1 ) verified their in vitro antibacterial activities. Putative biosynthetic pathway of macrocyclic polyketides through stepwise decarboxylative condensation initiated by malonate-acyl carrier protein further validated their structural and molecular attributes. CONCLUSIONS The studied siderophore-type macrocyclic polyketides from S. algae MTCC 12715 with significant anti-infective potential could be considered as promising candidates for pharmaceutical and biotechnological applications, especially against emerging multidrug-resistant pathogens. SIGNIFICANCE AND IMPACT OF THE STUDY This study exhibited the heterotrophic bacteria in association with intertidal macroalga as propitious biological resources to biosynthesize novel antibacterial agents.
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Affiliation(s)
- K Chakraborty
- Marine Bioprospecting Section of Marine Biotechnology Division, Central Marine Fisheries Research Institute, Ernakulam North, P.B. No. 1603, Cochin, India.,Faculty of Marine Sciences, Cochin University of Science and Technology, Kerala State, Lakeside Campus, Cochin, India
| | - V K Kizhakkekalam
- Marine Bioprospecting Section of Marine Biotechnology Division, Central Marine Fisheries Research Institute, Ernakulam North, P.B. No. 1603, Cochin, India.,Faculty of Marine Sciences, Cochin University of Science and Technology, Kerala State, Lakeside Campus, Cochin, India
| | - M Joy
- Marine Bioprospecting Section of Marine Biotechnology Division, Central Marine Fisheries Research Institute, Ernakulam North, P.B. No. 1603, Cochin, India.,Faculty of Marine Sciences, Cochin University of Science and Technology, Kerala State, Lakeside Campus, Cochin, India
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Anti-staphylococcal activity and mode of action of thioridazine photoproducts. Sci Rep 2020; 10:18043. [PMID: 33093568 PMCID: PMC7582912 DOI: 10.1038/s41598-020-74752-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Accepted: 10/01/2020] [Indexed: 02/06/2023] Open
Abstract
Antibiotic resistance became an increasing risk for population health threatening our ability to fight infectious diseases. The objective of this study was to evaluate the activity of laser irradiated thioridazine (TZ) against clinically-relevant bacteria in view to fight antibiotic resistance. TZ in ultrapure water solutions was irradiated (1–240 min) with 266 nm pulsed laser radiation. Irradiated solutions were characterized by UV–Vis and FTIR absorption spectroscopy, thin layer chromatography, laser-induced fluorescence, and dynamic surface tension measurements. Molecular docking studies were made to evaluate the molecular mechanisms of photoproducts action against Staphylococcus aureus and MRSA. More general, solutions were evaluated for their antimicrobial and efflux inhibitory activity against a panel of bacteria of clinical relevance. We observed an enhanced antimicrobial activity of TZ photoproducts against Gram-positive bacteria. This was higher than ciprofloxacin effects for methicillin- and ciprofloxacin-resistant Staphylococcus aureus. Molecular docking showed the Penicillin-binding proteins PBP3 and PBP2a inhibition by sulforidazine as a possible mechanism of action against Staphylococcus aureus and MRSA strains, respectively. Irradiated TZ reveals possible advantages in the treatment of infectious diseases produced by antibiotic-resistant Gram-positive bacteria. TZ repurposing and its photoproducts, obtained by laser irradiation, show accelerated and low-costs of development if compared to chemical synthesis.
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Qian Y, Allegretta G, Janardhanan J, Peng Z, Mahasenan KV, Lastochkin E, Gozun MMN, Tejera S, Schroeder VA, Wolter WR, Feltzer R, Mobashery S, Chang M. Exploration of the Structural Space in 4(3 H)-Quinazolinone Antibacterials. J Med Chem 2020; 63:5287-5296. [PMID: 32343145 DOI: 10.1021/acs.jmedchem.0c00153] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
We report herein the syntheses of 79 derivatives of the 4(3H)-quinazolinones and their structure-activity relationship (SAR) against methicillin-resistant Staphylococcus aureus (MRSA). Twenty one analogs were further evaluated in in vitro assays. Subsequent investigation of the pharmacokinetic properties singled out compound 73 ((E)-3-(5-carboxy-2-fluorophenyl)-2-(4-cyanostyryl)quinazolin-4(3H)-one) for further study. The compound synergized with piperacillin-tazobactam (TZP) both in vitro and in vivo in a clinically relevant mouse model of MRSA infection. The TZP combination lacks activity against MRSA, yet it synergized with compound 73 to kill MRSA in a bactericidal manner. The synergy is rationalized by the ability of the quinazolinones to bind to the allosteric site of penicillin-binding protein (PBP)2a, resulting in opening of the active site, whereby the β-lactam antibiotic now is enabled to bind to the active site in its mechanism of action. The combination effectively treats MRSA infection, for which many antibiotics (including TZP) have faced clinical obsolescence.
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Affiliation(s)
- Yuanyuan Qian
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Giuseppe Allegretta
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Jeshina Janardhanan
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Zhihong Peng
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Kiran V Mahasenan
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Elena Lastochkin
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Melissa Malia N Gozun
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Sara Tejera
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Valerie A Schroeder
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - William R Wolter
- Freimann Life Sciences Center, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Rhona Feltzer
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Shahriar Mobashery
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Mayland Chang
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
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Indole-based derivatives as potential antibacterial activity against methicillin-resistance Staphylococcus aureus (MRSA). Eur J Med Chem 2020; 194:112245. [DOI: 10.1016/j.ejmech.2020.112245] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 02/20/2020] [Accepted: 03/16/2020] [Indexed: 12/15/2022]
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40
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Shalaby MAW, Dokla EME, Serya RAT, Abouzid KAM. Penicillin binding protein 2a: An overview and a medicinal chemistry perspective. Eur J Med Chem 2020; 199:112312. [PMID: 32442851 DOI: 10.1016/j.ejmech.2020.112312] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 03/28/2020] [Accepted: 04/05/2020] [Indexed: 12/17/2022]
Abstract
Antimicrobial resistance is an imminent threat worldwide. Methicillin-resistant Staphylococcus aureus (MRSA) is one of the "superbug" family, manifesting resistance through the production of a penicillin binding protein, PBP2a, an enzyme that provides its transpeptidase activity to allow cell wall biosynthesis. PBP2a's low affinity to most β-lactams, confers resistance to MRSA against numerous members of this class of antibiotics. An Achilles' heel of MRSA, PBP2a represents a substantial target to design novel antibiotics to tackle MRSA threat via inhibition of the bacterial cell wall biosynthesis. In this review we bring into focus the PBP2a enzyme and examine the various aspects related to its role in conferring resistance to MRSA strains. Moreover, we discuss several antibiotics and antimicrobial agents designed to target PBP2a and their therapeutic potential to meet such a grave threat. In conclusion, we consider future perspectives for targeting MRSA infections.
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Affiliation(s)
- Menna-Allah W Shalaby
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Ain Shams University, Abbassia, 11566, Cairo, Egypt
| | - Eman M E Dokla
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Ain Shams University, Abbassia, 11566, Cairo, Egypt.
| | - Rabah A T Serya
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Ain Shams University, Abbassia, 11566, Cairo, Egypt
| | - Khaled A M Abouzid
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Ain Shams University, Abbassia, 11566, Cairo, Egypt; Department of Organic and Medicinal Chemistry, Faculty of Pharmacy, University of Sadat City, Sadat City, Egypt.
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41
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Chiang Y, Wong MTY, Essex JW. Molecular Dynamics Simulations of Antibiotic Ceftaroline at the Allosteric Site of Penicillin‐Binding Protein 2a (PBP2a). Isr J Chem 2020. [DOI: 10.1002/ijch.202000012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Ying‐Chih Chiang
- School of ChemistryUniversity of Southampton Southampton SO17 1BJ United Kingdom
| | - Mabel T. Y. Wong
- School of ChemistryUniversity of Southampton Southampton SO17 1BJ United Kingdom
| | - Jonathan W. Essex
- School of ChemistryUniversity of Southampton Southampton SO17 1BJ United Kingdom
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42
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Fisher JF, Mobashery S. Constructing and deconstructing the bacterial cell wall. Protein Sci 2020; 29:629-646. [PMID: 31747090 PMCID: PMC7021008 DOI: 10.1002/pro.3737] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 09/17/2019] [Accepted: 09/18/2019] [Indexed: 12/11/2022]
Abstract
The history of modern medicine cannot be written apart from the history of the antibiotics. Antibiotics are cytotoxic secondary metabolites that are isolated from Nature. The antibacterial antibiotics disproportionately target bacterial protein structure that is distinct from eukaryotic protein structure, notably within the ribosome and within the pathways for bacterial cell-wall biosynthesis (for which there is not a eukaryotic counterpart). This review focuses on a pre-eminent class of antibiotics-the β-lactams, exemplified by the penicillins and cephalosporins-from the perspective of the evolving mechanisms for bacterial resistance. The mechanism of action of the β-lactams is bacterial cell-wall destruction. In the monoderm (single membrane, Gram-positive staining) pathogen Staphylococcus aureus the dominant resistance mechanism is expression of a β-lactam-unreactive transpeptidase enzyme that functions in cell-wall construction. In the diderm (dual membrane, Gram-negative staining) pathogen Pseudomonas aeruginosa a dominant resistance mechanism (among several) is expression of a hydrolytic enzyme that destroys the critical β-lactam ring of the antibiotic. The key sensing mechanism used by P. aeruginosa is monitoring the molecular difference between cell-wall construction and cell-wall deconstruction. In both bacteria, the resistance pathways are manifested only when the bacteria detect the presence of β-lactams. This review summarizes how the β-lactams are sensed and how the resistance mechanisms are manifested, with the expectation that preventing these processes will be critical to future chemotherapeutic control of multidrug resistant bacteria.
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Affiliation(s)
- Jed F. Fisher
- Department of Chemistry and BiochemistryUniversity of Notre DameSouth BendIndiana
| | - Shahriar Mobashery
- Department of Chemistry and BiochemistryUniversity of Notre DameSouth BendIndiana
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43
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Mahasenan KV, Batuecas MT, De Benedetti S, Kim C, Rana N, Lee M, Hesek D, Fisher JF, Sanz-Aparicio J, Hermoso JA, Mobashery S. Catalytic Cycle of Glycoside Hydrolase BglX from Pseudomonas aeruginosa and Its Implications for Biofilm Formation. ACS Chem Biol 2020; 15:189-196. [PMID: 31877028 PMCID: PMC7995829 DOI: 10.1021/acschembio.9b00754] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
BglX is a heretofore uncharacterized periplasmic glycoside hydrolase (GH) of the human pathogen Pseudomonas aeruginosa. X-ray analysis identifies it as a protein homodimer. The two active sites of the homodimer comprise catalytic residues provided by each monomer. This arrangement is seen in <2% of the hydrolases of known structure. In vitro substrate profiling shows BglX is a catalyst for β-(1→2) and β-(1→3) saccharide hydrolysis. Saccharides with β-(1→4) or β-(1→6) bonds, and the β-(1→4) muropeptides from the cell-wall peptidoglycan, are not substrates. Additional structural insights from X-ray analysis (including structures of a mutant enzyme-derived Michaelis complex, two transition-state mimetics, and two enzyme-product complexes) enabled the comprehensive description of BglX catalysis. The half-chair (4H3) conformation of the transition-state oxocarbenium species, the approach of the hydrolytic water molecule to the oxocarbenium species, and the stepwise release of the two reaction products were also visualized. The substrate pattern for BglX aligns with the [β-(1→2)-Glc]x and [β-(1→3)-Glc]x periplasmic osmoregulated periplasmic glucans, and possibly with the Psl exopolysaccharides, of P. aeruginosa. Both polysaccharides are implicated in biofilm formation. Accordingly, we show that inactivation of the bglX gene of P. aeruginosa PAO1 attenuates biofilm formation.
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Affiliation(s)
- Kiran V Mahasenan
- Department of Chemistry and Biochemistry , University of Notre Dame , Notre Dame , Indiana 46556 , United States
| | - María T Batuecas
- Department of Crystallography and Structural Biology , Institute of Physical Chemistry "Rocasolano", CSIC , 28006 Madrid , Spain
| | - Stefania De Benedetti
- Department of Chemistry and Biochemistry , University of Notre Dame , Notre Dame , Indiana 46556 , United States
| | - Choon Kim
- Department of Chemistry and Biochemistry , University of Notre Dame , Notre Dame , Indiana 46556 , United States
| | - Neha Rana
- Department of Chemistry and Biochemistry , University of Notre Dame , Notre Dame , Indiana 46556 , United States
| | - Mijoon Lee
- Department of Chemistry and Biochemistry , University of Notre Dame , Notre Dame , Indiana 46556 , United States
| | - Dusan Hesek
- Department of Chemistry and Biochemistry , University of Notre Dame , Notre Dame , Indiana 46556 , United States
| | - Jed F Fisher
- Department of Chemistry and Biochemistry , University of Notre Dame , Notre Dame , Indiana 46556 , United States
| | - Julia Sanz-Aparicio
- Department of Crystallography and Structural Biology , Institute of Physical Chemistry "Rocasolano", CSIC , 28006 Madrid , Spain
| | - Juan A Hermoso
- Department of Crystallography and Structural Biology , Institute of Physical Chemistry "Rocasolano", CSIC , 28006 Madrid , Spain
| | - Shahriar Mobashery
- Department of Chemistry and Biochemistry , University of Notre Dame , Notre Dame , Indiana 46556 , United States
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44
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Structural basis of denuded glycan recognition by SPOR domains in bacterial cell division. Nat Commun 2019; 10:5567. [PMID: 31804467 PMCID: PMC6895207 DOI: 10.1038/s41467-019-13354-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 10/30/2019] [Indexed: 01/31/2023] Open
Abstract
SPOR domains are widely present in bacterial proteins that recognize cell-wall peptidoglycan strands stripped of the peptide stems. This type of peptidoglycan is enriched in the septal ring as a product of catalysis by cell-wall amidases that participate in the separation of daughter cells during cell division. Here, we document binding of synthetic denuded glycan ligands to the SPOR domain of the lytic transglycosylase RlpA from Pseudomonas aeruginosa (SPOR-RlpA) by mass spectrometry and structural analyses, and demonstrate that indeed the presence of peptide stems in the peptidoglycan abrogates binding. The crystal structures of the SPOR domain, in the apo state and in complex with different synthetic glycan ligands, provide insights into the molecular basis for recognition and delineate a conserved pattern in other SPOR domains. The biological and structural observations presented here are followed up by molecular-dynamics simulations and by exploration of the effect on binding of distinct peptidoglycan modifications.
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45
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Booth S, Lewis RJ. Structural basis for the coordination of cell division with the synthesis of the bacterial cell envelope. Protein Sci 2019; 28:2042-2054. [PMID: 31495975 PMCID: PMC6863701 DOI: 10.1002/pro.3722] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 08/29/2019] [Accepted: 08/29/2019] [Indexed: 01/02/2023]
Abstract
Bacteria are surrounded by a complex cell envelope made up of one or two membranes supplemented with a layer of peptidoglycan (PG). The envelope is responsible for the protection of bacteria against lysis in their oft-unpredictable environments and it contributes to cell integrity, morphology, signaling, nutrient/small-molecule transport, and, in the case of pathogenic bacteria, host-pathogen interactions and virulence. The cell envelope requires considerable remodeling during cell division in order to produce genetically identical progeny. Several proteinaceous machines are responsible for the homeostasis of the cell envelope and their activities must be kept coordinated in order to ensure the remodeling of the envelope is temporally and spatially regulated correctly during multiple cycles of cell division and growth. This review aims to highlight the complexity of the components of the cell envelope, but focusses specifically on the molecular apparatuses involved in the synthesis of the PG wall, and the degree of cross talk necessary between the cell division and the cell wall remodeling machineries to coordinate PG remodeling during division. The current understanding of many of the proteins discussed here has relied on structural studies, and this review concentrates particularly on this structural work.
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Affiliation(s)
- Simon Booth
- Institute for Cell and Molecular Biosciences, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
| | - Richard J. Lewis
- Institute for Cell and Molecular Biosciences, Faculty of Medical SciencesNewcastle UniversityNewcastle upon TyneUK
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46
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Roch M, Lelong E, Panasenko OO, Sierra R, Renzoni A, Kelley WL. Thermosensitive PBP2a requires extracellular folding factors PrsA and HtrA1 for Staphylococcus aureus MRSA β-lactam resistance. Commun Biol 2019; 2:417. [PMID: 31754647 PMCID: PMC6858329 DOI: 10.1038/s42003-019-0667-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 10/25/2019] [Indexed: 12/21/2022] Open
Abstract
Staphylococcus aureus is a major human pathogen and represents a clinical challenge because of widespread antibiotic resistance. Methicillin resistant Staphylococcus aureus (MRSA) is particularly problematic and originates by the horizontal acquisition of mecA encoding PBP2a, an extracellular membrane anchored transpeptidase, which confers resistance to β-lactam antibiotics by allosteric gating of its active site channel. Herein, we show that dual disruption of PrsA, a lipoprotein chaperone displaying anti-aggregation activity, together with HtrA1, a membrane anchored chaperone/serine protease, resulted in severe and synergistic attenuation of PBP2a folding that restores sensitivity to β-lactams such as oxacillin. Purified PBP2a has a pronounced unfolding transition initiating at physiological temperatures that leads to irreversible precipitation and complete loss of activity. The concordance of genetic and biochemical data highlights the necessity for extracellular protein folding factors governing MRSA β-lactam resistance. Targeting the PBP2a folding pathway represents a particularly attractive adjuvant strategy to combat antibiotic resistance.
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Affiliation(s)
- Mélanie Roch
- Department of Microbiology and Molecular Medicine, University Hospital and Medical School of Geneva, 1 rue Michel-Servet, Geneva, CH-1211 Switzerland
| | - Emmanuelle Lelong
- Service of Infectious Diseases and Department of Medical Specialties, University Hospital and Medical School of Geneva, 4 rue Gabrielle-Perret-Gentil, Geneva, CH-1206 Switzerland
| | - Olesya O. Panasenko
- Department of Microbiology and Molecular Medicine, University Hospital and Medical School of Geneva, 1 rue Michel-Servet, Geneva, CH-1211 Switzerland
- Service of Infectious Diseases and Department of Medical Specialties, University Hospital and Medical School of Geneva, 4 rue Gabrielle-Perret-Gentil, Geneva, CH-1206 Switzerland
| | - Roberto Sierra
- Department of Microbiology and Molecular Medicine, University Hospital and Medical School of Geneva, 1 rue Michel-Servet, Geneva, CH-1211 Switzerland
| | - Adriana Renzoni
- Service of Infectious Diseases and Department of Medical Specialties, University Hospital and Medical School of Geneva, 4 rue Gabrielle-Perret-Gentil, Geneva, CH-1206 Switzerland
| | - William L. Kelley
- Department of Microbiology and Molecular Medicine, University Hospital and Medical School of Geneva, 1 rue Michel-Servet, Geneva, CH-1211 Switzerland
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47
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Indole-nitroimidazole conjugates as efficient manipulators to decrease the genes expression of methicillin-resistant Staphylococcus aureus. Eur J Med Chem 2019; 179:723-735. [DOI: 10.1016/j.ejmech.2019.06.093] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 06/28/2019] [Accepted: 06/28/2019] [Indexed: 12/28/2022]
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48
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Speri E, Kim C, De Benedetti S, Qian Y, Lastochkin E, Fishovitz J, Fisher JF, Mobashery S. Cinnamonitrile Adjuvants Restore Susceptibility to β-Lactams against Methicillin-Resistant Staphylococcus aureus. ACS Med Chem Lett 2019; 10:1148-1153. [PMID: 31413798 DOI: 10.1021/acsmedchemlett.9b00169] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2019] [Accepted: 07/01/2019] [Indexed: 11/28/2022] Open
Abstract
β-Lactams are used routinely to treat Staphylococcus aureus infections. However, the emergence of methicillin-resistant S. aureus (MRSA) renders them clinically precarious. We describe a class of cinnamonitrile adjuvants that restore the activity of oxacillin (a penicillin member of the β-lactams) against MRSA. The lead adjuvants were tested against six important strains of MRSA, one vancomycin-intermediate S. aureus (VISA) strain, and one linezolid-resistant S. aureus strain. Five compounds out of 84 total compounds showed broad potentiation. At 8 μM (E)-3-(5-(3,4-dichlorobenzyl)-2-(trifluoromethoxy)phenyl)-2-(methylsulfonyl)acrylonitrile (26) potentiated oxacillin with a >4000-fold reduction of its MIC (from 256 to 0.06 mg·L-1). This class of adjuvants holds promise for reversal of the resistance phenotype of MRSA.
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Affiliation(s)
- Enrico Speri
- Department Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Choon Kim
- Department Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Stefania De Benedetti
- Department Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Yuanyuan Qian
- Department Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Elena Lastochkin
- Department Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Jennifer Fishovitz
- Department Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Jed F. Fisher
- Department Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Shahriar Mobashery
- Department Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
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49
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Abstract
Dating back to the 1960s, initial studies on the staphylococcal cell wall were driven by the need to clarify the mode of action of the first antibiotics and the resistance mechanisms developed by the bacteria. During the following decades, the elucidation of the biosynthetic path and primary composition of staphylococcal cell walls was propelled by advances in microbial cell biology, specifically, the introduction of high-resolution analytical techniques and molecular genetic approaches. The field of staphylococcal cell wall gradually gained its own significance as the complexity of its chemical structure and involvement in numerous cellular processes became evident, namely its versatile role in host interactions, coordination of cell division and environmental stress signaling.This chapter includes an updated description of the anatomy of staphylococcal cell walls, paying particular attention to information from the last decade, under four headings: high-resolution analysis of the Staphylococcus aureus peptidoglycan; variations in peptidoglycan composition; genetic determinants and enzymes in cell wall synthesis; and complex functions of cell walls. The latest contributions to a more precise picture of the staphylococcal cell envelope were possible due to recently developed state-of-the-art microscopy and spectroscopy techniques and to a wide combination of -omics approaches, that are allowing to obtain a more integrative view of this highly dynamic structure.
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Affiliation(s)
- Rita Sobral
- UCIBIO-REQUIMTE, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
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50
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Wang H, Jayaraman A, Menon R, Gejji V, Karthikeyan R, Fernando S. A non-beta-lactam antibiotic inhibitor for enterohemorrhagic Escherichia coli O104:H4. J Mol Med (Berl) 2019; 97:1285-1297. [PMID: 31254005 DOI: 10.1007/s00109-019-01803-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 04/25/2019] [Accepted: 05/21/2019] [Indexed: 01/29/2023]
Abstract
The overuse of antibiotics has caused an increased prevalence of drug-resistant bacteria. Bacterial resistance in E. coli is regulated via production of β-lactam-hydrolyzing β-lactamases enzymes. Escherichia coli O104: H4 is a multi-drug resistant strain known to resist β-lactam as well as several other antibiotics. Here, we report a molecular dynamic simulation-combined docking approach to identify, screen, and verify active pharmacophores against enterohemorrhagic Escherichia coli (EHEC). Experimental studies revealed a boronic acid cyclic monomer (BACM), a non-β-lactam compound, to inhibit the growth of E. coli O104: H4. In vitro Kirby Bauer disk diffusion susceptibility testing coupled interaction analysis suggests BACM inhibits E. coli O104:H4 growth by not only inhibiting the β-lactamase pathway but also via direct inhibition of the penicillin-binding protein. These results suggest that BACM could be used as a lead compound to develop potent drugs targeting beta-lactam resistant Gram-negative bacterial strains. KEY MESSAGES: • An in silico approach was reported to identify pharmacophores against E. coli O104: H4. • In vitro studies revealed a non-β-lactam compound to inhibit the growth of E. coli O104: H4. • This non-β-lactam compound could be used as a lead compound for targeting beta-lactam strains.
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Affiliation(s)
- Haoqi Wang
- Department of Biological and Agricultural Engineering, Texas A&M University, College Station, TX, USA
| | - Arul Jayaraman
- Department of Chemical Engineering, Texas A&M University, College Station, TX, USA
| | - Rani Menon
- Department of Chemical Engineering, Texas A&M University, College Station, TX, USA
| | - Varun Gejji
- Department of Biological and Agricultural Engineering, Texas A&M University, College Station, TX, USA
| | | | - Sandun Fernando
- Department of Biological and Agricultural Engineering, Texas A&M University, College Station, TX, USA.
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