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Zhang L, Tian X, Sun L, Mi K, Wang R, Gong F, Huang L. Bacterial Efflux Pump Inhibitors Reduce Antibiotic Resistance. Pharmaceutics 2024; 16:170. [PMID: 38399231 PMCID: PMC10892612 DOI: 10.3390/pharmaceutics16020170] [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: 01/09/2024] [Revised: 01/22/2024] [Accepted: 01/24/2024] [Indexed: 02/25/2024] Open
Abstract
Bacterial resistance is a growing problem worldwide, and the number of deaths due to drug resistance is increasing every year. We must pay great attention to bacterial resistance. Otherwise, we may go back to the pre-antibiotic era and have no drugs on which to rely. Bacterial resistance is the result of several causes, with efflux mechanisms widely recognised as a significant factor in the development of resistance to a variety of chemotherapeutic and antimicrobial medications. Efflux pump inhibitors, small molecules capable of restoring the effectiveness of existing antibiotics, are considered potential solutions to antibiotic resistance and have been an active area of research in recent years. This article provides a review of the efflux mechanisms of common clinical pathogenic bacteria and their efflux pump inhibitors and describes the effects of efflux pump inhibitors on biofilm formation, bacterial virulence, the formation of bacterial persister cells, the transfer of drug resistance among bacteria, and mismatch repair. Numerous efforts have been made in the past 20 years to find novel efflux pump inhibitors which are known to increase the effectiveness of medicines against multidrug-resistant strains. Therefore, the application of efflux pump inhibitors has excellent potential to address and reduce bacterial resistance.
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Affiliation(s)
- Lan Zhang
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (L.Z.); (X.T.); (L.S.); (K.M.); (R.W.); (F.G.)
- National Reference Laboratory of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiaoyuan Tian
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (L.Z.); (X.T.); (L.S.); (K.M.); (R.W.); (F.G.)
- National Reference Laboratory of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan 430070, China
| | - Lei Sun
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (L.Z.); (X.T.); (L.S.); (K.M.); (R.W.); (F.G.)
- National Reference Laboratory of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan 430070, China
| | - Kun Mi
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (L.Z.); (X.T.); (L.S.); (K.M.); (R.W.); (F.G.)
- National Reference Laboratory of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan 430070, China
| | - Ru Wang
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (L.Z.); (X.T.); (L.S.); (K.M.); (R.W.); (F.G.)
- MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan 430070, China
| | - Fengying Gong
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (L.Z.); (X.T.); (L.S.); (K.M.); (R.W.); (F.G.)
- MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan 430070, China
| | - Lingli Huang
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; (L.Z.); (X.T.); (L.S.); (K.M.); (R.W.); (F.G.)
- National Reference Laboratory of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan 430070, China
- MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan 430070, China
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan 430070, China
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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.
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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.
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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.
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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
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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.
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Li Y, Ge X. Molecular Dynamics Investigation of MFS Efflux Pump MdfA Reveals an Intermediate State between Its Inward and Outward Conformations. Int J Mol Sci 2022; 24:ijms24010356. [PMID: 36613823 PMCID: PMC9820426 DOI: 10.3390/ijms24010356] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 12/22/2022] [Accepted: 12/23/2022] [Indexed: 12/28/2022] Open
Abstract
Multidrug resistance poses a major challenge to antibiotic therapy. A principal cause of antibiotic resistance is through active export by efflux pumps embedded in the bacterial membrane. Major facilitator superfamily (MFS) efflux pumps constitute a major group of transporters, which are often related to quinolone resistance in clinical settings. Although a rocker-switch model is proposed for description of their conformational transitions, detailed changes in this process remain poorly understood. Here we used MdfA from E. coli as a representative MFS efflux pump to investigate factors that can affect its conformational transition in silico. Molecular dynamics (MD) simulations of MdfA's inward and outward conformations revealed an intermediate state between these two conformations. By comparison of the subtle differences between the intermediate state and the average state, we indicated that conformational transition from outward to inward was initiated by protonation of the periplasmic side. Subsequently, hydrophilic interaction of the periplasmic side with water was promoted and the regional structure of helix 1 was altered to favor this process. As the hydrophobic interaction between MdfA and membrane was also increased, energy was concentrated and stored for the opposite transition. In parallel, salt bridges at the cytoplasmic side were altered to lower probabilities to facilitate the entrance of substrate. In summary, we described the total and local changes during MdfA's conformational transition, providing insights for the development of potential inhibitors.
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Affiliation(s)
| | - Xizhen Ge
- Correspondence: ; Tel.: +86-10-5207-2337
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6
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Li Y, Ge X. Enhanced internal ionic interaction of MFS efflux pump MdfA contributes to its elevated antibiotic export. Phys Chem Chem Phys 2022; 25:788-795. [PMID: 36510750 DOI: 10.1039/d2cp05059e] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Infections caused by Gram-negative pathogens are difficult to manage due to their antibiotic resistance. Efflux pumps, which transport intracellular toxins out of the cytoplasm, play an important role in the detoxification of bacteria when treated with antibiotics. The major facilitator superfamily (MFS) is a kind of widely distributed efflux pumps and can actively export clinically important antibiotics such as ciprofloxacin, while the role of internal ionic interactions in regulating drug export remains poorly understood. Herein we used a representative MFS efflux pump MdfA to investigate the impact of internal ionic interactions on the antibiotic resistance of E. coli. First, we identified the internal salt bridges of MdfA and searched their natural variants across all the sequenced E. coli isolates. By constructing these variants, we discovered that extending the salt bridge on the cytoplasmic side (E136D) conferred an elevated antibiotic resistance level of E. coli, and the level was further enhanced by combining it with an artificial mutation K346R. By analyzing the trajectories of MdfA's variants in molecular dynamics (MD) simulations, we revealed that ionic interaction strengths on the two sides were proportionally enhanced, while the protein flexibility was not affected. Moreover, enhanced interactions resulted in a larger surface for MdfA's protonation, suggesting a higher possibility for its activation. Collectively, our data revealed the importance of internal interactions on the drug export of MdfA, offering insights for the development of novel inhibitors against MFS efflux pumps.
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Affiliation(s)
- Ying Li
- College of Biochemical Engineering, Beijing Union University, Beijing, 100023, China.
| | - Xizhen Ge
- College of Biochemical Engineering, Beijing Union University, Beijing, 100023, China.
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Seukep AJ, Mbuntcha HG, Kuete V, Chu Y, Fan E, Guo MQ. What Approaches to Thwart Bacterial Efflux Pumps-Mediated Resistance? Antibiotics (Basel) 2022; 11:antibiotics11101287. [PMID: 36289945 PMCID: PMC9598416 DOI: 10.3390/antibiotics11101287] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/16/2022] [Accepted: 09/18/2022] [Indexed: 12/03/2022] Open
Abstract
An effective response that combines prevention and treatment is still the most anticipated solution to the increasing incidence of antimicrobial resistance (AMR). As the phenomenon continues to evolve, AMR is driving an escalation of hard-to-treat infections and mortality rates. Over the years, bacteria have devised a variety of survival tactics to outwit the antibiotic’s effects, yet given their great adaptability, unexpected mechanisms are still to be discovered. Over-expression of efflux pumps (EPs) constitutes the leading strategy of bacterial resistance, and it is also a primary driver in the establishment of multidrug resistance (MDR). Extensive efforts are being made to develop antibiotic resistance breakers (ARBs) with the ultimate goal of re-sensitizing bacteria to medications to which they have become unresponsive. EP inhibitors (EPIs) appear to be the principal group of ARBs used to impair the efflux system machinery. Due to the high toxicity of synthetic EPIs, there is a growing interest in natural, safe, and innocuous ones, whereby plant extracts emerge to be excellent candidates. Besides EPIs, further alternatives are being explored including the development of nanoparticle carriers, biologics, and phage therapy, among others. What roles do EPs play in the occurrence of MDR? What weapons do we have to thwart EP-mediated resistance? What are the obstacles to their development? These are some of the core questions addressed in the present review.
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Affiliation(s)
- Armel Jackson Seukep
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 437004, China
- Department of Biomedical Sciences, Faculty of Health Sciences, University of Buea, Buea P.O. Box 63, Cameroon
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 437004, China
- Innovation Academy for Drug Discovery and Development, Chinese Academy of Sciences, Shanghai 201203, China
| | - Helene Gueaba Mbuntcha
- Department of Biochemistry, Faculty of Science, University of Dschang, Dschang P.O. Box 67, Cameroon
| | - Victor Kuete
- Department of Biochemistry, Faculty of Science, University of Dschang, Dschang P.O. Box 67, Cameroon
| | - 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 100005, 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 100005, China
- College of Life Sciences, Linyi University, Linyi 276005, China
- Correspondence: (E.F.); (M.-Q.G.)
| | - Ming-Quan Guo
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 437004, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 437004, China
- Innovation Academy for Drug Discovery and Development, Chinese Academy of Sciences, Shanghai 201203, China
- Correspondence: (E.F.); (M.-Q.G.)
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Huang L, Wu C, Gao H, Xu C, Dai M, Huang L, Hao H, Wang X, Cheng G. Bacterial Multidrug Efflux Pumps at the Frontline of Antimicrobial Resistance: An Overview. Antibiotics (Basel) 2022; 11:antibiotics11040520. [PMID: 35453271 PMCID: PMC9032748 DOI: 10.3390/antibiotics11040520] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 04/01/2022] [Accepted: 04/08/2022] [Indexed: 02/06/2023] Open
Abstract
Multidrug efflux pumps function at the frontline to protect bacteria against antimicrobials by decreasing the intracellular concentration of drugs. This protective barrier consists of a series of transporter proteins, which are located in the bacterial cell membrane and periplasm and remove diverse extraneous substrates, including antimicrobials, organic solvents, toxic heavy metals, etc., from bacterial cells. This review systematically and comprehensively summarizes the functions of multiple efflux pumps families and discusses their potential applications. The biological functions of efflux pumps including their promotion of multidrug resistance, biofilm formation, quorum sensing, and survival and pathogenicity of bacteria are elucidated. The potential applications of efflux pump-related genes/proteins for the detection of antibiotic residues and antimicrobial resistance are also analyzed. Last but not least, efflux pump inhibitors, especially those of plant origin, are discussed.
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Samreen, Qais FA, Ahmad I. In silico screening and in vitro validation of phytocompounds as multidrug efflux pump inhibitor against E. coli. J Biomol Struct Dyn 2022; 41:2189-2201. [PMID: 35067192 DOI: 10.1080/07391102.2022.2029564] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Multiple drug resistance (MDR) in bacteria has increased globally in recent times. This has reduced the efficacy of antibiotics and increasing the rate of therapeutic failure. Targeting efflux pump by natural and synthetic compounds is one of the strategies to develop an ideal broad-spectrum resistance-modifying agent. Very few inhibitors of AcrB from natural sources have been reported till date. In the current study, 19 phytocompounds were screened for efflux pump inhibitory activity against AcrB protein of E. coli TG1 using molecular docking studies. The molecular dynamics simulation provided stability the protein (AcrB) and its complex with chlorogenic acid under physiological conditions. Moreover, the detailed molecular insights of the binding were also explored. The Lipinski rule of 5 and the drug-likeness prediction was determined using Swiss ADME server, while toxicity prediction was done using admetSAR and PROTOX-II webservers. Chlorogenic acid showed the highest binding affinity (-9.1 kcal mol-1) with AcrB protein among all screened phytocompounds. Consequently, all the phytocompounds that accede to Lipinski's rule, demonstrated a high LD50 value indicating that they are non-toxic except the phytocompound reserpine. Chlorogenic acid and capsaicin are filtered out based on the synergy with tetracycline having FIC index of 0.25 and 0.28. The percentage increase of EtBr fluorescence by chlorogenic acid was 36.6% followed by piperine (24.2%). Chlorogenic acid may be a promising efflux pump inhibitor that might be employed in combination therapy with tetracycline against E. coli, based on the above relationship between in silico screening and in vitro positive efflux inhibitory activity.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Samreen
- Department of Agricultural Microbiology, Faculty of Agricultural Sciences, Aligarh Muslim University, Aligarh, India
| | - Faizan Abul Qais
- Department of Agricultural Microbiology, Faculty of Agricultural Sciences, Aligarh Muslim University, Aligarh, India
| | - Iqbal Ahmad
- Department of Agricultural Microbiology, Faculty of Agricultural Sciences, Aligarh Muslim University, Aligarh, India
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Cacciotto P, Basciu A, Oliva F, Malloci G, Zacharias M, Ruggerone P, Vargiu AV. Molecular rationale for the impairment of the MexAB-OprM efflux pump by a single mutation in MexA. Comput Struct Biotechnol J 2022; 20:252-260. [PMID: 35024097 PMCID: PMC8717590 DOI: 10.1016/j.csbj.2021.11.042] [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: 09/02/2021] [Revised: 11/29/2021] [Accepted: 11/30/2021] [Indexed: 11/16/2022] Open
Abstract
Efflux pumps of the Resistance-Nodulation-cell Division (RND) superfamily contribute to intrinsic and acquired resistance in Gram-negative pathogens by expelling chemically unrelated antibiotics with high efficiency. They are tripartite systems constituted by an inner-membrane-anchored transporter, an outer membrane factor protein, and a membrane fusion protein. Multimerization of the membrane fusion protein is an essential prerequisite for full functionality of these efflux pumps. In this work, we employed complementary computational techniques to investigate the stability of a dimeric unit of MexA (the membrane fusion protein of the MexAB-OprM RND efflux pump of Pseudomonas aeruginosa), and to provide a molecular rationale for the effect of the G72S substitution, which affects MexAB-OprM functionality by impairing the assembly of MexA. Our findings indicate that: i) dimers of this protein are stable in multiple µs-long molecular dynamics simulations; ii) the mutation drastically alters the conformational equilibrium of MexA, favouring a collapsed conformation that is unlikely to form dimers or higher order assemblies. Unveiling the mechanistic aspects underlying large conformational distortions induced by minor sequence changes is informative to efforts at interfering with the activity of this elusive bacterial weapon. In this respect, our work further confirms how molecular simulations can give important contribution and useful insights to characterize the mechanism of highly complex biological systems.
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Affiliation(s)
- Pierpaolo Cacciotto
- Dipartimento di Fisica, Università degli Studi di Cagliari, S.P. Monserrato-Sestu km 0.700, I-09042 Monserrato (CA), Italy
| | - Andrea Basciu
- Dipartimento di Fisica, Università degli Studi di Cagliari, S.P. Monserrato-Sestu km 0.700, I-09042 Monserrato (CA), Italy
| | - Francesco Oliva
- Dipartimento di Fisica, Università degli Studi di Cagliari, S.P. Monserrato-Sestu km 0.700, I-09042 Monserrato (CA), Italy
| | - Giuliano Malloci
- Dipartimento di Fisica, Università degli Studi di Cagliari, S.P. Monserrato-Sestu km 0.700, I-09042 Monserrato (CA), Italy
| | - Martin Zacharias
- Physics Department, Technische Universität München, James-Franck-Str. 1, 85748 Garching, Germany
| | - Paolo Ruggerone
- Dipartimento di Fisica, Università degli Studi di Cagliari, S.P. Monserrato-Sestu km 0.700, I-09042 Monserrato (CA), Italy
| | - Attilio V Vargiu
- Dipartimento di Fisica, Università degli Studi di Cagliari, S.P. Monserrato-Sestu km 0.700, I-09042 Monserrato (CA), Italy
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11
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Reduced Susceptibility and Increased Resistance of Bacteria against Disinfectants: A Systematic Review. Microorganisms 2021; 9:microorganisms9122550. [PMID: 34946151 PMCID: PMC8706950 DOI: 10.3390/microorganisms9122550] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 12/06/2021] [Accepted: 12/08/2021] [Indexed: 01/22/2023] Open
Abstract
Disinfectants are used to reduce the concentration of pathogenic microorganisms to a safe level and help to prevent the transmission of infectious diseases. However, bacteria have a tremendous ability to respond to chemical stress caused by biocides, where overuse and improper use of disinfectants can be reflected in a reduced susceptibility of microorganisms. This review aims to describe whether mutations and thus decreased susceptibility to disinfectants occur in bacteria during disinfectant exposure. A systematic literature review following PRISMA guidelines was conducted with the databases PubMed, Science Direct and Web of Science. For the final analysis, 28 sources that remained of interest were included. Articles describing reduced susceptibility or the resistance of bacteria against seven different disinfectants were identified. The important deviation of the minimum inhibitory concentration was observed in multiple studies for disinfectants based on triclosan and chlorhexidine. A reduced susceptibility to disinfectants and potentially related problems with antibiotic resistance in clinically important bacterial strains are increasing. Since the use of disinfectants in the community is rising, it is clear that reasonable use of available and effective disinfectants is needed. It is necessary to develop and adopt strategies to control disinfectant resistance.
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12
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Bharatham N, Bhowmik P, Aoki M, Okada U, Sharma S, Yamashita E, Shanbhag AP, Rajagopal S, Thomas T, Sarma M, Narjari R, Nagaraj S, Ramachandran V, Katagihallimath N, Datta S, Murakami S. Structure and function relationship of OqxB efflux pump from Klebsiella pneumoniae. Nat Commun 2021; 12:5400. [PMID: 34518546 PMCID: PMC8437966 DOI: 10.1038/s41467-021-25679-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 08/20/2021] [Indexed: 02/08/2023] Open
Abstract
OqxB is an RND (Resistance-Nodulation-Division) efflux pump that has emerged as a factor contributing to the antibiotic resistance in Klebsiella pneumoniae. OqxB underwent horizontal gene transfer and is now seen in other Gram-negative bacterial pathogens including Escherichia coli, Enterobacter cloacae and Salmonella spp., further disseminating multi-drug resistance. In this study, we describe crystal structure of OqxB with n-dodecyl-β-D-maltoside (DDM) molecules bound in its substrate-binding pocket, at 1.85 Å resolution. We utilize this structure in computational studies to predict the key amino acids contributing to the efflux of fluoroquinolones by OqxB, distinct from analogous residues in related transporters AcrB and MexB. Finally, our complementation assays with mutated OqxB and minimum inhibitory concentration (MIC) experiments with clinical isolates of E. coli provide further evidence that the predicted structural features are indeed involved in ciprofloxacin efflux.
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Affiliation(s)
- Nagakumar Bharatham
- grid.413008.e0000 0004 1765 8271Bugworks Research India Pvt. Ltd., Centre for Cellular and Molecular Platforms, GKVK, Bellary Rd, Bengaluru, Karnataka India ,grid.502290.cThe University of Trans-Disciplinary Health Sciences and Technology (TDU), Bengaluru, Karnataka India
| | - Purnendu Bhowmik
- grid.413008.e0000 0004 1765 8271Bugworks Research India Pvt. Ltd., Centre for Cellular and Molecular Platforms, GKVK, Bellary Rd, Bengaluru, Karnataka India ,grid.502290.cThe University of Trans-Disciplinary Health Sciences and Technology (TDU), Bengaluru, Karnataka India
| | - Maho Aoki
- grid.32197.3e0000 0001 2179 2105Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Ui Okada
- grid.32197.3e0000 0001 2179 2105Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Sreevalli Sharma
- grid.413008.e0000 0004 1765 8271Bugworks Research India Pvt. Ltd., Centre for Cellular and Molecular Platforms, GKVK, Bellary Rd, Bengaluru, Karnataka India ,grid.502290.cThe University of Trans-Disciplinary Health Sciences and Technology (TDU), Bengaluru, Karnataka India
| | - Eiki Yamashita
- grid.136593.b0000 0004 0373 3971Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Anirudh P. Shanbhag
- grid.413008.e0000 0004 1765 8271Bugworks Research India Pvt. Ltd., Centre for Cellular and Molecular Platforms, GKVK, Bellary Rd, Bengaluru, Karnataka India
| | - Sreenath Rajagopal
- grid.413008.e0000 0004 1765 8271Bugworks Research India Pvt. Ltd., Centre for Cellular and Molecular Platforms, GKVK, Bellary Rd, Bengaluru, Karnataka India
| | - Teby Thomas
- grid.418280.70000 0004 1794 3160St. John’s Research Institute, Bengaluru, Karnataka India
| | - Maitrayee Sarma
- grid.413008.e0000 0004 1765 8271Bugworks Research India Pvt. Ltd., Centre for Cellular and Molecular Platforms, GKVK, Bellary Rd, Bengaluru, Karnataka India
| | - Riya Narjari
- grid.413008.e0000 0004 1765 8271Bugworks Research India Pvt. Ltd., Centre for Cellular and Molecular Platforms, GKVK, Bellary Rd, Bengaluru, Karnataka India
| | | | - Vasanthi Ramachandran
- grid.413008.e0000 0004 1765 8271Bugworks Research India Pvt. Ltd., Centre for Cellular and Molecular Platforms, GKVK, Bellary Rd, Bengaluru, Karnataka India ,grid.502290.cThe University of Trans-Disciplinary Health Sciences and Technology (TDU), Bengaluru, Karnataka India
| | - Nainesh Katagihallimath
- grid.413008.e0000 0004 1765 8271Bugworks Research India Pvt. Ltd., Centre for Cellular and Molecular Platforms, GKVK, Bellary Rd, Bengaluru, Karnataka India ,grid.502290.cThe University of Trans-Disciplinary Health Sciences and Technology (TDU), Bengaluru, Karnataka India
| | - Santanu Datta
- grid.413008.e0000 0004 1765 8271Bugworks Research India Pvt. Ltd., Centre for Cellular and Molecular Platforms, GKVK, Bellary Rd, Bengaluru, Karnataka India
| | - Satoshi Murakami
- grid.32197.3e0000 0001 2179 2105Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
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13
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Wang Y, Alenazy R, Gu X, Polyak SW, Zhang P, Sykes MJ, Zhang N, Venter H, Ma S. Design and structural optimization of novel 2H-benzo[h]chromene derivatives that target AcrB and reverse bacterial multidrug resistance. Eur J Med Chem 2020; 213:113049. [PMID: 33279291 DOI: 10.1016/j.ejmech.2020.113049] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 10/21/2020] [Accepted: 11/23/2020] [Indexed: 10/22/2022]
Abstract
Drug efflux pumps have emerged as a new drug targets for the treatment of bacterial infections in view of its critical role in promoting multidrug resistance. Herein, novel chromanone and 2H-benzo[h]chromene derivatives were designed by means of integrated molecular design and structure-based pharmacophore modeling in an attempt to identify improved efflux pump inhibitors that target Escherichia coli AcrB. The compounds were tested for their efflux inhibitory activity, ability to inhibit efflux, and the effect on bacterial outer and inner membranes. Twenty-three novel structures were identified that synergized with antibacterials tested, inhibited Nile Red efflux, and acted specifically on the AcrB. Among them, WK2, WL7 and WL10 exhibiting broad-spectrum and high-efficiency efflux inhibitory activity were identified as potential ideal AcrB inhibitors. Molecular modeling further revealed that the strong π-π stacking interactions and hydrogen bond networks were the major contributors to tight binding of AcrB.
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Affiliation(s)
- Yinhu Wang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Wenhua Road, Jinan, 250012, China; School of Pharmacy, Liaocheng University, Liaocheng, China
| | - Rawaf Alenazy
- Clinical and Health Sciences, University of South Australia, Adelaide, SA, 5000, Australia; Department of Medical Laboratory, College of Applied Medical Sciences-Shaqra, Shaqra University, 11961, Saudi Arabia
| | - Xinjie Gu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Wenhua Road, Jinan, 250012, China
| | - Steven W Polyak
- Clinical and Health Sciences, University of South Australia, Adelaide, SA, 5000, Australia
| | - Panpan Zhang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Wenhua Road, Jinan, 250012, China
| | - Matthew J Sykes
- Clinical and Health Sciences, University of South Australia, Adelaide, SA, 5000, Australia
| | - Na Zhang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Wenhua Road, Jinan, 250012, China
| | - Henrietta Venter
- Clinical and Health Sciences, University of South Australia, Adelaide, SA, 5000, Australia.
| | - Shutao Ma
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Wenhua Road, Jinan, 250012, China.
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14
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A structure–activity relationship study of phenyl sesquiterpenoids on efflux inhibition against Staphylococcus aureus. Med Chem Res 2019. [DOI: 10.1007/s00044-019-02375-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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15
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Shriram V, Khare T, Bhagwat R, Shukla R, Kumar V. Inhibiting Bacterial Drug Efflux Pumps via Phyto-Therapeutics to Combat Threatening Antimicrobial Resistance. Front Microbiol 2018; 9:2990. [PMID: 30619113 PMCID: PMC6295477 DOI: 10.3389/fmicb.2018.02990] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 11/19/2018] [Indexed: 12/04/2022] Open
Abstract
Antibiotics, once considered the lifeline for treating bacterial infections, are under threat due to the emergence of threatening antimicrobial resistance (AMR). These drug-resistant microbes (or superbugs) are non-responsive to most of the commonly used antibiotics leaving us with few treatment options and escalating mortality-rates and treatment costs. The problem is further aggravated by the drying-pipeline of new and potent antibiotics effective particularly against the drug-resistant strains. Multidrug efflux pumps (EPs) are established as principal determinants of AMR, extruding multiple antibiotics out of the cell, mostly in non-specific manner and have therefore emerged as potent drug-targets for combating AMR. Plants being the reservoir of bioactive compounds can serve as a source of potent EP inhibitors (EPIs). The phyto-therapeutics with noteworthy drug-resistance-reversal or re-sensitizing activities may prove significant for reviving the otherwise fading antibiotics arsenal and making this combination-therapy effective. Contemporary attempts to potentiate the antibiotics with plant extracts and pure phytomolecules have gained momentum though with relatively less success against Gram-negative bacteria. Plant-based EPIs hold promise as potent drug-leads to combat the EPI-mediated AMR. This review presents an account of major bacterial multidrug EPs, their roles in imparting AMR, effective strategies for inhibiting drug EPs with phytomolecules, and current account of research on developing novel and potent plant-based EPIs for reversing their AMR characteristics. Recent developments including emergence of in silico tools, major success stories, challenges and future prospects are also discussed.
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Affiliation(s)
- Varsha Shriram
- Department of Botany, Prof. Ramkrishna More College, Savitribai Phule Pune University, Pune, India
| | - Tushar Khare
- Department of Biotechnology, Modern College of Arts, Science and Commerce (Savitribai Phule Pune University), Pune, India
| | - Rohit Bhagwat
- Department of Environmental Science, Savitribai Phule Pune University, Pune, India
| | - Ravi Shukla
- Centre for Advanced Materials and Industrial Chemistry, School of Science, RMIT University, Melbourne, VIC, Australia
| | - Vinay Kumar
- Department of Biotechnology, Modern College of Arts, Science and Commerce (Savitribai Phule Pune University), Pune, India.,Department of Environmental Science, Savitribai Phule Pune University, Pune, India
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16
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Vargiu AV, Ramaswamy VK, Malloci G, Malvacio I, Atzori A, Ruggerone P. Computer simulations of the activity of RND efflux pumps. Res Microbiol 2018; 169:384-392. [PMID: 29407044 DOI: 10.1016/j.resmic.2017.12.001] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 12/01/2017] [Accepted: 12/05/2017] [Indexed: 12/25/2022]
Abstract
The putative mechanism by which bacterial RND-type multidrug efflux pumps recognize and transport their substrates is a complex and fascinating enigma of structural biology. How a single protein can recognize a huge number of unrelated compounds and transport them through one or just a few mechanisms is an amazing feature not yet completely unveiled. The appearance of cooperativity further complicates the understanding of structure-dynamics-activity relationships in these complex machineries. Experimental techniques may have limited access to the molecular determinants and to the energetics of key processes regulating the activity of these pumps. Computer simulations are a complementary approach that can help unveil these features and inspire new experiments. Here we review recent computational studies that addressed the various molecular processes regulating the activity of RND efflux pumps.
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Affiliation(s)
- Attilio Vittorio Vargiu
- Department of Physics, University of Cagliari, Cittadella Universitaria, S.P. Monserrato-Sestu km 0.700, 09042 Monserrato (CA), Italy.
| | - Venkata Krishnan Ramaswamy
- Department of Physics, University of Cagliari, Cittadella Universitaria, S.P. Monserrato-Sestu km 0.700, 09042 Monserrato (CA), Italy
| | - Giuliano Malloci
- Department of Physics, University of Cagliari, Cittadella Universitaria, S.P. Monserrato-Sestu km 0.700, 09042 Monserrato (CA), Italy
| | - Ivana Malvacio
- Department of Physics, University of Cagliari, Cittadella Universitaria, S.P. Monserrato-Sestu km 0.700, 09042 Monserrato (CA), Italy
| | - Alessio Atzori
- Department of Physics, University of Cagliari, Cittadella Universitaria, S.P. Monserrato-Sestu km 0.700, 09042 Monserrato (CA), Italy
| | - Paolo Ruggerone
- Department of Physics, University of Cagliari, Cittadella Universitaria, S.P. Monserrato-Sestu km 0.700, 09042 Monserrato (CA), Italy.
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17
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López CA, Travers T, Pos KM, Zgurskaya HI, Gnanakaran S. Dynamics of Intact MexAB-OprM Efflux Pump: Focusing on the MexA-OprM Interface. Sci Rep 2017; 7:16521. [PMID: 29184094 PMCID: PMC5705723 DOI: 10.1038/s41598-017-16497-w] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 10/30/2017] [Indexed: 11/30/2022] Open
Abstract
Antibiotic efflux is one of the most critical mechanisms leading to bacterial multidrug resistance. Antibiotics are effluxed out of the bacterial cell by a tripartite efflux pump, a complex machinery comprised of outer membrane, periplasmic adaptor, and inner membrane protein components. Understanding the mechanism of efflux pump assembly and its dynamics could facilitate discovery of novel approaches to counteract antibiotic resistance in bacteria. We built here an intact atomistic model of the Pseudomonas aeruginosa MexAB-OprM pump in a Gram-negative membrane model that contained both inner and outer membranes separated by a periplasmic space. All-atom molecular dynamics (MD) simulations confirm that the fully assembled pump is stable in the microsecond timescale. Using a combination of all-atom and coarse-grained MD simulations and sequence covariation analysis, we characterized the interface between MexA and OprM in the context of the entire efflux pump. These analyses suggest a plausible mechanism by which OprM is activated via opening of its periplasmic aperture through a concerted interaction with MexA.
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Affiliation(s)
- Cesar A López
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico, 87545, United States
| | - Timothy Travers
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico, 87545, United States.,Center for Nonlinear Sciences, Los Alamos National Laboratory, Los Alamos, New Mexico, 87545, United States
| | - Klaas M Pos
- Institute of Biochemistry, Goethe University, Frankfurt am Main, Germany.,Cluster of Excellence Frankfurt, Goethe University, Frankfurt am Main, Germany
| | - Helen I Zgurskaya
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma, 73019, United States
| | - S Gnanakaran
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, New Mexico, 87545, United States.
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18
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Haynes KM, Abdali N, Jhawar V, Zgurskaya HI, Parks JM, Green AT, Baudry J, Rybenkov VV, Smith JC, Walker JK. Identification and Structure-Activity Relationships of Novel Compounds that Potentiate the Activities of Antibiotics in Escherichia coli. J Med Chem 2017. [PMID: 28650638 DOI: 10.1021/acs.jmedchem.7b00453] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
In Gram-negative bacteria, efflux pumps are able to prevent effective cellular concentrations from being achieved for a number of antibiotics. Small molecule adjuvants that act as efflux pump inhibitors (EPIs) have the potential to reinvigorate existing antibiotics that are currently ineffective due to efflux mechanisms. Through a combination of rigorous experimental screening and in silico virtual screening, we recently identified novel classes of EPIs that interact with the membrane fusion protein AcrA, a critical component of the AcrAB-TolC efflux pump in Escherichia coli. Herein, we present initial optimization efforts and structure-activity relationships around one of those previously described hits, NSC 60339 (1). From these efforts we identified two compounds, SLUPP-225 (17h) and SLUPP-417 (17o), which demonstrate favorable properties as potential EPIs in E. coli cells including the ability to penetrate the outer membrane, improved inhibition of efflux relative to 1, and potentiation of the activity of novobiocin and erythromycin.
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Affiliation(s)
- Keith M Haynes
- Department of Pharmacological & Physiological Science, Saint Louis University School of Medicine , St Louis, Missouri 63104, United States
| | - Narges Abdali
- Department of Chemistry and Biochemistry, University of Oklahoma , Norman, Oklahoma 73019, United States
| | - Varsha Jhawar
- Department of Chemistry and Biochemistry, University of Oklahoma , Norman, Oklahoma 73019, United States
| | - Helen I Zgurskaya
- Department of Chemistry and Biochemistry, University of Oklahoma , Norman, Oklahoma 73019, United States
| | - Jerry M Parks
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States.,Graduate School of Genome Science and Technology, University of Tennessee , Knoxville, Tennessee 37996, United States
| | - Adam T Green
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States.,Graduate School of Genome Science and Technology, University of Tennessee , Knoxville, Tennessee 37996, United States
| | - Jerome Baudry
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States.,Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee , Knoxville, Tennessee 37996, United States
| | - Valentin V Rybenkov
- Department of Chemistry and Biochemistry, University of Oklahoma , Norman, Oklahoma 73019, United States
| | - Jeremy C Smith
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States.,Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee , Knoxville, Tennessee 37996, United States
| | - John K Walker
- Department of Pharmacological & Physiological Science, Saint Louis University School of Medicine , St Louis, Missouri 63104, United States.,Department of Chemistry, Saint Louis University , St. Louis, Missouri 63104, United States
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19
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Schillaci D, Spanò V, Parrino B, Carbone A, Montalbano A, Barraja P, Diana P, Cirrincione G, Cascioferro S. Pharmaceutical Approaches to Target Antibiotic Resistance Mechanisms. J Med Chem 2017; 60:8268-8297. [PMID: 28594170 DOI: 10.1021/acs.jmedchem.7b00215] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
There is urgent need for new therapeutic strategies to fight the global threat of antibiotic resistance. The focus of this Perspective is on chemical agents that target the most common mechanisms of antibiotic resistance such as enzymatic inactivation of antibiotics, changes in cell permeability, and induction/activation of efflux pumps. Here we assess the current landscape and challenges in the treatment of antibiotic resistance mechanisms at both bacterial cell and community levels. We also discuss the potential clinical application of chemical inhibitors of antibiotic resistance mechanisms as add-on treatments for serious drug-resistant infections. Enzymatic inhibitors, such as the derivatives of the β-lactamase inhibitor avibactam, are closer to the clinic than other molecules. For example, MK-7655, in combination with imipenem, is in clinical development for the treatment of infections caused by carbapenem-resistant Enterobacteriaceae and Pseudomonas aeruginosa, which are difficult to treat. In addition, other molecules targeting multidrug-resistance mechanisms, such as efflux pumps, are under development and hold promise for the treatment of multidrug resistant infections.
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Affiliation(s)
- Domenico Schillaci
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Sezione di Chimica e Tecnologie Farmaceutiche, Università degli Studi di Palermo , Via Archirafi 32, 90123 Palermo, Italy
| | - Virginia Spanò
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Sezione di Chimica e Tecnologie Farmaceutiche, Università degli Studi di Palermo , Via Archirafi 32, 90123 Palermo, Italy
| | - Barbara Parrino
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Sezione di Chimica e Tecnologie Farmaceutiche, Università degli Studi di Palermo , Via Archirafi 32, 90123 Palermo, Italy
| | - Anna Carbone
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Sezione di Chimica e Tecnologie Farmaceutiche, Università degli Studi di Palermo , Via Archirafi 32, 90123 Palermo, Italy
| | - Alessandra Montalbano
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Sezione di Chimica e Tecnologie Farmaceutiche, Università degli Studi di Palermo , Via Archirafi 32, 90123 Palermo, Italy
| | - Paola Barraja
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Sezione di Chimica e Tecnologie Farmaceutiche, Università degli Studi di Palermo , Via Archirafi 32, 90123 Palermo, Italy
| | - Patrizia Diana
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Sezione di Chimica e Tecnologie Farmaceutiche, Università degli Studi di Palermo , Via Archirafi 32, 90123 Palermo, Italy
| | - Girolamo Cirrincione
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Sezione di Chimica e Tecnologie Farmaceutiche, Università degli Studi di Palermo , Via Archirafi 32, 90123 Palermo, Italy
| | - Stella Cascioferro
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Sezione di Chimica e Tecnologie Farmaceutiche, Università degli Studi di Palermo , Via Archirafi 32, 90123 Palermo, Italy
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20
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Phetsang W, Pelingon R, Butler MS, KC S, Pitt ME, Kaeslin G, Cooper MA, Blaskovich MAT. Fluorescent Trimethoprim Conjugate Probes To Assess Drug Accumulation in Wild Type and Mutant Escherichia coli. ACS Infect Dis 2016; 2:688-701. [PMID: 27737551 PMCID: PMC5067704 DOI: 10.1021/acsinfecdis.6b00080] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
![]()
Reduced
susceptibility to antimicrobials in Gram-negative bacteria may result
from multiple resistance mechanisms, including increased efflux pump
activity or reduced porin protein expression. Up-regulation of the
efflux pump system is closely associated with multidrug resistance
(MDR). To help investigate the role of efflux pumps on compound accumulation,
a fluorescence-based assay was developed using fluorescent derivatives
of trimethoprim (TMP), a broad-spectrum synthetic antibiotic that
inhibits an intracellular target, dihydrofolate reductase (DHFR).
Novel fluorescent TMP probes inhibited eDHFR activity
with comparable potency to TMP, but did not kill or inhibit growth
of wild type Escherichia coli. However,
bactericidal activity was observed against an efflux pump deficient E. coli mutant strain (ΔtolC). A simple and quick fluorescence assay was developed to measure
cellular accumulation of the TMP probe using either fluorescence spectroscopy
or flow cytometry, with validation by LC-MS/MS. This fluorescence
assay may provide a simple method to assess efflux pump activity with
standard laboratory equipment.
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Affiliation(s)
- Wanida Phetsang
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Ruby Pelingon
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Mark S. Butler
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Sanjaya KC
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Miranda E. Pitt
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Geraldine Kaeslin
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Matthew A. Cooper
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Mark A. T. Blaskovich
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
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