1
|
Duffey M, Jumde RP, da Costa RM, Ropponen HK, Blasco B, Piddock LJ. Extending the Potency and Lifespan of Antibiotics: Inhibitors of Gram-Negative Bacterial Efflux Pumps. ACS Infect Dis 2024; 10:1458-1482. [PMID: 38661541 PMCID: PMC11091901 DOI: 10.1021/acsinfecdis.4c00091] [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: 02/02/2024] [Revised: 03/14/2024] [Accepted: 03/20/2024] [Indexed: 04/26/2024]
Abstract
Efflux is a natural process found in all prokaryotic and eukaryotic cells that removes a diverse range of substrates from inside to outside. Many antibiotics are substrates of bacterial efflux pumps, and modifications to the structure or overexpression of efflux pumps are an important resistance mechanism utilized by many multidrug-resistant bacteria. Therefore, chemical inhibition of bacterial efflux to revitalize existing antibiotics has been considered a promising approach for antimicrobial chemotherapy over two decades, and various strategies have been employed. In this review, we provide an overview of bacterial multidrug resistance (MDR) efflux pumps, of which the resistance nodulation division (RND) efflux pumps are considered the most clinically relevant in Gram-negative bacteria, and describe over 50 efflux inhibitors that target such systems. Although numerous efflux inhibitors have been identified to date, none have progressed into clinical use because of formulation, toxicity, and pharmacokinetic issues or a narrow spectrum of inhibition. For these reasons, the development of efflux inhibitors has been considered a difficult and complex area of research, and few active preclinical studies on efflux inhibitors are in progress. However, recently developed tools, including but not limited to computational tools including molecular docking models, offer hope that further research on efflux inhibitors can be a platform for research and development of new bacterial efflux inhibitors.
Collapse
Affiliation(s)
- Maëlle Duffey
- Global
Antibiotic Research & Development Partnership (GARDP), Chemin Camille-Vidart 15, 1202 Geneva, Switzerland
| | - Ravindra P. Jumde
- Global
Antibiotic Research & Development Partnership (GARDP), Chemin Camille-Vidart 15, 1202 Geneva, Switzerland
| | - Renata M.A. da Costa
- Global
Antibiotic Research & Development Partnership (GARDP), Chemin Camille-Vidart 15, 1202 Geneva, Switzerland
| | - Henni-Karoliina Ropponen
- Global
Antibiotic Research & Development Partnership (GARDP), Chemin Camille-Vidart 15, 1202 Geneva, Switzerland
| | - Benjamin Blasco
- Global
Antibiotic Research & Development Partnership (GARDP), Chemin Camille-Vidart 15, 1202 Geneva, Switzerland
| | - Laura J.V. Piddock
- Global
Antibiotic Research & Development Partnership (GARDP), Chemin Camille-Vidart 15, 1202 Geneva, Switzerland
| |
Collapse
|
2
|
Schuster S, Vavra M, Wirth DAN, Kern WV. Comparative reassessment of AcrB efflux inhibitors reveals differential impact of specific pump mutations on the activity of potent compounds. Microbiol Spectr 2024; 12:e0304523. [PMID: 38170977 PMCID: PMC10846202 DOI: 10.1128/spectrum.03045-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 11/17/2023] [Indexed: 01/05/2024] Open
Abstract
Multidrug resistance poses global challenges, particularly with regard to Gram-negative bacterial infections. In view of the lack of new antibiotics, drug enhancers, such as efflux pump inhibitors (EPIs), have increasingly come into focus. A number of chemically diverse agents have been reported to inhibit AcrB, the main multidrug transporter in Escherichia coli, and homologs in other Gram-negative bacteria. However, due to the often varying methodologies used for their characterization, results remain difficult to compare. In this study, using a defined selection of antibiotics known to be efflux substrates, we reevaluated 38 published compounds for their in vitro EPI activity. When examined in an E. coli strain with stable wild-type AcrB overexpression, we found 17 compounds showing at least fourfold enhancing potency with more than 2 out of 10 test drugs (belonging to eight antibiotic classes). Pyranopyridines (MBX series) were confirmed as the most potent inhibitors among agents reported so far. A new and surprising finding was that their activity, unlike that of the pyridylpiperazine EPI BDM88855, was highly susceptible to the AcrB double-mutation G141D_N282Y, which had previously been shown to diminish drug enhancing of 1-(1-naphthylmethyl)piperazine in a predominantly substrate-specific manner. Conversely, transmembrane region mutation V411A, while eliminating the drug potentiating of the BDM compound, did not decrease the activity of the MBX EPIs. Besides comparative reassessment of the potency of reported EPIs, the study demonstrated the usefulness of mutagenesis approaches providing tools for an initial discrimination of EPIs regarding their mode of function.IMPORTANCEInfections with difficult-to-treat multidrug-resistant bacteria pose an urgent global threat in view of the stagnating development of new antimicrobial substances. Efflux pumps in Gram-negative pathogens are known to substantially contribute to multidrug resistance making them promising targets for chemotherapeutic interventions to restore the efficacy of conventional antibiotics. In the present study, the in vitro activity of previously reported efflux pump inhibitors was reassessed using standardized conditions. Relevant drug sensitizing activity could be proven for almost half of the tested compounds. Further characterization of potent inhibitors was achieved by investigating the impact of specific efflux pump mutations. A double-mutation previously known to decrease the activity of the arylpiperazine 1-(1-naphthylmethyl)piperazine also impaired that of the highly efficient pyranopyridine efflux pump inhibitors. Our findings provide direct comparability of reported efflux pump inhibitors and contribute to the elucidation of their mode of action.
Collapse
Affiliation(s)
- Sabine Schuster
- Division of Infectious Diseases, Department of Medicine II, University Hospital and Medical Center, Freiburg, Germany
| | - Martina Vavra
- Division of Infectious Diseases, Department of Medicine II, University Hospital and Medical Center, Freiburg, Germany
| | - Dave A. N. Wirth
- Division of Infectious Diseases, Department of Medicine II, University Hospital and Medical Center, Freiburg, Germany
| | - Winfried V. Kern
- Division of Infectious Diseases, Department of Medicine II, University Hospital and Medical Center, Freiburg, Germany
- Faculty of Medicine, Albert-Ludwigs University, Freiburg, Germany
| |
Collapse
|
3
|
Behera DU, Gaur M, Sahoo M, Subudhi E, Subudhi BB. Development of pharmacophore models for AcrB protein and the identification of potential adjuvant candidates for overcoming efflux-mediated colistin resistance. RSC Med Chem 2024; 15:127-138. [PMID: 38283226 PMCID: PMC10809322 DOI: 10.1039/d3md00483j] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 10/26/2023] [Indexed: 01/30/2024] Open
Abstract
Growing multi-drug resistance (MDR) among ESKAPE pathogens is a huge challenge. Increased resistance to last-resort antibiotics, like colistin, has further aggravated this. Efflux is identified as a major route of colistin resistance. So, finding an FDA-approved efflux inhibitor for potential application as an adjuvant to colistin was the primary objective of this study. E. coli-AcrB pump inhibitors and substrates were used to develop and validate the pharmacophoric model. Drugs confirming this pharmacophore were subjected to molecular docking to identify hits for the AcrB binding pocket. The efflux inhibition potential of the top hit was validated through the in vitro evaluation of the minimum inhibitory concentration (MIC) in combination with colistin. The checkerboard assay was done to demonstrate synergism, which was further corroborated by the Time-kill assay. Ten common pharmacophore hypotheses were successfully generated using substrate/inhibitors. Following enrichment analysis, AHHNR.100 was identified as the top-ranked hypothesis, and 207 unique compounds were found to conform to this hypothesis. The multi-step docking of these compounds against the AcrB protein revealed argatroban as the top non-antibiotic hit. This significantly inhibited the efflux activity of colistin-resistant clinical isolates K. pneumoniae (n = 1) and M. morganii (n = 2). Further, their combination with colistin enhanced the susceptibility of these isolates, and the effect was found to be synergistic. Accordingly, the time-kill assay of this combination showed 8-log and 2-log reductions against K. pneumoniae and M. morganii, respectively. In conclusion, this study found argatroban as a bacterial efflux inhibitor that can be potentially used to overcome efflux-mediated resistance.
Collapse
Affiliation(s)
- Dibyajyoti Uttameswar Behera
- Centre for Biotechnology, School of Pharmaceutical Sciences, Siksha 'O' Anusandhan (Deemed to be University) Kalinga Nagar, Ghatikia Bhubaneswar-751003 Odisha India +91 9861075829
| | - Mahendra Gaur
- Drug Development and Analysis Laboratory, School of Pharmaceutical Sciences, Siksha 'O' Anusandhan (Deemed to be University) Kalinga Nagar, Ghatikia Bhubaneswar-751003 Odisha India +91 7978085389
- Department of Biotechnology & Food Technology, Punjabi University Patiala 147002 India
| | - Maheswata Sahoo
- Centre for Biotechnology, School of Pharmaceutical Sciences, Siksha 'O' Anusandhan (Deemed to be University) Kalinga Nagar, Ghatikia Bhubaneswar-751003 Odisha India +91 9861075829
| | - Enketeswara Subudhi
- Centre for Biotechnology, School of Pharmaceutical Sciences, Siksha 'O' Anusandhan (Deemed to be University) Kalinga Nagar, Ghatikia Bhubaneswar-751003 Odisha India +91 9861075829
| | - Bharat Bhusan Subudhi
- Drug Development and Analysis Laboratory, School of Pharmaceutical Sciences, Siksha 'O' Anusandhan (Deemed to be University) Kalinga Nagar, Ghatikia Bhubaneswar-751003 Odisha India +91 7978085389
| |
Collapse
|
4
|
Chauhan SS, Gupta A, Srivastava A, Parthasarathi R. Discovering targeted inhibitors for Escherichia coli efflux pump fusion proteins using computational and structure-guided approaches. J Comput Chem 2024; 45:13-24. [PMID: 37656428 DOI: 10.1002/jcc.27215] [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: 05/30/2023] [Revised: 07/18/2023] [Accepted: 08/14/2023] [Indexed: 09/02/2023]
Abstract
Multidrug resistance pathogens causing infections and illness remain largely untreated clinically. Efflux pumps are one of the primary processes through which bacteria develop resistance by transferring antibiotics from the interior of their cells to the outside environment. Inhibiting these pumps by developing efficient derivatives appears to be a promising strategy for restoring antibiotic potency. This investigation explores literature-reported inhibitors of E. coli efflux pump fusion proteins AcrB-AcrA and identify potential chemical derivatives of these inhibitors to overcome the limitations. Using computational and structure-guided approaches, a study was conducted with the selected inhibitors (AcrA:25-AcrB:59) obtained by data mining and their derivatives (AcrA:857-AcrB:3891) to identify their inhibitory effect on efflux pump using virtual screening, molecular docking and density functional theory (DFT) calculations. The finding indicates that Compound 2 (ZINC000072136376) has shown better binding and a significant inhibitory effect on AcrA, while Compound 3 (ZINC000072266819) has shown stronger binding and substantial inhibition effect on both non-mutant and mutated AcrB subunits. The identified derivatives could exhibit a better inhibitor and provide a potential approach for restoring the actions of resistant antibiotics.
Collapse
Affiliation(s)
- Shweta Singh Chauhan
- Computational Toxicology Facility, Toxicoinformatics & Industrial Research, CSIR-Indian Institute of Toxicology Research, Lucknow, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Anshika Gupta
- Computational Toxicology Facility, Toxicoinformatics & Industrial Research, CSIR-Indian Institute of Toxicology Research, Lucknow, India
| | - Aashna Srivastava
- Computational Toxicology Facility, Toxicoinformatics & Industrial Research, CSIR-Indian Institute of Toxicology Research, Lucknow, India
| | - Ramakrishnan Parthasarathi
- Computational Toxicology Facility, Toxicoinformatics & Industrial Research, CSIR-Indian Institute of Toxicology Research, Lucknow, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| |
Collapse
|
5
|
Sahoo M, Behera DU, Gaur M, Subudhi E. Molecular docking, molecular dynamics simulation, and MM/PBSA analysis of ginger phytocompounds as a potential inhibitor of AcrB for treating multidrug-resistant Klebsiella pneumoniae infections. J Biomol Struct Dyn 2024:1-17. [PMID: 38165647 DOI: 10.1080/07391102.2023.2299741] [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: 08/17/2023] [Accepted: 12/20/2023] [Indexed: 01/04/2024]
Abstract
The emergence of Multidrug resistance (MDR) in human pathogens has defected the existing antibiotics and compelled us to understand more about the basic science behind alternate anti-infective drug discovery. Soon, proteome analysis identified AcrB efflux pump protein as a promising drug target using plant-driven phytocompounds used in traditional medicine systems with lesser side effects. Thus, the present study aims to explore the novel, less toxic, and natural inhibitors of Klebsiella pneumoniae AcrB pump protein from 69 Zingiber officinale phyto-molecules available in the SpiceRx database through computational-biology approaches. AcrB protein's homology-modelling was carried out to get a 3D structure. The multistep-docking (HTVS, SP, and XP) were employed to eliminate less-suitable compounds in each step based on the docking score. The chosen hit-compounds underwent induced-fit docking (IFD). Based on the XP GScore, the top three compounds, epicatechin (-10.78), 6-gingerol (-9.71), and quercetin (-9.09) kcal/mol, were selected for further calculation of binding free energy (MM/GBSA). Furthermore, the short-listed compounds were assessed for their drug-like properties based on in silico ADMET properties and Pa, Pi values. In addition, the molecular dynamics simulation (MDS) studies for 250 ns elucidated the binding mechanism of epicatechin, 6-gingerol, and quercetin to AcrB. From the dynamic binding free energy calculations using MM/PBSA, 6-gingerol exhibited a strong binding affinity towards AcrB. Further, the 6-gingerol complex's energy fluctuation was observed from the free energy landscape. In conclusion, 6-gingerol has a promising inhibiting potential against the AcrB efflux pump and thus necessitates further validation through in vitro and in vivo experiments.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Maheswata Sahoo
- Centre for Biotechnology, Siksha 'O' Anusandhan (Deemed to be University), Bhubaneswar, Odisha, India
| | | | - Mahendra Gaur
- Drug Development, and Analysis Laboratory, School of Pharmaceutical Sciences, Siksha 'O' Anusandhan (Deemed to be University), Bhubaneswar, India
- Department of Biotechnology, Punjabi University, Patiala, India
| | - Enketeswara Subudhi
- Centre for Biotechnology, Siksha 'O' Anusandhan (Deemed to be University), Bhubaneswar, Odisha, India
| |
Collapse
|
6
|
Pisoni LA, Semple SJ, Liu S, Sykes MJ, Venter H. Combined Structure- and Ligand-Based Approach for the Identification of Inhibitors of AcrAB-TolC in Escherichia coli. ACS Infect Dis 2023; 9:2504-2522. [PMID: 37888944 DOI: 10.1021/acsinfecdis.3c00350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
The inhibition of efflux pumps is a promising approach to combating multidrug-resistant bacteria. We have developed a combined structure- and ligand-based model, using OpenEye software, for the identification of inhibitors of AcrB, the inner membrane protein component of the AcrAB-TolC efflux pump in Escherichia coli. From a database of 1391 FDA-approved drugs, 23 compounds were selected to test for efflux inhibition in E. coli. Seven compounds, including ivacaftor (25), butenafine (19), naftifine (27), pimozide (30), thioridazine (35), trifluoperazine (37), and meloxicam (26), enhanced the activity of at least one antimicrobial substrate and inhibited the efflux pump-mediated removal of the substrate Nile Red from cells. Ivacaftor (25) inhibited efflux dose dependently, had no effect on an E. coli strain with genomic deletion of the gene encoding AcrB, and did not damage the bacterial outer membrane. In the presence of a sub-minimum inhibitory concentration (MIC) of the outer membrane permeabilizer colistin, ivacaftor at 1 μg/mL reduced the MICs of erythromycin and minocycline by 4- to 8-fold. The identification of seven potential AcrB inhibitors shows the merits of a combined structure- and ligand-based approach to virtual screening.
Collapse
Affiliation(s)
- Lily A Pisoni
- Health and Biomedical Innovation, Clinical and Health Sciences, University of South Australia, Adelaide, South Australia 5000, Australia
- Quality Use of Medicines and Pharmacy Research Centre, Clinical and Health Sciences, University of South Australia, Adelaide, South Australia 5000, Australia
| | - Susan J Semple
- Quality Use of Medicines and Pharmacy Research Centre, Clinical and Health Sciences, University of South Australia, Adelaide, South Australia 5000, Australia
| | - Sida Liu
- Health and Biomedical Innovation, Clinical and Health Sciences, University of South Australia, Adelaide, South Australia 5000, Australia
| | - Matthew J Sykes
- Health and Biomedical Innovation, Clinical and Health Sciences, University of South Australia, Adelaide, South Australia 5000, Australia
| | - Henrietta Venter
- Health and Biomedical Innovation, Clinical and Health Sciences, University of South Australia, Adelaide, South Australia 5000, Australia
| |
Collapse
|
7
|
Phan TV, Nguyen VTV, Le MT, Nguyen BGD, Vu TT, Thai KM. Identification of efflux pump inhibitors for Pseudomonas aeruginosa MexAB-OprM via ligand-based pharmacophores, 2D-QSAR, molecular docking, and molecular dynamics approaches. Mol Divers 2023:10.1007/s11030-023-10758-9. [PMID: 37919619 DOI: 10.1007/s11030-023-10758-9] [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: 10/04/2023] [Accepted: 10/24/2023] [Indexed: 11/04/2023]
Abstract
Efflux pumps have been reported as one of the significant mechanisms by which bacteria evade the effects of multiple antibiotics. The tripartite efflux pump MexAB-OprM in Pseudomonas aeruginosa is one of the most significant multidrug efflux systems due to its broad resistance to antibiotics such as chloramphenicol, fluoroquinolones, lipophilic β-lactam antibiotics, nalidixic acid, novobiocin, rifampicin, and tetracycline. A promising strategy to overcome this resistance mechanism is to combine antibiotics with efflux pump inhibitors (EPIs), which can increase their intracellular concentration to enhance their biological activities. Based on 143 EPIs with chemically diverse skeletons, the 3D pharmacophore and 2D-QSAR modelings were developed and used for the virtual screening on 9.2 million compounds including ZINC15, DrugBank, and Traditional Chinese Medicine databases to identify new EPIs. The molecular docking was also performed to evaluate the binding affinity of potential EPIs to the distal-binding pocket of MexB and resulted in 611 potential EPIs. The structure-activity relationship analyses suggested that nitrogen heterocyclic compounds, piperazine and pyridine scaffolds, and amide derivatives are the most favorable chemically features for MexAB inhibitory activities. The results from molecular dynamics analysis in 100 ns indicated that ZINC009296881 and ZINC009200074 were the most potential MexB inhibitors with strong binding affinity to the distal pocket and MM/GBSA ∆Gbind values of - 38.97 and - 30.19 kcal mol-1, respectively. The predicted pharmacokinetic properties and toxicity of these compounds indicated their potential oral drugs. Multistep virtual screening of EPIs for MexAB-OprM, efflux pump multidrug resistant of P. aeruginosa.
Collapse
Affiliation(s)
- Thien-Vy Phan
- Faculty of Pharmacy, University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, 700000, Vietnam
- Faculty of Pharmacy, Nguyen Tat Thanh University, Ho Chi Minh City, 700000, Vietnam
| | - Vu-Thuy-Vy Nguyen
- Faculty of Pharmacy, University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, 700000, Vietnam
- Faculty of Pharmacy, Nguyen Tat Thanh University, Ho Chi Minh City, 700000, Vietnam
| | - Minh-Tri Le
- Faculty of Pharmacy, University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, 700000, Vietnam
- School of Medicine, Vietnam National University Ho Chi Minh City, Linh Trung Ward., Thu Duc Dist, Ho Chi Minh City, 700000, Vietnam
| | | | - Thanh-Thao Vu
- Faculty of Pharmacy, University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, 700000, Vietnam
| | - Khac-Minh Thai
- Faculty of Pharmacy, University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, 700000, Vietnam.
| |
Collapse
|
8
|
Mangiaterra G, Cedraro N, Vaiasicca S, Citterio B, Frangipani E, Biavasco F, Vignaroli C. Involvement of Acquired Tobramycin Resistance in the Shift to the Viable but Non-Culturable State in Pseudomonas aeruginosa. Int J Mol Sci 2023; 24:11618. [PMID: 37511375 PMCID: PMC10380639 DOI: 10.3390/ijms241411618] [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: 06/23/2023] [Revised: 07/14/2023] [Accepted: 07/17/2023] [Indexed: 07/30/2023] Open
Abstract
Persistent and viable but non-culturable (VBNC) Pseudomonas aeruginosa cells are mainly responsible for the recurrence and non-responsiveness to antibiotics of cystic fibrosis (CF) lung infections. The sub-inhibitory antibiotic concentrations found in the CF lung in between successive therapeutic cycles can trigger the entry into the VBNC state, albeit with a strain-specific pattern. Here, we analyzed the VBNC cell induction in the biofilms of two CF P. aeruginosa isolates, exposed to starvation with/without antibiotics, and investigated the putative genetic determinants involved. Total viable bacterial cells were quantified by the validated ecfX-targeting qPCR protocol and the VBNC cells were estimated as the difference between qPCR and cultural counts. The isolates were both subjected to whole genome sequencing, with attention focused on their carriage of aminoglycoside resistance genes and on identifying mutated toxin-antitoxin and quorum sensing systems. The obtained results suggest the variable contribution of different antibiotic resistance mechanisms to VBNC cell abundance, identifying a major contribution from tobramycin efflux, mediated by MexXY efflux pump overexpression. The genome analysis evidenced putative mutation hotspots, which deserve further investigation. Therefore, drug efflux could represent a crucial mechanism through which the VBNC state is entered and a potential target for anti-persistence strategies.
Collapse
Affiliation(s)
- Gianmarco Mangiaterra
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, Via S. Chiara 27, 61029 Urbino, Italy
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Nicholas Cedraro
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Salvatore Vaiasicca
- Department of Molecular and Clinical Sciences, Polytechnic University of Marche, Via Tronto 10/a, 60020 Ancona, Italy
| | - Barbara Citterio
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, Via S. Chiara 27, 61029 Urbino, Italy
| | - Emanuela Frangipani
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, Via S. Chiara 27, 61029 Urbino, Italy
| | - Francesca Biavasco
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Carla Vignaroli
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
| |
Collapse
|
9
|
Alobaidallah MSA, García V, De Mets R, Wellner SM, Thomsen LE, Herrero-Fresno A, Olsen JE. Uncovering the Important Genetic Factors for Growth during Cefotaxime-Gentamicin Combination Treatment in blaCTX-M-1 Encoding Escherichia coli. Antibiotics (Basel) 2023; 12:993. [PMID: 37370312 DOI: 10.3390/antibiotics12060993] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 05/26/2023] [Accepted: 05/29/2023] [Indexed: 06/29/2023] Open
Abstract
Due to the rapid spread of CTX-M type ESBLs, the rate of resistance to third-generation cephalosporin has increased among Gram-negative bacteria, especially in Escherichia coli, and there is a need to find ways to re-sensitize ESBL E. coli to cephalosporin treatment. A previous study showed that genes involved in protein synthesis were significantly up-regulated in the presence of subinhibitory concentration of cefotaxime (CTX) in a CTX-M-1-producing E. coli. In this study, the interaction between CTX and gentamicin (GEN), targeting protein synthesis, was evaluated in MG1655/pTF2, and the MIC of CTX was strongly reduced (128-fold) in the presence of this combnation therapy. Since the underlying mechanism behind this synergy is not known, we constructed a saturated transposon mutant library in MG1655/pTF2::blaCTX-M-1 containing 315,925 unique transposon insertions to measure mutant depletion upon exposure to CTX, GEN, and combination treatment of CTX and GEN by Transposon Directed Insertion-site Sequencing (TraDIS). We identified 57 genes that were depleted (log2FC ≤ -2 and with q.value ≤ 0.01) during exposure to CTX, 18 for GEN, and 31 for combination treatment of CTX and GEN. For validation, we deleted eight genes that were either uniquely identified in combination treatment, overlapped with monotherapy of GEN, or were shared between combination treatment and monotherapy with CTX and GEN. Of these genes, we found that the inactivation of dnaK, mnmA, rsgA, and ybeD increased the efficacy of both CTX and GEN treatment, the inactivation of cpxR and yafN increased the efficacy of only CTX, and the inactivation of mnmA, rsgA, and ybeD resulted in increased synergy between CTX and GEN. Thus, the study points to putative targets for helper drugs that can restore susceptibility to these important drugs, and it indicates that genes involved in protein synthesis are essential for the synergy between these two drugs. In summary, the study identified mutants that sensitize ESBL-producing E. coli to CTX and a combination of CTX and GEN, and it increased our understanding of the mechanism behind synergy between β-lactam and aminoglycoside drugs. This forms a framework for developing new strategies to combat infections caused by resistant bacteria.
Collapse
Affiliation(s)
- Mosaed Saleh A Alobaidallah
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870 Frederiksberg, Denmark
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud bin Abdulaziz University for Health Sciences, Jeddah 21423, Saudi Arabia
- King Abdullah International Medical Research Center, Jeddah 22384, Saudi Arabia
| | - Vanesa García
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870 Frederiksberg, Denmark
- Laboratorio de Referencia de Escherichia coli (LREC), Departamento de Microbioloxía e Parasitoloxía, Facultade de Veterinaria, Universidade de Santiago de Compostela (USC), 27002 Lugo, Spain
| | - Richard De Mets
- Department of Biomedical Sciences, Core Facility for Integrated Microscopy, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Sandra M Wellner
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870 Frederiksberg, Denmark
| | - Line E Thomsen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870 Frederiksberg, Denmark
| | - Ana Herrero-Fresno
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870 Frederiksberg, Denmark
- National Food Institute, Technical University of Denmark, 2800 Lyngby, Denmark
| | - John Elmerdahl Olsen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 1870 Frederiksberg, Denmark
| |
Collapse
|
10
|
Athar M, Gervasoni S, Catte A, Basciu A, Malloci G, Ruggerone P, Vargiu AV. Tripartite efflux pumps of the RND superfamily: what did we learn from computational studies? MICROBIOLOGY (READING, ENGLAND) 2023; 169. [PMID: 36972322 DOI: 10.1099/mic.0.001307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
Abstract
Bacterial resistance to antibiotics has been long recognized as a priority to address for human health. Among all micro-organisms, the so-called multi-drug resistant (MDR) bacteria, which are resistant to most, if not all drugs in our current arsenal, are particularly worrisome. The World Health Organization has prioritized the ESKAPE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacter species) pathogens, which include four Gram-negative bacterial species. In these bacteria, active extrusion of antimicrobial compounds out of the cell by means of 'molecular guns' known as efflux pumps is a main determinant of MDR phenotypes. The resistance-nodulation-cell division (RND) superfamily of efflux pumps connecting the inner and outer membrane in Gram-negative bacteria is crucial to the onset of MDR and virulence, as well as biofilm formation. Thus, understanding the molecular basis of the interaction of antibiotics and inhibitors with these pumps is key to the design of more effective therapeutics. With the aim to contribute to this challenge, and complement and inspire experimental research, in silico studies on RND efflux pumps have flourished in recent decades. Here, we review a selection of such investigations addressing the main determinants behind the polyspecificity of these pumps, the mechanisms of substrate recognition, transport and inhibition, as well as the relevance of their assembly for proper functioning, and the role of protein-lipid interactions. The journey will end with a perspective on the role of computer simulations in addressing the challenges posed by these beautifully complex machineries and in supporting the fight against the spread of MDR bacteria.
Collapse
Affiliation(s)
- Mohd Athar
- Physics Department, University of Cagliari, Cittadella Universitaria, SP 8 km 0.700, 09042, Monserrato (CA), Italy
| | - Silvia Gervasoni
- Physics Department, University of Cagliari, Cittadella Universitaria, SP 8 km 0.700, 09042, Monserrato (CA), Italy
| | - Andrea Catte
- Physics Department, University of Cagliari, Cittadella Universitaria, SP 8 km 0.700, 09042, Monserrato (CA), Italy
| | - Andrea Basciu
- Physics Department, University of Cagliari, Cittadella Universitaria, SP 8 km 0.700, 09042, Monserrato (CA), Italy
| | - Giuliano Malloci
- Physics Department, University of Cagliari, Cittadella Universitaria, SP 8 km 0.700, 09042, Monserrato (CA), Italy
| | - Paolo Ruggerone
- Physics Department, University of Cagliari, Cittadella Universitaria, SP 8 km 0.700, 09042, Monserrato (CA), Italy
| | - Attilio Vittorio Vargiu
- Physics Department, University of Cagliari, Cittadella Universitaria, SP 8 km 0.700, 09042, Monserrato (CA), Italy
| |
Collapse
|
11
|
Oyedara OO, Fadare OA, Franco-Frías E, Heredia N, García S. Computational assessment of phytochemicals of medicinal plants from Mexico as potential inhibitors of Salmonella enterica efflux pump AcrB protein. J Biomol Struct Dyn 2023; 41:1776-1789. [PMID: 34996337 DOI: 10.1080/07391102.2021.2024261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The AcrAB-TolC efflux pump (EP) confers multidrug resistance to Salmonella enterica, a major etiological agent of foodborne infections. Phytochemicals that inhibit the functions of AcrAB-TolC EP present ideal candidates for reversal of antibiotic resistance. Progressive technological advancements, have facilitated the development of computational methods that offer a rapid low-cost approach to screen and identify phytochemicals with inhibitory potential against EP. In this study, 71 phytochemicals derived from plants used for medicinal purposes in Mexico were screened for their potential as inhibitors of Salmonella AcrB protein using in silico approaches including molecular docking and molecular dynamics (MD) simulation. Consequently, naringenin, 5-methoxypsoralen, and licarin A were identified as candidate inhibitors of AcrB protein. The three phytochemicals bound distal/deep pocket (DP) and hydrophobic trap (HPT) residues of AcrB protein critical for interactions with inhibitors, with estimated binding free energies of -95.5 kJ/mol, -97.4 kJ/mol, and -143.8 kJ/mol for naringenin, 5-methoxypsoralen, and licarin A, respectively. Data from the 50 ns MD simulation study revealed stability of the protein-ligand complex and alterations in the AcrB protein DP conformation upon binding of phytochemicals to the DP and HPT regions. Based on the estimated binding free energy and interactions with three out of five residues lining the hydrophobic trap, licarin A demonstrated the highest inhibitory potential, supporting its further application as a candidate for overcoming drug resistance in pathogens. Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Omotayo O Oyedara
- Departamento de Microbiología e Inmunología, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, San Nicolás de los Garza, Nuevo León, México.,Department of Microbiology, Faculty of Basic and Applied Sciences, Osun State University, Osogbo, Nigeria
| | | | - Eduardo Franco-Frías
- Departamento de Microbiología e Inmunología, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, San Nicolás de los Garza, Nuevo León, México
| | - Norma Heredia
- Departamento de Microbiología e Inmunología, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, San Nicolás de los Garza, Nuevo León, México
| | - Santos García
- Departamento de Microbiología e Inmunología, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, San Nicolás de los Garza, Nuevo León, México
| |
Collapse
|
12
|
Phan TV, Nguyen VTV, Nguyen CHH, Vu TT, Tran TD, Le MT, Trinh DTT, Tran VH, Thai KM. Discovery of AcrAB-TolC pump inhibitors: Virtual screening and molecular dynamics simulation approach. J Biomol Struct Dyn 2023; 41:12503-12520. [PMID: 36762699 DOI: 10.1080/07391102.2023.2175381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 01/04/2023] [Indexed: 02/11/2023]
Abstract
AcrAB-TolC tripartite efflux pump, which belongs to the RND superfamily, is a main multi-drug efflux system of Escherichia coli (E. coli) because of the broad resistance on various antibiotics. With the discovering of efflux pump inhibitors (EPIs), a combination between these and antibiotics is one of the most promising therapies. Therefore, building a virtual screening model with prediction capacities for the efflux pump inhibitory activities of candidates from DrugBank and ZINC15 dataset, is one of the key goals of this project. Based on the database of 170 diverse chemical structures collected from 28 research journals, two 2D-QSAR models and a 3D-pharmacophore model have been performed. On the AcrB protein (PDB 4DX7), two binding sites have been discovered that match to the hydrophobic trap in the distal pocket and the switch loop in the proximal pocket. After virtual screening processes, twenty candidate AcrAB-TolC inhibitors have been subjected to molecular dynamics simulations, binding free energy calculations and ADMET predictions. The results indicate that three compounds namely DB09233, DB02581, and DB15224 are potential inhibitors with ΔGbind of -42.30 ± 4.58, -40.76 ± 7.30 and -31.06 ± 7.63 kcal.mol-1, respectively.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Thien-Vy Phan
- Faculty of Pharmacy, University of Medicine and Pharmacy at Ho Chi Minh city, Ho Chi Minh City, Vietnam
- Department of Pharmacy, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam
| | - Vu-Thuy-Vy Nguyen
- Faculty of Pharmacy, University of Medicine and Pharmacy at Ho Chi Minh city, Ho Chi Minh City, Vietnam
- Department of Pharmacy, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam
| | | | - Thanh-Thao Vu
- Faculty of Pharmacy, University of Medicine and Pharmacy at Ho Chi Minh city, Ho Chi Minh City, Vietnam
| | - Thanh-Dao Tran
- Faculty of Pharmacy, University of Medicine and Pharmacy at Ho Chi Minh city, Ho Chi Minh City, Vietnam
| | - Minh-Tri Le
- Faculty of Pharmacy, University of Medicine and Pharmacy at Ho Chi Minh city, Ho Chi Minh City, Vietnam
- School of Medicine, Vietnam National University Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Dieu-Thuong Thi Trinh
- Faculty of Traditional Medicine, University of Medicine and Pharmacy, Ho Chi Minh City, Vietnam
| | - Viet-Hung Tran
- Institute of Drug, Quality Control, Ho Chi Minh City, Vietnam
| | - Khac-Minh Thai
- Faculty of Pharmacy, University of Medicine and Pharmacy at Ho Chi Minh city, Ho Chi Minh City, Vietnam
| |
Collapse
|
13
|
Chodkowski JL, Shade A. A coevolution experiment between Flavobacterium johnsoniae and Burkholderia thailandensis reveals parallel mutations that reduce antibiotic susceptibility. MICROBIOLOGY (READING, ENGLAND) 2023; 169. [PMID: 36724091 DOI: 10.1099/mic.0.001267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
One interference mechanism of bacterial competition is the production of antibiotics. Bacteria exposed to antibiotics can resist antibiotic inhibition through intrinsic or acquired mechanisms. Here, we performed a coevolution experiment to understand the long-term consequences of antibiotic production and antibiotic susceptibility for two environmental bacterial strains. We grew five independent lines of the antibiotic-producing environmental strain, Burkholderia thailandensis E264, and the antibiotic-inhibited environmental strain, Flavobacterium johnsoniae UW101, together and separately on agar plates for 7.5 months (1.5 month incubations), transferring each line five times to new agar plates. We observed that the F. johnsoniae ancestor could tolerate the B. thailandensis-produced antibiotic through efflux mechanisms, but that the coevolved lines had reduced susceptibility. We then sequenced genomes from the coevolved and monoculture F. johnsoniae lines, and uncovered mutational ramifications for the long-term antibiotic exposure. The coevolved genomes from F. johnsoniae revealed four potential mutational signatures of reduced antibiotic susceptibility that were not observed in the evolved monoculture lines. Two mutations were found in tolC: one corresponding to a 33 bp deletion and the other corresponding to a nonsynonymous mutation. A third mutation was observed as a 1 bp insertion coding for a RagB/SusD nutrient uptake protein. The last mutation was a G83R nonsynonymous mutation in acetyl-coA carboxylayse carboxyltransferase subunit alpha (AccA). Deleting the 33 bp from tolC in the F. johnsoniae ancestor reduced antibiotic susceptibility, but not to the degree observed in coevolved lines. Furthermore, the accA mutation matched a previously described mutation conferring resistance to B. thailandensis-produced thailandamide. Analysis of B. thailandensis transposon mutants for thailandamide production revealed that thailandamide was bioactive against F. johnsoniae, but also suggested that additional B. thailandensis-produced antibiotics were involved in the inhibition of F. johnsoniae. This study reveals how multi-generational interspecies interactions, mediated through chemical exchange, can result in novel interaction-specific mutations, some of which may contribute to reductions in antibiotic susceptibility.
Collapse
Affiliation(s)
- John L Chodkowski
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
| | - Ashley Shade
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA.,Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA.,Program in Ecology, Evolution and Behavior, Michigan State University, East Lansing, MI 48824, USA.,Univ Lyon, CNRS, INSA Lyon, Université Claude Bernard Lyon 1, Ecole Centrale de Lyon, Ampère, UMR5005, 69134, Ecully cedex, France
| |
Collapse
|
14
|
Update on the Discovery of Efflux Pump Inhibitors against Critical Priority Gram-Negative Bacteria. Antibiotics (Basel) 2023; 12:antibiotics12010180. [PMID: 36671381 PMCID: PMC9854755 DOI: 10.3390/antibiotics12010180] [Citation(s) in RCA: 31] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 01/10/2023] [Accepted: 01/11/2023] [Indexed: 01/18/2023] Open
Abstract
Antimicrobial resistance (AMR) has become a major problem in public health leading to an estimated 4.95 million deaths in 2019. The selective pressure caused by the massive and repeated use of antibiotics has led to bacterial strains that are partially or even entirely resistant to known antibiotics. AMR is caused by several mechanisms, among which the (over)expression of multidrug efflux pumps plays a central role. Multidrug efflux pumps are transmembrane transporters, naturally expressed by Gram-negative bacteria, able to extrude and confer resistance to several classes of antibiotics. Targeting them would be an effective way to revive various options for treatment. Many efflux pump inhibitors (EPIs) have been described in the literature; however, none of them have entered clinical trials to date. This review presents eight families of EPIs active against Escherichia coli or Pseudomonas aeruginosa. Structure-activity relationships, chemical synthesis, in vitro and in vivo activities, and pharmacological properties are reported. Their binding sites and their mechanisms of action are also analyzed comparatively.
Collapse
|
15
|
Chetri S. The culmination of multidrug-resistant efflux pumps vs. meager antibiotic arsenal era: Urgent need for an improved new generation of EPIs. Front Microbiol 2023; 14:1149418. [PMID: 37138605 PMCID: PMC10149990 DOI: 10.3389/fmicb.2023.1149418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Accepted: 03/13/2023] [Indexed: 05/05/2023] Open
Abstract
Efflux pumps function as an advanced defense system against antimicrobials by reducing the concentration of drugs inside the bacteria and extruding the substances outside. Various extraneous substances, including antimicrobials, toxic heavy metals, dyes, and detergents, have been removed by this protective barrier composed of diverse transporter proteins found in between the cell membrane and the periplasm within the bacterial cell. In this review, multiple efflux pump families have been analytically and widely outlined, and their potential applications have been discussed in detail. Additionally, this review also discusses a variety of biological functions of efflux pumps, including their role in the formation of biofilms, quorum sensing, their survivability, and the virulence in bacteria, and the genes/proteins associated with efflux pumps have also been explored for their potential relevance to antimicrobial resistance and antibiotic residue detection. A final discussion centers around efflux pump inhibitors, particularly those derived from plants.
Collapse
|
16
|
Phan TV, Nguyen CHH, Nguyen VTV. 3D-Pharmacophore and Molecular Docking Studies for AcrAB-TolC Efflux Pump Potential Inhibitors from DrugBank and Traditional Chinese Medical Database. Open Access Maced J Med Sci 2022. [DOI: 10.3889/oamjms.2022.11081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Background: Due to the widespread resistance to several antibiotics, the AcrAB-TolC tripartite efflux pump is the primary multi-drug efflux system of Escherichia coli. One of the most promising treatments since the discovery of efflux pump inhibitors is the combination of them with antibiotics.
AIM: Based on the efflux pump inhibitor database and the structure of AcrB, the research was created the virtual screening models with prediction capabilities for the efflux pump inhibitory effects of candidates from the DrugBank and Traditional Chinese Medical databank.
Methods: The pharmacophore models were developed by MOE 2015.10 software using a database of 119 efflux pump inhibitors discovered in 12 research publications and belonged to different structural classes. The binding site was found on the AcrB protein (PDB: 4DX7) by LeadIT 2.0.2 software that corresponds to the hydrophobic trap in the proximal pocket.
Results: The potential inhibitors which satisfied the pharmacophore model and had docking scores under -20 kJ.mol-1 have been established. In which, TCM_20290, DB00303, DB04642, DB08116, TCM_29530, and 2,5-dimethyl-3-O-D-glucopyranosyl-naphthol have the best docking scores of -32.76, -26.59, -26.14, -25.62, -24.88, and -22.82 kJ.mol-1, respectively.
Conclusions: After the screening, the result was obtained six compounds may be potential efflux pump inhibitors that can be used for additional studies. In the future, further in vitro and in vivo research should be required to confirm the effects of these compounds. The ongoing battle against antibiotic resistance shows promise with the finding on initiators that can obstruct AcrAB–TolC multidrug efflux pumps.
Keywords: AcrAB-TolC, inhibitors, Escherichia coli, pharmacophore, molecular docking.
Collapse
|
17
|
New Chalcone-Triazole Hybrids with Promising Antimicrobial Activity in Multidrug Resistance Strains. Int J Mol Sci 2022; 23:ijms232214291. [PMID: 36430768 PMCID: PMC9697807 DOI: 10.3390/ijms232214291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/09/2022] [Accepted: 11/16/2022] [Indexed: 11/19/2022] Open
Abstract
Resistance to antibiotics is an emerging problem worldwide, which leads to an increase in morbidity and mortality rates. Several mechanisms are attributed to bacterial resistance, overexpression of efflux pumps being one of the most prominent. As an attempt to develop new effective antimicrobial drugs, which could be able to act against resistant bacterial strains and considering the antimicrobial potential of flavonoids and triazolyl flavonoid derivatives, in particular chalcones, a small library of chalcone derivatives was synthesized and evaluated for its potential to act as antimicrobials and/or adjuvants in combination with antibiotics towards resistant bacteria. Although only compound 7 was able to act as antibacterial, compounds 1, 2, 4, 5, 7, and 9 revealed to be able to potentiate the activity of antibiotics in resistant bacteria. Moreover, five compounds (3, 5-8) demonstrated to be effective inhibitors of efflux pumps in Salmonella enterica serovar Typhimurium SL1344, and four compounds (1, 3, 7, and 10) showed higher ability than reserpine to inhibit biofilm formation of resistant Staphylococcus aureus 272123. Together, our results showed the potential of these compounds regarding reversion of bacterial resistance.
Collapse
|
18
|
Drug Efflux Pump Inhibitors: A Promising Approach to Counter Multidrug Resistance in Gram-Negative Pathogens by Targeting AcrB Protein from AcrAB-TolC Multidrug Efflux Pump from Escherichia coli. BIOLOGY 2022; 11:biology11091328. [PMID: 36138807 PMCID: PMC9495857 DOI: 10.3390/biology11091328] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 08/26/2022] [Accepted: 08/27/2022] [Indexed: 11/17/2022]
Abstract
Simple Summary Multidrug-resistant bacterial infections, especially that caused by Gram-negative bacteria, have posed serious health issues worldwide. Bacteria have different mechanisms that can confer multidrug resistance to bacteria, among these mechanisms are drug efflux pumps that play the main role in conferring multidrug resistance by recognizing then expelling a wide range of compounds, especially antibiotics, and reducing their concentration to sub-toxic levels. Small molecule inhibitors that target drug efflux pumps especially the AcrAB-TolC multidrug efflux pump, from E. coli, appear as a new promising and attractive approach that could increase the required accumulation of antimicrobials to eliminate bacteria as well as leading to reverse antibiotic resistance and prevent the development of resistance in clinically relevant bacterial pathogens and enhances the activity of antibiotics or prolong their effectiveness. Abstract Infections caused by multidrug resistance (MDR) of Gram-negative bacteria have become one of the most severe public health problems worldwide. The main mechanism that confers MDR to bacteria is drug efflux pumps, as they expel a wide range of compounds, especially antibiotics. Among the different types of drug efflux pumps, the resistance nodulation division (RND) superfamily confers MDR to various Gram-negative bacteria species. The AcrAB-TolC multidrug efflux pump, from E. coli, a member of RND, is the best-characterized example and an excellent model for understanding MDR because of an abundance of functional and structural data. Small molecule inhibitors that target the AcrAB-TolC drug efflux pump represent a new solution to reversing MDR in Gram-negative bacteria and restoring the efficacy of various used drugs that are clinically relevant to these pathogens, especially in the high shortage of drugs for multidrug-resistant Gram-negative bacteria. This review will investigate solutions of MDR in Gram-negative bacteria by studying the inhibition of the AcrAB-TolC multidrug efflux pump.
Collapse
|
19
|
Uddin Mahamud AGMS, Nahar S, Ashrafudoulla M, Park SH, Ha SD. Insights into antibiofilm mechanisms of phytochemicals: Prospects in the food industry. Crit Rev Food Sci Nutr 2022; 64:1736-1763. [PMID: 36066482 DOI: 10.1080/10408398.2022.2119201] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The recalcitrance of microbial aggregation or biofilm in the food industry underpins the emerging antimicrobial resistance among foodborne pathogens, exacerbating the phenomena of food spoilage, processing and safety management failure, and the prevalence of foodborne illnesses. The challenges of growing tolerance to current chemical and disinfectant-based antibiofilm strategies have driven the urgency in finding a less vulnerable to bacterial resistance, effective alternative antibiofilm agent. To address these issues, various novel strategies are suggested in current days to combat bacterial biofilm. Among the innovative approaches, phytochemicals have already demonstrated their excellent performance in preventing biofilm formation and bactericidal actions against resident bacteria within biofilms. However, the diverse group of phytochemicals and their different modes of action become a barrier to applying them against specific pathogenic biofilm-formers. This phenomenon mandates the need to elucidate the multi-mechanistic actions of phytochemicals to design an effective novel antibiofilm strategy. Therefore, this review critically illustrates the structure - activity relationship, functional sites of actions, and target molecules of diverse phytochemicals regarding multiple major antibiofilm mechanisms and reversal mechanisms of antimicrobial resistance. The implementation of the in-depth knowledge will hopefully aid future studies for developing phytochemical-based next-generation antimicrobials.
Collapse
Affiliation(s)
- A G M Sofi Uddin Mahamud
- School of Food Science and Technology, Chung-Ang University, Anseong-si, Gyeonggi-do, Republic of Korea
| | - Shamsun Nahar
- School of Food Science and Technology, Chung-Ang University, Anseong-si, Gyeonggi-do, Republic of Korea
| | - Md Ashrafudoulla
- School of Food Science and Technology, Chung-Ang University, Anseong-si, Gyeonggi-do, Republic of Korea
| | - Si Hong Park
- Department of Food Science and Technology, Oregon State University, Corvallis, OR, USA
| | - Sang-Do Ha
- School of Food Science and Technology, Chung-Ang University, Anseong-si, Gyeonggi-do, Republic of Korea
| |
Collapse
|
20
|
Song L, Hu X, Ren X, Liu J, Liu X. Antibacterial Modes of Herbal Flavonoids Combat Resistant Bacteria. Front Pharmacol 2022; 13:873374. [PMID: 35847042 PMCID: PMC9278433 DOI: 10.3389/fphar.2022.873374] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 05/17/2022] [Indexed: 12/21/2022] Open
Abstract
The increasing dissemination of multidrug resistant (MDR) bacterial infections endangers global public health. How to develop effective antibacterial agents against resistant bacteria is becoming one of the most urgent demands to solve the drug resistance crisis. Traditional Chinese medicine (TCM) with multi-target antibacterial actions are emerging as an effective way to combat the antibacterial resistance. Based on the innovative concept of organic wholeness and syndrome differentiation, TCM use in antibacterial therapies is encouraging. Herein, advances on flavonoid compounds of heat-clearing Chinese medicine exhibit their potential for the therapy of resistant bacteria. In this review, we focus on the antibacterial modes of herbal flavonoids. Additionally, we overview the targets of flavonoid compounds and divide them into direct-acting antibacterial compounds (DACs) and host-acting antibacterial compounds (HACs) based on their modes of action. We also discuss the associated functional groups of flavonoid compounds and highlight recent pharmacological activities against diverse resistant bacteria to provide the candidate drugs for the clinical infection.
Collapse
Affiliation(s)
- Lianyu Song
- Beijing Traditional Chinese Veterinary Engineering Center and Beijing Key Laboratory of Traditional Chinese Veterinary Medicine, Beijing University of Agriculture, Changping, China
| | - Xin Hu
- Animal Science and Technology College, Beijing University of Agriculture, Changping, China
| | - Xiaomin Ren
- Beijing Traditional Chinese Veterinary Engineering Center and Beijing Key Laboratory of Traditional Chinese Veterinary Medicine, Beijing University of Agriculture, Changping, China
| | - Jing Liu
- Animal Science and Technology College, Beijing University of Agriculture, Changping, China
| | - Xiaoye Liu
- Beijing Traditional Chinese Veterinary Engineering Center and Beijing Key Laboratory of Traditional Chinese Veterinary Medicine, Beijing University of Agriculture, Changping, China
- Animal Science and Technology College, Beijing University of Agriculture, Changping, China
- *Correspondence: Xiaoye Liu,
| |
Collapse
|
21
|
Sundaramoorthy NS, Shankaran P, Gopalan V, Nagarajan S. New tools to mitigate drug resistance in Enterobacteriaceae - Escherichia coli and Klebsiella pneumoniae. Crit Rev Microbiol 2022:1-20. [PMID: 35649163 DOI: 10.1080/1040841x.2022.2080525] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Treatment to common bacterial infections are becoming ineffective of late, owing to the emergence and dissemination of antibiotic resistance globally. Escherichia coli and Klebsiella pneumoniae are the most notorious microorganisms and are among the critical priority pathogens listed by WHO in 2017. These pathogens are the predominant cause of sepsis, urinary tract infections (UTIs), pneumonia, meningitis and pyogenic liver abscess. Concern arises due to the resistance of bacteria to most of the beta lactam antibiotics like penicillin, cephalosporin, monobactams and carbapenems, even to the last resort antibiotics like colistin. Preventing influx by modulation of porins, extruding the antibiotics by overexpression of efflux pumps, mutations of drug targets/receptors, biofilm formation, altering the drug molecules and rendering them ineffective are few resistance mechanisms that are adapted by Enterobacteriaeceae upon exposure to antibiotics. The situation is exacerbated due to the process of horizontal gene transfer (HGT), wherein the genes encoding resistance mechanisms are transferred to the neighbouring bacteria through plasmids/phages/uptake of free DNA. Carbapenemases, other beta lactamases and mcr genes coding for colistin resistance are widely disseminated leading to limited/no therapeutic options against those infections. Development of new antibiotics can be viewed as a possible solution but it involves major investment, time and labour despite which, the bacteria can easily adapt to the new antibiotic and evolve resistance in a relatively short time. Targeting the resistance mechanisms can be one feasible alternative to tackle these multidrug resistant (MDR) pathogens. Removal of plasmid (plasmid curing) causing resistance, use of bacteriophages and bacteriotherapy can be other potential approaches to combat infections caused by MDR E. coli and K. pneumoniae. The present review discusses the efficacies of these therapies in mitigating these infections, which can be potentially used as an adjuvant therapy along with existing antibiotics.
Collapse
Affiliation(s)
- Niranjana Sri Sundaramoorthy
- Center for Research on Infectious Diseases, School of Chemical and Biotechnology, SASTRA deemed University, Thanjavur, Tamil Nadu, India
| | - Prakash Shankaran
- Center for Research on Infectious Diseases, School of Chemical and Biotechnology, SASTRA deemed University, Thanjavur, Tamil Nadu, India
| | - Vidhya Gopalan
- Department of Virology, Kings Institute of Preventative Medicine, Guindy, Chennai, Tamil Nadu, India
| | - Saisubramanian Nagarajan
- Center for Research on Infectious Diseases, School of Chemical and Biotechnology, SASTRA deemed University, Thanjavur, Tamil Nadu, India
| |
Collapse
|
22
|
Rahmati A, Shakib P, Javadi A, Zolfaghari MR. Synthesis and Evaluation of Antimicrobial Activities of Gold and ZnO Nanoparticles on Inhibiting the MexAB-OprM Efflux Pump in Pseudomonas aeruginosa Isolates. BIONANOSCIENCE 2022. [DOI: 10.1007/s12668-022-00992-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
23
|
Phenolic Compound Ethyl 3,4-Dihydroxybenzoate Retards Drug Efflux and Potentiates Antibiotic Activity. Antibiotics (Basel) 2022; 11:antibiotics11040497. [PMID: 35453250 PMCID: PMC9029221 DOI: 10.3390/antibiotics11040497] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 04/04/2022] [Accepted: 04/06/2022] [Indexed: 12/04/2022] Open
Abstract
The World Health Organization indicated that antibiotic resistance is one of the greatest threats to health, food security, and development in the world. Drug resistance efflux pumps are essential for antibiotic resistance in bacteria. Here, we evaluated the plant phenolic compound ethyl 3,4-dihydroxybenzoate (EDHB) for its efflux pump inhibitory (EPI) activity against drug-resistant Escherichia coli. The half-maximal inhibitory concentration, modulation assays, and time-kill studies indicated that EDHB has limited antibacterial activity but can potentiate the activity of antibiotics for drug-resistant E. coli. Dye accumulation/efflux and MALDI-TOF studies showed that EDHB not only significantly increases dye accumulation and reduces dye efflux but also increases the extracellular amount of antibiotics in the drug-resistant E. coli, indicating its interference with substrate translocation via a bacterial efflux pump. Molecular docking analysis using AutoDock Vina indicated that EDHB putatively posed within the distal binding pocket of AcrB and in close interaction with the residues by H-bonds and hydrophobic contacts. Additionally, EDHB showed an elevated postantibiotic effect on drug-resistant E. coli. Our toxicity assays showed that EDHB did not change the bacterial membrane permeability and exhibited mild human cell toxicity. In summary, these findings indicate that EDHB could serve as a potential EPI for drug-resistant E. coli.
Collapse
|
24
|
In Silico and In Vitro Screening of Natural Compounds as Broad-Spectrum β-Lactamase Inhibitors against Acinetobacter baumannii New Delhi Metallo-β-lactamase-1 (NDM-1). BIOMED RESEARCH INTERNATIONAL 2022; 2022:4230788. [PMID: 35372567 PMCID: PMC8966755 DOI: 10.1155/2022/4230788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 02/10/2022] [Accepted: 02/17/2022] [Indexed: 11/18/2022]
Abstract
Antibiotic resistance is one of the significant problems globally; there is an increase in resistance with introducing every new class of antibiotics. Further, this has become one of the reasons for arising of new resistance mechanisms in Acinetobacter baumannii. In this study, we have screened natural compounds as a possible inhibitor against the NDM-1 β-lactamase enzyme from A. baumannii using a combination of in silico methods and in vitro evaluation. The database of natural compounds was screened against NDM-1 protein, using Glide docking, followed by QM-polarised ligand docking (QPLD). When the screened hits were validated in vitro, withaferin A and mangiferin had good IC50 values in reducing the activity of NDM-1 enzymes, and their fractional inhibitory concentration index (FICI) was ascertained in combination with imipenem. The withaferin A and mangiferin-NDM-1 docking complexes were analyzed for structural stability by molecular dynamic simulation analysis using GROMACS for 100 ns. The molecular properties of the natural compounds were then calculated using density functional theory (DFT). Withaferin A and mangiferin showed promising inhibitory activity and can be a natural compound candidate inhibitor synergistically used along with carbapenems against NDM-1 producing A. baumannii.
Collapse
|
25
|
Gan WK, Liew HS, Pua LJW, Ng XY, Fong KW, Cheong SL, Liew YK, Low ML. Novel Cu(II) Schiff Base Complex Combination with Polymyxin B/Phenylalanine-Arginine β-Naphthylamide Against Various Bacterial Strains. Int J Pept Res Ther 2022. [DOI: 10.1007/s10989-021-10358-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
|
26
|
Effect of black pepper essential oil on quorum sensing and efflux pump systems in the fish-borne spoiler Pseudomonas psychrophila KM02 identified by RNA-seq, RT-qPCR and molecular docking analyses. Food Control 2021. [DOI: 10.1016/j.foodcont.2021.108284] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
|
27
|
Flavonoids as Inhibitors of Bacterial Efflux Pumps. Molecules 2021; 26:molecules26226904. [PMID: 34833994 PMCID: PMC8625893 DOI: 10.3390/molecules26226904] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 11/09/2021] [Accepted: 11/12/2021] [Indexed: 11/17/2022] Open
Abstract
Flavonoids are widely occurring secondary plant constituents, and are abundant in vegetable and fruit diets as well as herbal medicines. Therapeutic treatment options for bacterial infections are limited due to the spread of antimicrobial resistances. Hence, in a number of studies during the last few years, different classes of plant secondary metabolites as resistance-modifying agents have been carried out. In this review, we present the role of flavonoids as inhibitors of bacterial efflux pumps. Active compounds could be identified in the subclasses of chalcones, flavan-3-ols, flavanones, flavones, flavonols, flavonolignans and isoflavones; by far the majority of compounds were aglycones, although some glycosides like kaempferol glycosides with p-coumaroyl acylation showed remarkable results. Staphylococcus aureus NorA pump was the focus of many studies, followed by mycobacteria, whereas Gram-negative bacteria are still under-investigated.
Collapse
|
28
|
Agreles MAA, Cavalcanti IDL, Cavalcanti IMF. The Role of Essential Oils in the Inhibition of Efflux Pumps and Reversion of Bacterial Resistance to Antimicrobials. Curr Microbiol 2021; 78:3609-3619. [PMID: 34432112 DOI: 10.1007/s00284-021-02635-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 08/17/2021] [Indexed: 01/09/2023]
Abstract
Due to the deaths from infections caused by multidrug-resistant microorganisms worldwide, the World Health Organization considers antibiotic resistance to be a critical global public health problem. Bacterial resistance mechanisms are diverse and can be acquired through the overexpression of transmembrane proteins that are called efflux pumps, which act by expelling drugs from the intracellular environment, thereby preventing their action and contributing to the severity of infections. Efflux pumps are one of the main mechanisms of bacterial resistance, and it is important to identify new molecules that are capable of inhibiting the action of efflux pumps and circumvent the problem of resistance linked to the expression of these transmembrane proteins. The plants are promising candidates for obtaining biologically active substances, such as essential oils, with antimicrobial activity and inhibitors of efflux pumps, which can help in the resensitization of bacterial strains resistant to antibiotics. Therefore, this review aims to present the recently reported inhibitory activity of essential oils against bacterial pathogens that produce efflux pumps.
Collapse
Affiliation(s)
- Maria Anndressa Alves Agreles
- Laboratory of Immunopathology Keizo Asami (LIKA), Federal University of Pernambuco (UFPE), Av. Prof. Moraes Rego, 1235, Cidade Universitária, Recife, Pernambuco, CEP: 50670-901, Brazil
| | - Iago Dillion Lima Cavalcanti
- Laboratory of Immunopathology Keizo Asami (LIKA), Federal University of Pernambuco (UFPE), Av. Prof. Moraes Rego, 1235, Cidade Universitária, Recife, Pernambuco, CEP: 50670-901, Brazil
| | - Isabella Macário Ferro Cavalcanti
- Laboratory of Immunopathology Keizo Asami (LIKA), Federal University of Pernambuco (UFPE), Av. Prof. Moraes Rego, 1235, Cidade Universitária, Recife, Pernambuco, CEP: 50670-901, Brazil.
- Laboratory of Microbiology and Immunology, Academic Center of Vitória (CAV), Federal University of Pernambuco (UFPE), Rua do Alto do Reservatório s/n, Bela Vista, Vitória de Santo Antão, Pernambuco, CEP: 55608-680, Brazil.
| |
Collapse
|
29
|
Saha SB, Gupta VK, Ramteke PW. uCARE Chem Suite and uCAREChemSuiteCLI: Tools for bacterial resistome prediction. Genes Dis 2021; 8:721-729. [PMID: 34291144 PMCID: PMC8278538 DOI: 10.1016/j.gendis.2020.06.008] [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: 04/11/2020] [Revised: 06/08/2020] [Accepted: 06/21/2020] [Indexed: 11/23/2022] Open
Abstract
In the era of antibiotic resistance, in silico prediction of bacterial resistome profiles, likely to be associated with inactivation of new potential antibiotics is of utmost importance. Despite this, to the best of our knowledge, no tool exists for such prediction. Therefore, under the rationale that drugs with similar structures have similar resistome profiles, we developed two models, a deterministic model and a stochastic model, to predict the bacterial resistome likely to neutralize uncharacterized but potential chemical structures. The current version of the tool involves the prediction of a resistome for Escherichia coli and Pseudomonas aeruginosa. The deterministic model on omitting two diverse but relatively less characterized drug classes, polyketides and polypeptides showed an accuracy of 87%, a sensitivity of 85%, and a precision of 89%, whereas the stochastic model predicted antibiotic classes of the test set compounds with an accuracy of 72%, a sensitivity of 75%, and a precision of 83%. The models have been implemented in both a standalone package and an online server, uCAREChemSuiteCLI and uCARE Chem Suite, respectively. In addition to resistome prediction, the online version of the suite enables the user to visualize the chemical structure, classify compounds in 19 predefined drug classes, perform pairwise alignment, and cluster with database compounds using a graphical user interface. Availability uCARE Chem Suite can be browsed at: https://sauravsaha.shinyapps.io/ucarechemsuite2/, and uCAREChemSuiteCLI can be installed from: 1. CRAN (https://cran.r-project.org/package=uCAREChemSuiteCLI) and 2. GitHub (https://github.com/sauravbsaha/uCAREChemSuiteCLI).
Collapse
Affiliation(s)
- Saurav Bhaskar Saha
- Department of Computational Biology and Bioinformatics, JIBB, SHUATS, Prayagraj, Uttar Pradesh, 211007, India
| | - Vijai Kumar Gupta
- Department of Chemistry and Biotechnology, School of Science, Tallinn University of Technology, Akadeemia Tee 15, Tallinn, 12618, Estonia
| | | |
Collapse
|
30
|
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.
Collapse
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
| |
Collapse
|
31
|
Parthasarathy A, Borrego EJ, Savka MA, Dobson RCJ, Hudson AO. Amino acid-derived defense metabolites from plants: A potential source to facilitate novel antimicrobial development. J Biol Chem 2021; 296:100438. [PMID: 33610552 PMCID: PMC8024917 DOI: 10.1016/j.jbc.2021.100438] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 02/16/2021] [Accepted: 02/17/2021] [Indexed: 12/23/2022] Open
Abstract
For millennia, humanity has relied on plants for its medicines, and modern pharmacology continues to reexamine and mine plant metabolites for novel compounds and to guide improvements in biological activity, bioavailability, and chemical stability. The critical problem of antibiotic resistance and increasing exposure to viral and parasitic diseases has spurred renewed interest into drug treatments for infectious diseases. In this context, an urgent revival of natural product discovery is globally underway with special attention directed toward the numerous and chemically diverse plant defensive compounds such as phytoalexins and phytoanticipins that combat herbivores, microbial pathogens, or competing plants. Moreover, advancements in “omics,” chemistry, and heterologous expression systems have facilitated the purification and characterization of plant metabolites and the identification of possible therapeutic targets. In this review, we describe several important amino acid–derived classes of plant defensive compounds, including antimicrobial peptides (e.g., defensins, thionins, and knottins), alkaloids, nonproteogenic amino acids, and phenylpropanoids as potential drug leads, examining their mechanisms of action, therapeutic targets, and structure–function relationships. Given their potent antibacterial, antifungal, antiparasitic, and antiviral properties, which can be superior to existing drugs, phytoalexins and phytoanticipins are an excellent resource to facilitate the rational design and development of antimicrobial drugs.
Collapse
Affiliation(s)
- Anutthaman Parthasarathy
- Rochester Institute of Technology, Thomas H. Gosnell School of Life Sciences, Rochester, New York, USA
| | - Eli J Borrego
- Rochester Institute of Technology, Thomas H. Gosnell School of Life Sciences, Rochester, New York, USA
| | - Michael A Savka
- Rochester Institute of Technology, Thomas H. Gosnell School of Life Sciences, Rochester, New York, USA
| | - Renwick C J Dobson
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch, New Zealand; Bio21 Molecular Science and Biotechnology Institute, Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria, Australia
| | - André O Hudson
- Rochester Institute of Technology, Thomas H. Gosnell School of Life Sciences, Rochester, New York, USA.
| |
Collapse
|
32
|
|
33
|
Serçinoğlu O, Senturk D, Altinisik Kaya FE, Avci FG, Frlan R, Tomašič T, Ozbek P, Orelle C, Jault JM, Sariyar Akbulut B. Identification of novel inhibitors of the ABC transporter BmrA. Bioorg Chem 2020; 105:104452. [PMID: 33212311 DOI: 10.1016/j.bioorg.2020.104452] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 10/23/2020] [Accepted: 11/01/2020] [Indexed: 01/02/2023]
Abstract
The resistance of microbes to commonly used antibiotics has become a worldwide health problem. A major underlying mechanism of microbial antibiotic resistance is the export of drugs from bacterial cells. Drug efflux is mediated through the action of multidrug resistance efflux pumps located in the bacterial cell membranes. The critical role of bacterial efflux pumps in antibiotic resistance has directed research efforts to the identification of novel efflux pump inhibitors that can be used alongside antibiotics in clinical settings. Here, we aimed to find potential inhibitors of the archetypical ATP-binding cassette (ABC) efflux pump BmrA of Bacillus subtilis via virtual screening of the Mu.Ta.Lig. Chemotheca small molecule library. Molecular docking calculations targeting the nucleotide-binding domain of BmrA were performed using AutoDock Vina. Following a further drug-likeness filtering step based on Lipinski's Rule of Five, top 25 scorers were identified. These ligands were then clustered into separate groups based on their contact patterns with the BmrA nucleotide-binding domain. Six ligands with distinct contact patterns were used for further in vitro inhibition assays based on intracellular ethidium bromide accumulation. Using this methodology, we identified two novel inhibitors of BmrA from the Chemotheca small molecule library.
Collapse
Affiliation(s)
- Onur Serçinoğlu
- Department of Bioengineering, Recep Tayyip Erdogan University, Fener 53100, Rize, Turkey
| | - Duygu Senturk
- Department of Bioengineering, Marmara University, Kadikoy 34722, Istanbul, Turkey
| | | | - Fatma Gizem Avci
- Department of Bioengineering, Uskudar University, Uskudar 34662, Istanbul, Turkey
| | - Rok Frlan
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva 7, 1000 Ljubljana, Slovenia
| | - Tihomir Tomašič
- University of Ljubljana, Faculty of Pharmacy, Aškerčeva 7, 1000 Ljubljana, Slovenia
| | - Pemra Ozbek
- Department of Bioengineering, Marmara University, Kadikoy 34722, Istanbul, Turkey
| | - Cédric Orelle
- University of Lyon, CNRS, UMR5086 "Molecular Microbiology and Structural Biochemistry", 7 passage du Vercors, 69367 Lyon Cedex 7, France
| | - Jean-Michel Jault
- University of Lyon, CNRS, UMR5086 "Molecular Microbiology and Structural Biochemistry", 7 passage du Vercors, 69367 Lyon Cedex 7, France
| | | |
Collapse
|
34
|
Jewboonchu J, Saetang J, Saeloh D, Siriyong T, Rungrotmongkol T, Voravuthikunchai SP, Tipmanee V. Atomistic insight and modeled elucidation of conessine towards Pseudomonas aeruginosa efflux pump. J Biomol Struct Dyn 2020; 40:1480-1489. [PMID: 33025857 DOI: 10.1080/07391102.2020.1828169] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Drug-resistant Pseudomonas aeruginosa efflux pump extrudes antibiotics from cells for survival. Efflux pump inhibitor (EPI) thus becomes an interesting alternative to handle the drug-resistant bacteria. Conessine, a natural steroidal alkaloid from Holarrhena antidysenterica, previously exhibited efflux pump inhibitory potential. Our molecular docking and molecular dynamics (MD) studies provided atomistic information as well as the interaction of conessine with bacterial MexB efflux pump in phospholipid bilayer membrane to further the previous experimental report. Herein, the binding site and proposed mode of action of conessine were identified compared to known/commercial EPIs such as PAβN or designed-synthetic P9D. Our results explained conessine binding mode of action as an effective agent against the MexB efflux pump. The MD simulation also suggested that conessine was able to affect glycine loop (G-loop) flexibility, and the reduced G-loop flexibility due to conessine could hinder an antibiotics extrusion. In addition, our study suggested the conessine core structure buried in a hydrophobic region in the efflux pump similar to other known EPIs. Our finding could cope as a key for the design and development of the conessine derivative as novel EPI against P. aeruginosa.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Juntamanee Jewboonchu
- EZ-Mol-Design Laboratory and Department of Biomedical Sciences, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand
| | - Jirakrit Saetang
- EZ-Mol-Design Laboratory and Department of Surgery, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand
| | - Dennapa Saeloh
- Faculty of Medical Technology, Prince of Songkla University, Songkhla, Thailand
| | - Thanyaluck Siriyong
- Faculty of Thai Traditional Medicine, Prince of Songkla University, Songkhla, Thailand
| | - Thanyada Rungrotmongkol
- Biocatalyst and Environmental Biotechnology Research Unit, Department of Biochemistry, Faculty of Science, and Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok, Thailand
| | - Supayang Piyawan Voravuthikunchai
- Natural Product Research Center of Excellence, and Department of Microbiology, Faculty of Science, Prince of Songkla University, Songkhla, Thailand
| | - Varomyalin Tipmanee
- EZ-Mol-Design Laboratory and Department of Biomedical Sciences, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand
| |
Collapse
|
35
|
Efflux pumps as interventions to control infection caused by drug-resistance bacteria. Drug Discov Today 2020; 25:2307-2316. [PMID: 33011344 DOI: 10.1016/j.drudis.2020.09.028] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 08/06/2020] [Accepted: 09/24/2020] [Indexed: 12/30/2022]
Abstract
Antibiotic resistance has become a global concern for healthcare workers and physicians. Efflux pumps are one of the major mechanisms of resistance. Hence, we describe examples of natural efflux pump inhibitors used to combat antibiotic resistance.
Collapse
|
36
|
Matin MM, Chakraborty P, Alam MS, Islam MM, Hanee U. Novel mannopyranoside esters as sterol 14α-demethylase inhibitors: Synthesis, PASS predication, molecular docking, and pharmacokinetic studies. Carbohydr Res 2020; 496:108130. [PMID: 32863019 PMCID: PMC7427576 DOI: 10.1016/j.carres.2020.108130] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 08/02/2020] [Accepted: 08/09/2020] [Indexed: 12/18/2022]
Abstract
Direct unimolar one-step valeroylation of methyl α-d-mannopyranoside (MDM) furnished mainly 6-O-valeroate. However, similar reaction catalyzed by DMAP resulted 3,6-di-O-valeroate (21%) and 6-O-valeroate (47%) indicating reactivity sequence as 6-OH>3-OH>2-OH,4-OH. To get potential antimicrobial agents, 6-O-valeroate was converted into four 2,3,4-di-O-acyl esters, and 3,6-di-O-valeroate was converted into 2,4-di-O-acetate. Direct tetra-O-valeroylation of MDM gave a mixture of 2,3,4,6-tetra-O-valeroate and 2,3,6-tri-O-valeroate indicating that the C2-OH is more reactive than the equatorial C4-OH. The activity spectra analysis along with in vitro antimicrobial evaluation clearly indicated that these novel MDM esters had better antifungal activities over antibacterial agents. In this connection, molecular docking indicated that these MDM esters acted as competitive inhibitors of sterol 14α-demethylase (CYP51), an essential enzyme for clinical target to cure several infectious diseases. Furthermore, pharmacokinetic studies revealed that these MDM esters may be worth considering as potent candidates for oral and topical administration. Structure activity relationship (SAR) affirmed that saturated valeric chain (C5) in combination with caprylic (C8) chains was more promising CYP51 inhibitor over conventional antifungal antibiotics.
Collapse
Affiliation(s)
- Mohammed M Matin
- Bioorganic and Medicinal Chemistry Laboratory, Department of Chemistry, Faculty of Science, University of Chittagong, Chattogram, 4331, Bangladesh.
| | - Priyanka Chakraborty
- Bioorganic and Medicinal Chemistry Laboratory, Department of Chemistry, Faculty of Science, University of Chittagong, Chattogram, 4331, Bangladesh
| | - Muhammad S Alam
- Molecular Modeling & Drug Design Laboratory, Bangladesh Council of Scientific & Industrial Research (BCSIR) Laboratories, Chattogram, 4220, Bangladesh
| | - Mohammad M Islam
- Department of Biochemistry and Molecular Biology, Faculty of Biological Science, University of Chittagong, Chattogram, 4331, Bangladesh
| | - Umme Hanee
- Bioorganic and Medicinal Chemistry Laboratory, Department of Chemistry, Faculty of Science, University of Chittagong, Chattogram, 4331, Bangladesh
| |
Collapse
|
37
|
Rathi E, Kumar A, Kini SG. Computational approaches in efflux pump inhibitors: current status and prospects. Drug Discov Today 2020; 25:1883-1890. [PMID: 32712312 DOI: 10.1016/j.drudis.2020.07.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 07/02/2020] [Accepted: 07/13/2020] [Indexed: 01/02/2023]
Abstract
Treatment of bacterial infections is currently threatened by the development of antibiotic resistance and a poor pipeline of new antibiotics. Efflux pumps (EPs) are an integral part of the defense machinery of bacteria, preventing the entry of molecules, such as antibiotics, into the intracellular environment and resulting in antibiotic resistance. Therefore, research has focused on the discovery of novel EP inhibitors (EPIs), such as PAβN, D13-9001, and MBX2319. however, there are still no US Food and Drug Administration (FDA)-approved drugs targeting EPs because of the inadequate assimilation of the inhibitors. Here, we discuss the use of computational approaches for molecular mechanistic studies of EPIs to help direct future research.
Collapse
Affiliation(s)
- Ekta Rathi
- Department of Pharmaceutical Chemistry, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, 576104, India
| | - Avinash Kumar
- Department of Pharmaceutical Chemistry, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, 576104, India
| | - Suvarna G Kini
- Department of Pharmaceutical Chemistry, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, 576104, India.
| |
Collapse
|
38
|
Abstract
Efflux is an important mechanism in Gram-negative bacteria conferring multidrug resistance. Inhibition of efflux is an encouraging strategy to restore the antibacterial activity of antibiotics. Chlorpromazine and amitriptyline have been shown to behave as efflux inhibitors. However, their mode of action is poorly understood. Exposure of Salmonella enterica serovar Typhimurium and Escherichia coli to chlorpromazine selected for mutations within genes encoding RamR and MarR, regulators of the multidrug tripartite efflux pump AcrAB-TolC. Further experiments with S. Typhimurium containing AcrB D408A (a nonfunctional efflux pump) and chlorpromazine or amitriptyline resulted in the reversion of the mutant acrB allele to the wild type. Together, this suggests these drugs are AcrB efflux substrates. Subsequent docking studies with AcrB from S. Typhimurium and E. coli, followed by molecular dynamics simulations and free energy calculations showed that chlorpromazine and amitriptyline bind at the hydrophobic trap, a preferred binding site for substrates and inhibitors within the distal binding pocket of AcrB. Based on these simulations, we suggest that chlorpromazine and amitriptyline inhibit AcrB-mediated efflux by interfering with substrate binding. Our findings provide evidence that these drugs are substrates and inhibitors of AcrB, yielding molecular details of their mechanism of action and informing drug discovery of new efflux inhibitors.IMPORTANCE Efflux pumps of the resistance nodulation-cell division (RND) superfamily are major contributors to multidrug resistance for most of the Gram-negative ESKAPE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) pathogens. The development of inhibitors of these pumps would be highly desirable; however, several issues have thus far hindered all efforts at designing new efflux inhibitory compounds devoid of adverse effects. An alternative route to de novo design relies on the use of marketed drugs, for which side effects on human health have been already assessed. In this work, we provide experimental evidence that the antipsychotic drugs chlorpromazine and amitriptyline are inhibitors of the AcrB transporter, the engine of the major RND efflux pumps in Escherichia coli and Salmonella enterica serovar Typhimurium. Furthermore, in silico calculations have provided a molecular-level picture of the inhibition mechanism, allowing rationalization of experimental data and paving the way for similar studies with other classes of marketed compounds.
Collapse
|
39
|
Wu Y, Lou L, Xie ZR. A Pilot Study of All-Computational Drug Design Protocol-From Structure Prediction to Interaction Analysis. Front Chem 2020; 8:81. [PMID: 32117898 PMCID: PMC7028743 DOI: 10.3389/fchem.2020.00081] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 01/24/2020] [Indexed: 11/13/2022] Open
Abstract
Speeding up the drug discovery process is of great significance. To achieve that, high-efficiency methods should be exploited. The conventional wet-bench methods hardly meet the high-speed demand due to time-consuming experiments. Conversely, in silico approaches are much more efficient for drug discovery and design. However, in silico approaches usually serve as a supportive role in research processes. To fully exert the strength of computational methods, we propose a protocol which integrates various in silico approaches, from de novo protein structure prediction to ligand-protein interaction simulation. As a proof of concept, human SK2/calmodulin complex was used as a target for validation. First, we obtained a predicted structure of SK2/calmodulin and predicted binding sites which were consistent with the literature data. Then we investigated the ligand-protein interaction via virtual mutagenesis, flexible docking, and binding affinity calculation. As a result, the binding energies of mutants have similar trends compared with the EC50 values (R = 0.6 for NS309 in V481 mutants). The results indicate that our protocol can be applied to the drug design of structure unknown proteins. Our study also demonstrates that the integration of in silico approaches is feasible and it facilitates the acceleration of new drug discovery.
Collapse
Affiliation(s)
- Yifei Wu
- Computational Drug Discovery Laboratory, School of Electrical and Computer Engineering, College of Engineering, University of Georgia, Athens, GA, United States
| | - Lei Lou
- Computational Drug Discovery Laboratory, School of Electrical and Computer Engineering, College of Engineering, University of Georgia, Athens, GA, United States
| | - Zhong-Ru Xie
- Computational Drug Discovery Laboratory, School of Electrical and Computer Engineering, College of Engineering, University of Georgia, Athens, GA, United States
| |
Collapse
|
40
|
Identification of Mycobacterium tuberculosis CtpF as a target for designing new antituberculous compounds. Bioorg Med Chem 2019; 28:115256. [PMID: 31879181 DOI: 10.1016/j.bmc.2019.115256] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 12/04/2019] [Accepted: 12/06/2019] [Indexed: 01/08/2023]
Abstract
The emergence of tuberculosis (TB) produced by multi-drug resistance (MDR) and extensively-drug resistance (XDR) Mycobacterium tuberculosis (Mtb), encourages the development of new antituberculous compounds, as well as the identification of novel drug targets. In this regard, plasma membrane P-type ATPases are interesting targets because they play a crucial role in ion homeostasis and mycobacterial survival. We focused on Mtb CtpF, a calcium P-type ATPase that responds to a broad number of intraphagosomal conditions, as a novel target. In this study, we evaluated the capacity of cyclopiazonic acid (CPA), a well-known inhibitor of the sarco-endoplasmic reticulum Ca2+-ATPase (SERCA), to inhibit the ATPase activity of CtpF and the Mtb growth demonstrating that CtpF is a druggable target. A homology modeling of CtpF was generated for molecular docking studies of CtpF with CPA and key pharmacophoric features were identified, which were used to perform a pharmacophore-based virtual screening of the ZINC database, and to identify CtpF inhibitor candidates. Molecular docking-based virtual screening and MM-BGSA calculations of candidates allowed identifying six compounds with the best binding energies. The compounds displayed in vitro minimum inhibitory concentrations (MIC) ranging from 50 to 100 μg/mL, growth inhibitions from 29.5 to 64.0% on Mtb, and inhibitions of Ca2+-dependent ATPase activity in Mtb membrane vesicles (IC50) ranging from 4.1 to 35.8 μM. The compound ZINC63908257 was the best candidate by displaying a MIC of 50 μg/mL and a Ca2+ P-type ATPase inhibition of 45% with IC50 = 4.4 μM. Overall, the results indicate that CtpF is a druggable target for designing new antituberculous compounds.
Collapse
|
41
|
Measuring Small Molecule Binding to Escherichia coli AcrB by Surface Plasmon Resonance. Methods Mol Biol 2019. [PMID: 31773650 DOI: 10.1007/978-1-0716-0163-1_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Antimicrobial resistance (AMR) is rapidly becoming one of the great healthcare challenges. A common mechanism employed by pathogenic bacteria to avoid the action of certain antibiotics is to overexpress efflux pumps that can extrude these drugs from the cell rendering them ineffective. Small molecule inhibitors that target bacterial efflux pumps provide a route toward reversing AMR. Here, we describe the application of surface plasmon resonance (SPR) technology to characterize protein:small molecule interactions between the inner membrane protein AcrB subunit of the Escherichia coli AcrA-AcrB-TolC efflux pump and its substrates and novel inhibitors. The SPR assay provides quantitative data about the kinetics of binding that can help guide the development of new chemotherapies to combat AMR.
Collapse
|
42
|
Reza A, Sutton JM, Rahman KM. Effectiveness of Efflux Pump Inhibitors as Biofilm Disruptors and Resistance Breakers in Gram-Negative (ESKAPEE) Bacteria. Antibiotics (Basel) 2019; 8:antibiotics8040229. [PMID: 31752382 PMCID: PMC6963839 DOI: 10.3390/antibiotics8040229] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 11/07/2019] [Accepted: 11/12/2019] [Indexed: 12/21/2022] Open
Abstract
Antibiotic resistance represents a significant threat to the modern healthcare provision. The ESKAPEE pathogens (Enterococcus faecium., Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter spp. and Escherichia coli), in particular, have proven to be especially challenging to treat, due to their intrinsic and acquired ability to rapidly develop resistance mechanisms in response to environmental threats. The development of biofilm has been characterised as an essential contributing factor towards antimicrobial-resistance and tolerance. Several studies have implicated the involvement of efflux pumps in antibiotic resistance, both directly, via drug extrusion and indirectly, through the formation of biofilm. As a result, the underlying mechanism of these pumps has attracted considerable interest due to the potential of targeting these protein structures and developing novel adjunct therapies. Subsequent investigations have revealed the ability of efflux pump-inhibitors (EPIs) to block drug-extrusion and disrupt biofilm formation, thereby, potentiating antibiotics and reversing resistance of pathogen towards them. This review will discuss the potential of EPIs as a possible solution to antimicrobial resistance, examining different challenges to the design of these compounds, with an emphasis on Gram-negative ESKAPEE pathogens.
Collapse
Affiliation(s)
- Akif Reza
- Institute of Pharmaceutical Science, King’s College London, London, SE1 9NH, UK;
| | - J. Mark Sutton
- National Infections Service, Public Health England, Porton Down, Salisbury, Wiltshire SP4 0JG, UK;
| | - Khondaker Miraz Rahman
- Institute of Pharmaceutical Science, King’s College London, London, SE1 9NH, UK;
- Correspondence: ; Tel.: +44-(0)207-848-1891
| |
Collapse
|
43
|
Plant-derived secondary metabolites as the main source of efflux pump inhibitors and methods for identification. J Pharm Anal 2019; 10:277-290. [PMID: 32923005 PMCID: PMC7474127 DOI: 10.1016/j.jpha.2019.11.002] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 10/05/2019] [Accepted: 11/04/2019] [Indexed: 12/25/2022] Open
Abstract
The upsurge of multiple drug resistance (MDR) bacteria substantially diminishes the effectiveness of antibiotic arsenal and therefore intensifies the rate of therapeutic failure. The major factor in MDR is efflux pump-mediated resistance. A unique pump can make bacteria withstand a wide range of structurally diverse compounds. Therefore, their inhibition is a promising route to eliminate resistance phenomenon in bacteria. Phytochemicals are excellent alternatives as resistance-modifying agents. They can directly kill bacteria or interact with the crucial events of pathogenicity, thereby decreasing the ability of bacteria to develop resistance. Numerous botanicals display noteworthy efflux pumps inhibitory activities. Edible plants are of growing interest. Likewise, some plant families would be excellent sources of efflux pump inhibitors (EPIs) including Apocynaceae, Berberidaceae, Convolvulaceae, Cucurbitaceae, Fabaceae, Lamiaceae, and Zingiberaceae. Easily applicable methods for screening plant-derived EPIs include checkerboard synergy test, berberine uptake assay and ethidium bromide test. In silico high-throughput virtual detection can be evaluated as a criterion of excluding compounds with efflux substrate-like characteristics, thereby improving the selection process and extending the identification of EPIs. To ascertain the efflux activity inhibition, real-time PCR and quantitative mass spectrometry can be applied. This review emphasizes on efflux pumps and their roles in transmitting bacterial resistance and an update plant-derived EPIs and strategies for identification. Active efflux as the main resistance strategy in bacteria. Phytochemicals as promising alternatives against efflux pumps-mediated MDR. Herbals-based efflux pump inhibitors screening, the methods.
Collapse
|
44
|
Cooper R, Kirketerp-Møller K. Non-antibiotic antimicrobial interventions and antimicrobial stewardship in wound care. J Wound Care 2019; 27:355-377. [PMID: 29883284 DOI: 10.12968/jowc.2018.27.6.355] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Control of wound infection today relies largely on antibiotics, but the continual emergence of antibiotic-resistant microorganisms threatens a return to the pre-antibiotic era when physicians used antiseptics to prevent and manage infection. Some of those antiseptics are still used today, and others have become available. A diverse variety of non-antibiotic antimicrobial interventions are found on modern formularies. Unlike the mode of action of antibiotics, which affect specific cellular target sites of pathogens, many non-antibiotic antimicrobials affect multiple cellular target sites in a non-specific way. Although this reduces the likelihood of selecting for resistant strains of microorganisms, some have emerged and cross-resistance between antibiotics and antiseptics has been detected. With the prospect of a post-antibiotic era looming, ways to maintain and extend our antimicrobial armamentarium must be found. In this narrative review, current and emerging non-antibiotic antimicrobial strategies will be considered and the need for antimicrobial stewardship in wound care will be explained.
Collapse
Affiliation(s)
- Rose Cooper
- Professor of Microbiology, Department of Biomedical Science, Cardiff School of Health Sciences, Cardiff Metropolitan University, Western Avenue, Cardiff, UK
| | - Klaus Kirketerp-Møller
- Orthopaedic Surgeon, Copenhagen Wound Healing Center, Department of Dermatology and Wounds, Bispebjerg University Hospital, Bispebjerg Bakke 23, DK-2400 Copenhagen NV
| |
Collapse
|
45
|
Rohini K, Ramanathan K, Shanthi V. Multi-Dimensional Screening Strategy for Drug Repurposing with Statistical Framework—A New Road to Influenza Drug discovery. Cell Biochem Biophys 2019; 77:319-333. [DOI: 10.1007/s12013-019-00887-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Accepted: 09/16/2019] [Indexed: 12/17/2022]
|
46
|
Shaheen A, Afridi WA, Mahboob S, Sana M, Zeeshan N, Ismat F, Mirza O, Iqbal M, Rahman M. Reserpine Is the New Addition into the Repertoire of AcrB Efflux Pump Inhibitors. Mol Biol 2019. [DOI: 10.1134/s0026893319040113] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
47
|
Sheng Z, Sun Y, Yin Z, Tang K, Cao Z. Advances in computational approaches in identifying synergistic drug combinations. Brief Bioinform 2019; 19:1172-1182. [PMID: 28475767 DOI: 10.1093/bib/bbx047] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Indexed: 12/21/2022] Open
Abstract
Accumulated empirical clinical experience, supported by animal or cell line models, has initiated efforts of predicting synergistic combinatorial drugs with more-than-additive effect compared with the sum of the individual agents. Aiming to construct better computational models, this review started from the latest updated data resources of combinatorial drugs, then summarized the reported mechanism of the known synergistic combinations from aspects of drug molecular and pharmacological patterns, target network properties and compound functional annotation. Based on above, we focused on the main in silico strategies recently published, covering methods of molecular modeling, mathematical simulation, optimization of combinatorial targets and pattern-based statistical/learning model. Future thoughts are also discussed related to the role of natural compounds, drug combination with immunotherapy and management of adverse effects. Overall, with particular emphasis on mechanism of action of drug synergy, this review may serve as a rapid reference to design improved models for combinational drugs.
Collapse
Affiliation(s)
- Zhen Sheng
- School of Life Sciences and Technology, Tongji University
| | - Yi Sun
- School of Life Sciences and Technology, Tongji University
| | - Zuojing Yin
- School of Life Sciences and Technology, Tongji University
| | - Kailin Tang
- Advanced Institute of Translational Medicine, Tongji University
| | - Zhiwei Cao
- School of Life Sciences and Technology, Tongji University
| |
Collapse
|
48
|
The search of potential inhibitors of the AcrAB-TolC system of multidrug-resistant Escherichia coli: an in silico approach. Appl Microbiol Biotechnol 2019; 103:6309-6318. [PMID: 31209525 DOI: 10.1007/s00253-019-09954-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 05/09/2019] [Accepted: 05/28/2019] [Indexed: 01/07/2023]
Abstract
The number of infections caused by multidrug antibiotic resistance (MDR) species is increasing globally. The efflux pump system, AcrAB-TolC, confers Escherichia coli resistance to many antibiotics and results in poor treatment outcomes. Different rational drug design techniques were employed to search for a safe and effective AcrAB-TolC system inhibitor. Ligand docking was performed to analyze the binding of different ArcB substrates and/or inhibitors in the different AcrAB crystal structure binding sites. The validated docking site using the established docking preferences was used to perform virtual high-throughput screening on a large library of compounds. Domperidone, a known and safe over-the-counter antiemetic drug, was proposed as an effective ArcB inhibitor. Microbiological studies confirmed the computational results and domperidone reversed the resistance to the antibiotics: levofloxacin and ciprofloxacin in the MDR E. coli stains with an effect that surpassed the effect of the known efflux pump inhibitor, reserpine. In addition, it was able to increase both antibiotic effects on susceptible strains. This finding suggests that the antibiotic-domperidone combination can be used clinically to treat infections caused by multidrug-resistant E. coli strains.
Collapse
|
49
|
Uhlenbrock L, Ditz R, Strube J. Process Engineering Accelerating an Economic Industrialization Towards a Bio-Based World. Molecules 2019; 24:molecules24101853. [PMID: 31091783 PMCID: PMC6571845 DOI: 10.3390/molecules24101853] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 05/02/2019] [Accepted: 05/10/2019] [Indexed: 12/02/2022] Open
Abstract
The transition towards a bio-based world is a challenging undertaking. This perspective paper, from an engineering point of view, aims to provide an overview of existing projects and academic disciplines highlighting the potential benefit of increased interdisciplinary exchanges. Furthermore, the current utilization of biomass to produce biogas is discussed, including an economic assessment, showing the need for new strategies of biomass valorization. One solution could be the development of separation processes for the isolation of secondary plant metabolites, which have been especially valuable for pharmaceutical applications, e.g., taxotere ® and artemisinin. The economic feasibility is demonstrated in a case study, evaluating the purification potential of curcuminoids from Curcuma longa L. Subsequently, the conclusion discusses the limitations of large-scale industrial applications and the need for new separation techniques as a step towards a bio-based world.
Collapse
Affiliation(s)
- Lukas Uhlenbrock
- Institute for Separation and Process Technology, Clausthal University of Technology, 38678 Clausthal-Zellerfeld, Germany.
| | - Reinhard Ditz
- Institute for Separation and Process Technology, Clausthal University of Technology, 38678 Clausthal-Zellerfeld, Germany.
| | - Jochen Strube
- Institute for Separation and Process Technology, Clausthal University of Technology, 38678 Clausthal-Zellerfeld, Germany.
| |
Collapse
|
50
|
Chandar B, Bhattacharya D. Role of Natural Product in Modulation of Drug Transporters and New Delhi Metallo-β Lactamases. Curr Top Med Chem 2019; 19:874-885. [PMID: 30987566 DOI: 10.2174/1871529x19666190415110724] [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: 02/17/2019] [Revised: 03/20/2019] [Accepted: 04/05/2019] [Indexed: 11/22/2022]
Abstract
A rapid growth in drug resistance has brought options for treating antimicrobial resistance to a halt. Bacteria have evolved to accumulate a multitude of genes that encode resistance for a single drug within a single cell. Alternations of drug transporters are one of the causes for the development of resistance in drug interactions. Conversely, the production of enzymes also inactivates most antibiotics. The discovery of newer classes of antibiotics and drugs from natural products is urgently needed. Alternative medicines play an integral role in countries across the globe but many require validation for treatment strategies. It is essential to explore this chemical diversity in order to find novel drugs with specific activities which can be used as alternative drug targets. This review describes the interaction of drugs with resistant pathogens with a special focus on natural product-derived efflux pump and carbapenemase inhibitors.
Collapse
Affiliation(s)
- Brinda Chandar
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma, United States
| | - Debdutta Bhattacharya
- ICMRRegional Medical Research Centre (Dept. of Health Research, Govt. of India), Chandrasekharpur, Bhubaneswar, India
| |
Collapse
|