1
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Haque S, Ahmad F, Mathkor DM, Makhdoom H, Johargy AK, Faidah H, Babalghith AO, Jalal NA, Alhindi Z, Bantun F. Binding selectivity analysis of new delhi metallo-beta-lactamase-1 inhibitors using molecular dynamics simulations: Exploring possibilities for decoding antimicrobial drug resistance. J Infect Public Health 2024; 17:1108-1116. [PMID: 38714123 DOI: 10.1016/j.jiph.2024.04.018] [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: 02/14/2024] [Revised: 03/25/2024] [Accepted: 04/21/2024] [Indexed: 05/09/2024] Open
Abstract
BACKGROUND New Delhi metallo-beta-lactamase-1 (NDM1) confers resistance to several bacterial species against a broad range of beta-lactam antibiotics and turning them into superbugs that pose a significant threat to healthcare systems worldwide. As such, it is a potentially relevant biological target for counteracting bacterial infections. Given the lack of effective treatment options against NDM1 producing bacteria, finding a reliable inhibitor for the NDM1 enzyme is crucial. METHODS Using molecular dynamics simulations, the binding selectivities and affinities of three ligands, viz. PNK, 3S0, and N1G were investigated against NDM1. RESULTS The results indicate that N1G binds with more affinity to NDM1 than PNK and 3S0. The binding energy decomposition analysis revealed that residues I35, W93, H189, K211, and N220 showed significant binding energies with PNK, 3S0, and N1G, and hence are crucially involved in the binding of the ligands to NDM1. Molecular dynamics trajectory analysis further elicited that the ligands influence dynamic flexibility of NDM1 morphology, which contributes to the partial selectivities of PNK, 3S0, and N1G. CONCLUSIONS This in silico study offers a vital information for developing potential NDM1 inhibitors with high selectivity. Nevertheless, in vitro and in vivo experimental validation is mandated to extend the possible applications of these ligands as NDM1 inhibitors that succor in combating antimicrobial resistance.
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Affiliation(s)
- Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing and Health Sciences, Jazan University, Jazan 45142, Saudi Arabia; Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Beirut, Lebanon.
| | - Faraz Ahmad
- Department of Biotechnology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, India.
| | - Darin Mansor Mathkor
- Research and Scientific Studies Unit, College of Nursing and Health Sciences, Jazan University, Jazan 45142, Saudi Arabia.
| | - Hatim Makhdoom
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taibah University, Madinah, Saudi Arabia.
| | - Ayman K Johargy
- Department of Microbiology and Parasitology, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia.
| | - Hani Faidah
- Department of Microbiology and Parasitology, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia.
| | - Ahmad O Babalghith
- Department of Medical Genetics, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia.
| | - Naif A Jalal
- Department of Microbiology and Parasitology, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia.
| | - Zain Alhindi
- Department of Clinical Laboratory Sciences, Faculty of Applied Medical Sciences, Umm Al-Qura University, Makkah, Saudi Arabia.
| | - Farkad Bantun
- Department of Microbiology and Parasitology, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia.
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2
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Kamo T, Kuroda K, Nimura S, Guo Y, Kondo S, Nukaga M, Hoshino T. Development of Inhibitory Compounds for Metallo-beta-lactamase through Computational Design and Crystallographic Analysis. Biochemistry 2024; 63:1278-1286. [PMID: 38690676 DOI: 10.1021/acs.biochem.4c00069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2024]
Abstract
Metallo-β-lactamases (MBL) deactivate β-lactam antibiotics through a catalytic reaction caused by two zinc ions at the active center. Since MBLs deteriorate a wide range of antibiotics, they are dangerous factors for bacterial multidrug resistance. In this work, organic synthesis, computational design, and crystal structure analysis were performed to obtain potent MBL inhibitors based on a previously identified hit compound. The hit compound comprised 3,4-dihydro-2(1H)-quinolinone linked with a phenyl-ether-methyl group via a thiazole ring. In the first step, the thiazole ring was replaced with a tertiary amine to avoid the planar structure. In the second step, we virtually modified the compound by keeping the quinolinone backbone. Every modified compound was bound to a kind of MBL, imipenemase-1 (IMP-1), and the binding pose was optimized by a molecular mechanics calculation. The binding scores were evaluated for the respective optimized binding poses. Given the predicted binding poses and calculated binding scores, candidate compounds were determined for organic syntheses. The inhibitory activities of the synthesized compounds were measured by an in vitro assay for two kinds of MBLs, IMP-1 and New Delhi metallo-β-lactamase (NDM-1). A quinolinone connected with an amine bound with methyl-phenyl-ether-propyl and cyclohexyl-ethyl showed a 50% inhibitory concentration of 4.8 μM. An X-ray crystal analysis clarified the binding structure of a synthesized compound to IMP-1. The δ-lactam ring of quinolinone was hydrolyzed, and the generated carboxyl group was coordinated with zinc ions. The findings on the chemical structure and binding pose are expected to be a base for developing MBL inhibitors.
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Affiliation(s)
- Taichi Kamo
- Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8675, Japan
| | - Keiichi Kuroda
- Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8675, Japan
| | - Saki Nimura
- Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8675, Japan
| | - Yan Guo
- Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8675, Japan
| | - Shota Kondo
- Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8675, Japan
| | - Michiyoshi Nukaga
- Faculty of Pharmaceutical Sciences, Josai International University, Gumyo, Togane City, Chiba 283-8555, Japan
| | - Tyuji Hoshino
- Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8675, Japan
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3
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Ye D, Li X, Zhao L, Liu S, Jia X, Wang Z, Du J, Ge L, Shen J, Xia X. Oxidized glutathione reverts carbapenem resistance in bla NDM-1-carrying Escherichia coli. EMBO Mol Med 2024; 16:1051-1062. [PMID: 38565805 PMCID: PMC11099006 DOI: 10.1038/s44321-024-00061-x] [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: 12/21/2023] [Revised: 03/13/2024] [Accepted: 03/15/2024] [Indexed: 04/04/2024] Open
Abstract
The emergence of drug-resistant Enterobacteriaceae carrying plasmid-mediated β-lactamase genes has become a significant threat to public health. Organisms in the Enterobacteriaceae family containing New Delhi metallo-β-lactamase‑1 (NDM-1) and its variants, which are capable of hydrolyzing nearly all β-lactam antibacterial agents, including carbapenems, are referred to as superbugs and distributed worldwide. Despite efforts over the past decade, the discovery of an NDM-1 inhibitor that can reach the clinic remains a challenge. Here, we identified oxidized glutathione (GSSG) as a metabolic biomarker for blaNDM-1 using a non-targeted metabolomics approach and demonstrated that GSSG supplementation could restore carbapenem susceptibility in Escherichia coli carrying blaNDM-1 in vitro and in vivo. We showed that exogenous GSSG promotes the bactericidal effects of carbapenems by interfering with intracellular redox homeostasis and inhibiting the expression of NDM-1 in drug-resistant E. coli. This study establishes a metabolomics-based strategy to potentiate metabolism-dependent antibiotic efficacy for the treatment of antibiotic-resistant bacteria.
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Affiliation(s)
- Dongyang Ye
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Xiaowei Li
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Liang Zhao
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Saiwa Liu
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Xixi Jia
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Zhinan Wang
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Jingjing Du
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Lirui Ge
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Jianzhong Shen
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China.
| | - Xi Xia
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China.
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4
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Moussa AY. Endophytes: a uniquely tailored source of potential antibiotic adjuvants. Arch Microbiol 2024; 206:207. [PMID: 38581477 PMCID: PMC10998792 DOI: 10.1007/s00203-024-03891-y] [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: 12/25/2023] [Revised: 02/06/2024] [Accepted: 02/08/2024] [Indexed: 04/08/2024]
Abstract
Multidrug microbial resistance is risking an annual loss of more than 10 million people' lives by 2050. Solutions include the rational use of antibiotics and the use of drugs that reduce resistance or completely obliterate them. Here endophytes come to play due to their high-yield production and inherent nature to produce antimicrobial molecules. Around 40%, 45% and 17% of antibacterial agents were obtained from fungi, actinomycetes, and bacteria, respectively, whose secondary metabolites revealed effectiveness against resistant microbes such as MRSA, MRSE, and Shigella flexneri. Endophyte's role was not confined to bactericidal effect but extended to other mechanisms against MDR microbes, among which was the adjuvant role or the "magic bullets". Scarce focus was given to antibiotic adjuvants, and many laboratories today just screen for the antimicrobial activity without considering combinations with traditional antibiotics, which means real loss of promising resistance combating molecules. While some examples of synthetic adjuvants were introduced in the last decade, the number is still far from covering the disused antibiotics and restoring them back to clinical use. The data compiled in this article demonstrated the significance of quorum sensing as a foreseen mechanism for adjuvants from endophytes secondary metabolites, which call for urgent in-depth studies of their molecular mechanisms. This review, comprehensively and for the first time, sheds light on the significance of endophytes secondary metabolites in solving AMR problem as AB adjuvants.
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Affiliation(s)
- Ashaimaa Y Moussa
- Department of Pharmacognosy, Faculty of Pharmacy, Ain-Shams University, African Union Organization Street, Abbassia, Cairo, 11566, Egypt.
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5
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Hibbert T, Krpetic Z, Latimer J, Leighton H, McHugh R, Pottenger S, Wragg C, James CE. Antimicrobials: An update on new strategies to diversify treatment for bacterial infections. Adv Microb Physiol 2024; 84:135-241. [PMID: 38821632 DOI: 10.1016/bs.ampbs.2023.12.002] [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: 06/02/2024]
Abstract
Ninety-five years after Fleming's discovery of penicillin, a bounty of antibiotic compounds have been discovered, modified, or synthesised. Diversification of target sites, improved stability and altered activity spectra have enabled continued antibiotic efficacy, but overwhelming reliance and misuse has fuelled the global spread of antimicrobial resistance (AMR). An estimated 1.27 million deaths were attributable to antibiotic resistant bacteria in 2019, representing a major threat to modern medicine. Although antibiotics remain at the heart of strategies for treatment and control of bacterial diseases, the threat of AMR has reached catastrophic proportions urgently calling for fresh innovation. The last decade has been peppered with ground-breaking developments in genome sequencing, high throughput screening technologies and machine learning. These advances have opened new doors for bioprospecting for novel antimicrobials. They have also enabled more thorough exploration of complex and polymicrobial infections and interactions with the healthy microbiome. Using models of infection that more closely resemble the infection state in vivo, we are now beginning to measure the impacts of antimicrobial therapy on host/microbiota/pathogen interactions. However new approaches are needed for developing and standardising appropriate methods to measure efficacy of novel antimicrobial combinations in these contexts. A battery of promising new antimicrobials is now in various stages of development including co-administered inhibitors, phages, nanoparticles, immunotherapy, anti-biofilm and anti-virulence agents. These novel therapeutics need multidisciplinary collaboration and new ways of thinking to bring them into large scale clinical use.
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Affiliation(s)
- Tegan Hibbert
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences (IVES), University of Liverpool, Liverpool, UK
| | - Zeljka Krpetic
- School of Science, Engineering, and Environment, University of Salford, Salford, UK
| | - Joe Latimer
- School of Science, Engineering, and Environment, University of Salford, Salford, UK
| | - Hollie Leighton
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences (IVES), University of Liverpool, Liverpool, UK
| | - Rebecca McHugh
- School of Infection and Immunity, University of Glasgow, Glasgow, UK
| | - Sian Pottenger
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences (IVES), University of Liverpool, Liverpool, UK
| | - Charlotte Wragg
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection, Veterinary and Ecological Sciences (IVES), University of Liverpool, Liverpool, UK
| | - Chloë E James
- School of Science, Engineering, and Environment, University of Salford, Salford, UK.
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6
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Li H, Duan S, Li L, Zhao G, Wei L, Zhang B, Ma Y, Wu MX, Mao Y, Lu M. Bio-Responsive Sliver Peroxide-Nanocarrier Serves as Broad-Spectrum Metallo-β-lactamase Inhibitor for Combating Severe Pneumonia. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2310532. [PMID: 38095435 DOI: 10.1002/adma.202310532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 12/04/2023] [Indexed: 12/22/2023]
Abstract
Metallo-β-lactamases (MBLs) represent a prevalent resistance mechanism in Gram-negative bacteria, rendering last-line carbapenem-related antibiotics ineffective. Here, a bioresponsive sliver peroxide (Ag2 O2 )-based nanovesicle, named Ag2 O2 @BP-MT@MM, is developed as a broad-spectrum MBL inhibitor for combating MBL-producing bacterial pneumonia. Ag2 O2 nanoparticle is first orderly modified with bovine serum albumin and polydopamine to co-load meropenem (MER) and [5-(p-fluorophenyl)-2-ureido]-thiophene-3-carboxamide (TPCA-1) and then encapsulated with macrophage membrane (MM) aimed to target inflammatory lung tissue specifically. The resultant Ag2 O2 @BP-MT@MM effectively abrogates MBL activity by displacing the Zn2+ cofactor in MBLs with Ag+ and displays potent bactericidal and anti-inflammatory properties, specific targeting abilities, and great bioresponsive characteristics. After intravenous injection, the nanoparticles accumulate prominently at infection sites through MM-mediated targeting . Ag+ released from Ag2 O2 decomposition at the infection sites effectively inhibits MBL activity and overcomes the resistance of MBL-producing bacteria to MER, resulting in synergistic elimination of bacteria in conjunction with MER. In two murine infection models of NDM-1+ Klebsiella pneumoniae-induced severe pneumonia and NDM-1+ Escherichia coli-induced sepsis-related bacterial pneumonia, the nanoparticles significantly reduce bacterial loading, pro-inflammatory cytokine levels locally and systemically, and the recruitment and activation of neutrophils and macrophages. This innovative approach presents a promising new strategy for combating infections caused by MBL-producing carbapenem-resistant bacteria.
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Affiliation(s)
- Hanqing Li
- Department of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China
- Department of Orthopaedics, Shanghai Key Laboratory for Prevention and Treatment of Bone and Joint Diseases, Shanghai Institute of Traumatology and Orthopaedics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Shuxian Duan
- Department of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China
| | - Lixia Li
- Department of Pharmacy, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China
| | - Gang Zhao
- Department of Orthopaedics, Shanghai Key Laboratory for Prevention and Treatment of Bone and Joint Diseases, Shanghai Institute of Traumatology and Orthopaedics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Li Wei
- Department of Orthopaedics, Shanghai Key Laboratory for Prevention and Treatment of Bone and Joint Diseases, Shanghai Institute of Traumatology and Orthopaedics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Bohan Zhang
- Department of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China
| | - Yingying Ma
- Department of Orthopaedics, Shanghai Key Laboratory for Prevention and Treatment of Bone and Joint Diseases, Shanghai Institute of Traumatology and Orthopaedics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Mei X Wu
- Wellman Center for Photomedicine, Massachusetts General Hospital Department of Dermatology, Harvard Medical School, 50 Blossom Street, Boston, MA, 02114, USA
| | - Yanfei Mao
- Department of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China
| | - Min Lu
- Department of Orthopaedics, Shanghai Key Laboratory for Prevention and Treatment of Bone and Joint Diseases, Shanghai Institute of Traumatology and Orthopaedics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
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7
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Shi X, Dai Y, Lan Z, Wang S, Cui L, Xiao C, Zhao K, Li X, Liu W, Zhang Q. Interplay between the β-lactam side chain and an active-site mobile loop of NDM-1 in penicillin hydrolysis as a potential target for mechanism-based inhibitor design. Int J Biol Macromol 2024; 262:130041. [PMID: 38336327 DOI: 10.1016/j.ijbiomac.2024.130041] [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: 10/09/2023] [Revised: 02/04/2024] [Accepted: 02/06/2024] [Indexed: 02/12/2024]
Abstract
Metallo-β-lactamases (MβLs) stand as significant resistant mechanism against β-lactam antibiotics in Gram-negative bacteria. The worldwide dissemination of New Delhi metallo-β-lactamases (NDMs) intensifies antimicrobial resistance, posing severe threats to human health due to the absence of inhibitors available in clinical therapy. L3, a flexible β-hairpin loop flanking the active site in MβLs, has been proven to wield influence over the reaction process by assuming a crucial role in substrate recognition and intermediate stabilization. In principle, it potentially retards product release from the enzyme, consequently reducing the overall turnover rate although the details regarding this aspect remain inadequately elucidated. In this study, we crystallized NDM-1 in complex with three penicillin substrates, conducted molecular dynamics simulations, and measured the steady-state kinetic parameters. These analyses consistently unveiled substantial disparities in their interactions with loop L3. We further synthesized a penicillin V derivative with increased hydrophobicity in the R1 side chain and co-crystallized it with NDM-1. Remarkably, this compound exhibited much stronger dynamic interplay with L3 during molecular dynamics simulation, showed much lower Km and kcat values, and demonstrated moderate inhibitory capacity to NDM-1 catalyzed meropenem hydrolysis. The data presented here may provide a strategic approach for designing mechanism-based MβL inhibitors focusing on structural elements external to the enzyme's active center.
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Affiliation(s)
- Xiangrui Shi
- Department of Obstetrics and Gynecology, Daping Hospital, Army Medical University, Chongqing 400042, China
| | - Yujie Dai
- Department of Obstetrics and Gynecology, Daping Hospital, Army Medical University, Chongqing 400042, China
| | - Zhu Lan
- Institute of Immunology, Army Medical University, Chongqing 400038, China
| | - Sheng Wang
- College of Life Science and Technology, Huazhong University of Science and Technology, 1037 Luoyu Avenue, Wuhan, Hubei 430074, China
| | - Liwei Cui
- Institute of Immunology, Army Medical University, Chongqing 400038, China
| | - Chengliang Xiao
- College of Life Science and Technology, Huazhong University of Science and Technology, 1037 Luoyu Avenue, Wuhan, Hubei 430074, China
| | - Kunhong Zhao
- Key Laboratory of Green Pesticide and Agricultural Bioengineering, Minister of Education, Guizhou University, Guiyang 550025, China
| | - Xiangyang Li
- Key Laboratory of Green Pesticide and Agricultural Bioengineering, Minister of Education, Guizhou University, Guiyang 550025, China.
| | - Wei Liu
- Institute of Immunology, Army Medical University, Chongqing 400038, China.
| | - Qinghua Zhang
- Department of Obstetrics and Gynecology, Daping Hospital, Army Medical University, Chongqing 400042, China.
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8
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Chung SF, Tam SY, Wong WT, So PK, Cheong WL, Mak CW, Lee LMY, Chan PH, Wong KY, Leung YC. Fluorescently Modified NDM-1: A Versatile Drug Sensor for Rapid In Vitro β-Lactam Antibiotic and Inhibitor Screening. ACS OMEGA 2024; 9:9161-9169. [PMID: 38434906 PMCID: PMC10906033 DOI: 10.1021/acsomega.3c08117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 01/14/2024] [Accepted: 01/25/2024] [Indexed: 03/05/2024]
Abstract
We successfully developed a fluorescent drug sensor from clinically relevant New Delhi metallo-β-lactamase-1 (NDM-1). The F70 residue was chosen to be replaced with a cysteine for conjugation with thiol-reactive fluorescein-5-maleimide to form fluorescent F70Cf, where "f" refers to fluorescein-5-maleimide. Our proteolytic studies of unlabeled F70C and labeled F70Cf monitored by electrospray ionization-mass spectrometry (ESI-MS) revealed that fluorescein-5-maleimide was specifically linked to C70 in 1:1 mole ratio (F70C:fluorophore). Our drug sensor (F70Cf) can detect the β-lactam antibiotics cefotaxime and cephalothin by giving stronger fluorescence in the initial binding phase and then declining fluorescence signals as a result of the hydrolysis of the antibiotics into acid products. F70Cf can also detect non-β-lactam inhibitors (e.g., l-captopril, d-captopril, dl-thiorphan, and thanatin). In all cases, F70Cf exhibits stronger fluorescence due to inhibitor binding and subsequently sustained fluorescence signals in a later stage. Native ESI-MS results show that F70Cf can bind to all four inhibitors. Moreover, our drug sensor is compatible with a high-throughput microplate reader and has the capability to perform in vitro drug screening.
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Affiliation(s)
- Sai-Fung Chung
- State
Key Laboratory of Chemical Biology and Drug Discovery, Department
of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hunghom, Kowloon, Hong Kong, China
- Lo
Ka Chung Research Centre for Natural Anti-Cancer Drug Development, The Hong Kong Polytechnic University, Hunghom, Kowloon, Hong Kong, China
| | - Suet-Ying Tam
- State
Key Laboratory of Chemical Biology and Drug Discovery, Department
of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hunghom, Kowloon, Hong Kong, China
- Lo
Ka Chung Research Centre for Natural Anti-Cancer Drug Development, The Hong Kong Polytechnic University, Hunghom, Kowloon, Hong Kong, China
| | - Wai-Ting Wong
- State
Key Laboratory of Chemical Biology and Drug Discovery, Department
of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hunghom, Kowloon, Hong Kong, China
| | - Pui-Kin So
- State
Key Laboratory of Chemical Biology and Drug Discovery, Department
of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hunghom, Kowloon, Hong Kong, China
| | - Wing-Lam Cheong
- Department
of Science, School of Science and Technology, Hong Kong Metropolitan University, Hong Kong, Hong Kong
| | - Chun-Wing Mak
- State
Key Laboratory of Chemical Biology and Drug Discovery, Department
of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hunghom, Kowloon, Hong Kong, China
| | - Leo Man-Yuen Lee
- State
Key Laboratory of Chemical Biology and Drug Discovery, Department
of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hunghom, Kowloon, Hong Kong, China
| | - Pak-Ho Chan
- State
Key Laboratory of Chemical Biology and Drug Discovery, Department
of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hunghom, Kowloon, Hong Kong, China
| | - Kwok-Yin Wong
- State
Key Laboratory of Chemical Biology and Drug Discovery, Department
of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hunghom, Kowloon, Hong Kong, China
| | - Yun-Chung Leung
- State
Key Laboratory of Chemical Biology and Drug Discovery, Department
of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hunghom, Kowloon, Hong Kong, China
- Lo
Ka Chung Research Centre for Natural Anti-Cancer Drug Development, The Hong Kong Polytechnic University, Hunghom, Kowloon, Hong Kong, China
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9
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Kondratieva A, Palica K, Frøhlich C, Hovd RR, Leiros HKS, Erdelyi M, Bayer A. Fluorinated captopril analogues inhibit metallo-β-lactamases and facilitate structure determination of NDM-1 binding pose. Eur J Med Chem 2024; 266:116140. [PMID: 38242072 DOI: 10.1016/j.ejmech.2024.116140] [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: 10/26/2023] [Revised: 12/31/2023] [Accepted: 01/09/2024] [Indexed: 01/21/2024]
Abstract
Bacterial resistance to the majority of clinically used β-lactam antibiotics is a global health threat and, consequently, the driving force for the development of metallo-β-lactamase (MBL) inhibitors. The rapid evolution of new MBLs calls for new strategies and tools for inhibitor development. In this study, we designed and developed a series of trifluoromethylated captopril analogues as probes for structural studies of enzyme-inhibitor binding. The new compounds showed activity comparable to the non-fluorinated inhibitors against the New Delhi Metallo-β-lactamase-1 (NDM-1). The most active compound, a derivative of D-captopril, exhibited an IC50 value of 0.3 μM. Several compounds demonstrated synergistic effects, restoring the effect of meropenem and reducing the minimum inhibitory concentration (MIC) values in NDM-1 (up to 64-fold), VIM-2 (up to 8-fold) and IMP-26 (up to 8-fold) harbouring Escherichia coli. NMR spectroscopy and molecular docking of one representative inhibitor determined the binding pose in NDM-1, demonstrating that fluorinated analogues of inhibitors are a valuable tool for structural studies of MBL-inhibitor complexes.
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Affiliation(s)
- Alexandra Kondratieva
- Department of Chemistry, UiT The Arctic University of Norway, NO-9037, Tromsø, Norway
| | - Katarzyna Palica
- Department of Chemistry - BMC, Organic Chemistry, Uppsala University, 752 37, Uppsala, Sweden
| | - Christopher Frøhlich
- Department of Pharmacy, UiT The Arctic University of Norway, NO-9037, Tromsø, Norway
| | | | - Hanna-Kirsti S Leiros
- Department of Chemistry, UiT The Arctic University of Norway, NO-9037, Tromsø, Norway
| | - Mate Erdelyi
- Department of Chemistry - BMC, Organic Chemistry, Uppsala University, 752 37, Uppsala, Sweden
| | - Annette Bayer
- Department of Chemistry, UiT The Arctic University of Norway, NO-9037, Tromsø, Norway.
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10
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Park S, Fan J, Chamakuri S, Palaniappan M, Sharma K, Qin X, Wang J, Tan Z, Judge A, Hu L, Sankaran B, Li F, Prasad BVV, Matzuk MM, Palzkill T. Exploiting the Carboxylate-Binding Pocket of β-Lactamase Enzymes Using a Focused DNA-Encoded Chemical Library. J Med Chem 2024; 67:620-642. [PMID: 38117688 DOI: 10.1021/acs.jmedchem.3c01834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2023]
Abstract
β-Lactamase enzymes hydrolyze and thereby provide bacterial resistance to the important β-lactam class of antibiotics. The OXA-48 and NDM-1 β-lactamases cause resistance to the last-resort β-lactams, carbapenems, leading to a serious public health threat. Here, we utilized DNA-encoded chemical library (DECL) technology to discover novel β-lactamase inhibitors. We exploited the β-lactamase enzyme-substrate binding interactions and created a DECL targeting the carboxylate-binding pocket present in all β-lactamases. A library of 106 compounds, each containing a carboxylic acid or a tetrazole as an enzyme recognition element, was designed, constructed, and used to identify OXA-48 and NDM-1 inhibitors with micromolar to nanomolar potency. Further optimization led to NDM-1 inhibitors with increased potencies and biological activities. This work demonstrates that the carboxylate-binding pocket-targeting DECL, designed based on substrate binding information, aids in inhibitor identification and led to the discovery of novel non-β-lactam pharmacophores for the development of β-lactamase inhibitors for enzymes of different structural and mechanistic classes.
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Affiliation(s)
- Suhyeorn Park
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Jiayi Fan
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Srinivas Chamakuri
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Murugesan Palaniappan
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Kiran Sharma
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Xuan Qin
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Jian Wang
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Zhi Tan
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Allison Judge
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Liya Hu
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Banumathi Sankaran
- Berkeley Center for Structural Biology, Advanced Light Source, Lawrence Berkeley National Lab, Berkeley, California 94720, United States
| | - Feng Li
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - B V Venkataram Prasad
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Martin M Matzuk
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
- Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Timothy Palzkill
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
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11
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Jacobs LMC, Consol P, Chen Y. Drug Discovery in the Field of β-Lactams: An Academic Perspective. Antibiotics (Basel) 2024; 13:59. [PMID: 38247618 PMCID: PMC10812508 DOI: 10.3390/antibiotics13010059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 12/21/2023] [Accepted: 12/23/2023] [Indexed: 01/23/2024] Open
Abstract
β-Lactams are the most widely prescribed class of antibiotics that inhibit penicillin-binding proteins (PBPs), particularly transpeptidases that function in peptidoglycan synthesis. A major mechanism of antibiotic resistance is the production of β-lactamase enzymes, which are capable of hydrolyzing β-lactam antibiotics. There have been many efforts to counter increasing bacterial resistance against β-lactams. These studies have mainly focused on three areas: discovering novel inhibitors against β-lactamases, developing new β-lactams less susceptible to existing resistance mechanisms, and identifying non-β-lactam inhibitors against cell wall transpeptidases. Drug discovery in the β-lactam field has afforded a range of research opportunities for academia. In this review, we summarize the recent new findings on both β-lactamases and cell wall transpeptidases because these two groups of enzymes are evolutionarily and functionally connected. Many efforts to develop new β-lactams have aimed to inhibit both transpeptidases and β-lactamases, while several promising novel β-lactamase inhibitors have shown the potential to be further developed into transpeptidase inhibitors. In addition, the drug discovery progress against each group of enzymes is presented in three aspects: understanding the targets, screening methodology, and new inhibitor chemotypes. This is to offer insights into not only the advancement in this field but also the challenges, opportunities, and resources for future research. In particular, cyclic boronate compounds are now capable of inhibiting all classes of β-lactamases, while the diazabicyclooctane (DBO) series of small molecules has led to not only new β-lactamase inhibitors but potentially a new class of antibiotics by directly targeting PBPs. With the cautiously optimistic successes of a number of new β-lactamase inhibitor chemotypes and many questions remaining to be answered about the structure and function of cell wall transpeptidases, non-β-lactam transpeptidase inhibitors may usher in the next exciting phase of drug discovery in this field.
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Affiliation(s)
| | | | - Yu Chen
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA; (L.M.C.J.); (P.C.)
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12
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Jin W, Xu C, Dong N, Chen K, Zhang D, Ning J, Li Y, Zhang G, Ke J, Hou A, Chen L, Chen S, Chan KF. Identification of isothiazolones analogues as potent bactericidal agents against antibiotic resistant CRE and MRSA strains. BMC Chem 2023; 17:183. [PMID: 38104171 PMCID: PMC10724953 DOI: 10.1186/s13065-023-01100-3] [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: 05/29/2023] [Accepted: 12/08/2023] [Indexed: 12/19/2023] Open
Abstract
Carbapenem-resistant Enterobacterales (CRE) has emerged as a worldwide spread nosocomial superbug exhibiting antimicrobial resistance (AMR) to all current antibiotics, leaving limited options for treating its infection. To discovery novel antibiotics against CRE, we designed and synthesized a series of 14 isothiazol-3(2H)-one analogues subjected to antibacterial activity evaluation against Escherichia coli (E. coli) BL21 (NDM-1) and clinical strain E. coli HN88 for investigating their structure-activity relationships (SAR). The results suggested that 5-chloroisothiazolone core with an N-(4-chlorophenyl) substitution 5a was the most potent antibacterial activity against the E. coli BL21 (NDM-1) with MIC value of less than 0.032 μg/mL, which was at least 8000-fold higher than the positive control Meropenem (MRM). It also displayed 2048-fold potent than the positive control MRM against E. coli HN88. Additionally, SAR analysis supported the conclusion that compounds with a chloro-group substituted on the 5-position of the heterocyclic ring was much more potent than other positions. The board spectrum analysis suggested that compound 5a showed a promising antimicrobial activity on MRSA and CRE pathogens. Meanwhile, cytotoxicity study of compound 5a suggested that it had a therapeutic index value of 875, suggesting future therapeutic potential. In vivo efficacy study declared that compound 5a could also protect the BALB/c mice against American type culture collection (ATCC) 43,300. Further screening of our compounds against a collection of CRE strains isolated from patients indicated that compound 5 g displayed much stronger antibacterial activity compared with MRM. In conclusion, our studies indicated that isothiazolones analogues could be potent bactericidal agents against CRE and MRSA pathogens.
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Affiliation(s)
- Wenbin Jin
- Key Laboratory of External Drug Delivery System and Preparation Technology in Universities of Yunnan and Faculty of Chinese Materia Medica, Yunnan University of Chinese Medicine, Kunming, Yunnan, China.
- State Key Laboratory of Chemical Biology and Drug Discovery and Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China.
| | - Chen Xu
- State Key Laboratory of Chemical Biology and Drug Discovery and Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
- School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Ning Dong
- State Key Laboratory of Chemical Biology and Drug Discovery and Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
- Department of Medical Microbiology, School of Biology and Basic Medical Sciences, Suzhou Medical College of Soochow University, Suzhou, China
| | - Kaichao Chen
- State Key Laboratory of Chemical Biology and Drug Discovery and Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China
| | - Die Zhang
- Key Laboratory of External Drug Delivery System and Preparation Technology in Universities of Yunnan and Faculty of Chinese Materia Medica, Yunnan University of Chinese Medicine, Kunming, Yunnan, China
| | - Jinhua Ning
- Key Laboratory of External Drug Delivery System and Preparation Technology in Universities of Yunnan and Faculty of Chinese Materia Medica, Yunnan University of Chinese Medicine, Kunming, Yunnan, China
| | - Yunbing Li
- Department of Medical Microbiology, School of Biology and Basic Medical Sciences, Suzhou Medical College of Soochow University, Suzhou, China
| | - Guangfen Zhang
- Department of Medical Microbiology, School of Biology and Basic Medical Sciences, Suzhou Medical College of Soochow University, Suzhou, China
| | - Jin Ke
- Key Laboratory of External Drug Delivery System and Preparation Technology in Universities of Yunnan and Faculty of Chinese Materia Medica, Yunnan University of Chinese Medicine, Kunming, Yunnan, China
| | - Anguo Hou
- Key Laboratory of External Drug Delivery System and Preparation Technology in Universities of Yunnan and Faculty of Chinese Materia Medica, Yunnan University of Chinese Medicine, Kunming, Yunnan, China
| | - Linyun Chen
- Key Laboratory of External Drug Delivery System and Preparation Technology in Universities of Yunnan and Faculty of Chinese Materia Medica, Yunnan University of Chinese Medicine, Kunming, Yunnan, China
| | - Sheng Chen
- Department of Food Science and Nutrition, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China.
| | - Kin-Fai Chan
- State Key Laboratory of Chemical Biology and Drug Discovery and Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China.
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13
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Bersani M, Failla M, Vascon F, Gianquinto E, Bertarini L, Baroni M, Cruciani G, Verdirosa F, Sannio F, Docquier JD, Cendron L, Spyrakis F, Lazzarato L, Tondi D. Structure-Based Optimization of 1,2,4-Triazole-3-Thione Derivatives: Improving Inhibition of NDM-/VIM-Type Metallo-β-Lactamases and Synergistic Activity on Resistant Bacteria. Pharmaceuticals (Basel) 2023; 16:1682. [PMID: 38139809 PMCID: PMC10747250 DOI: 10.3390/ph16121682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Revised: 11/21/2023] [Accepted: 11/26/2023] [Indexed: 12/24/2023] Open
Abstract
The worldwide emergence and dissemination of Gram-negative bacteria expressing metallo-β-lactamases (MBLs) menace the efficacy of all β-lactam antibiotics, including carbapenems, a last-line treatment usually restricted to severe pneumonia and urinary tract infections. Nonetheless, no MBL inhibitor is yet available in therapy. We previously identified a series of 1,2,4-triazole-3-thione derivatives acting as micromolar inhibitors of MBLs in vitro, but devoid of synergistic activity in microbiological assays. Here, via a multidisciplinary approach, including molecular modelling, synthesis, enzymology, microbiology, and X-ray crystallography, we optimized this series of compounds and identified low micromolar inhibitors active against clinically relevant MBLs (NDM-1- and VIM-type). The best inhibitors increased, to a certain extent, the susceptibility of NDM-1- and VIM-4-producing clinical isolates to meropenem. X-ray structures of three selected inhibitors in complex with NDM-1 elucidated molecular recognition at the base of potency improvement, confirmed in silico predicted orientation, and will guide further development steps.
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Affiliation(s)
- Matteo Bersani
- Department of Drug Science and Technology, University of Turin, Via Pietro Giuria 9, 10125 Turin, Italy; (M.B.); (M.F.); (E.G.); (F.S.)
| | - Mariacristina Failla
- Department of Drug Science and Technology, University of Turin, Via Pietro Giuria 9, 10125 Turin, Italy; (M.B.); (M.F.); (E.G.); (F.S.)
| | - Filippo Vascon
- Department of Biology, University of Padua, Viale G. Colombo 3, 35121 Padua, Italy; (F.V.); (L.C.)
| | - Eleonora Gianquinto
- Department of Drug Science and Technology, University of Turin, Via Pietro Giuria 9, 10125 Turin, Italy; (M.B.); (M.F.); (E.G.); (F.S.)
| | - Laura Bertarini
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy;
| | - Massimo Baroni
- Kinetic Business Centre, Molecular Discovery Ltd., Elstree, Borehamwood, Hertfordshire WD6 4PJ, UK;
| | - Gabriele Cruciani
- Department of Chemistry, Biology and Biotechnology, Università Degli Studi di Perugia, Via Elce di Sotto, 06132 Perugia, Italy;
| | - Federica Verdirosa
- Department of Medical Biotechnologies, University of Siena, Viale Bracci 16, 53100 Siena, Italy; (F.V.); (F.S.); (J.-D.D.)
| | - Filomena Sannio
- Department of Medical Biotechnologies, University of Siena, Viale Bracci 16, 53100 Siena, Italy; (F.V.); (F.S.); (J.-D.D.)
| | - Jean-Denis Docquier
- Department of Medical Biotechnologies, University of Siena, Viale Bracci 16, 53100 Siena, Italy; (F.V.); (F.S.); (J.-D.D.)
- Laboratoire de Bactériologie Moléculaire, Centre d’Ingénierie des Protéines-InBioS, Université de Liège, B-4000 Liège, Belgium
| | - Laura Cendron
- Department of Biology, University of Padua, Viale G. Colombo 3, 35121 Padua, Italy; (F.V.); (L.C.)
| | - Francesca Spyrakis
- Department of Drug Science and Technology, University of Turin, Via Pietro Giuria 9, 10125 Turin, Italy; (M.B.); (M.F.); (E.G.); (F.S.)
| | - Loretta Lazzarato
- Department of Drug Science and Technology, University of Turin, Via Pietro Giuria 9, 10125 Turin, Italy; (M.B.); (M.F.); (E.G.); (F.S.)
| | - Donatella Tondi
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy;
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14
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Palica K, Deufel F, Skagseth S, Di Santo Metzler GP, Thoma J, Andersson Rasmussen A, Valkonen A, Sunnerhagen P, Leiros HKS, Andersson H, Erdelyi M. α-Aminophosphonate inhibitors of metallo-β-lactamases NDM-1 and VIM-2. RSC Med Chem 2023; 14:2277-2300. [PMID: 38020072 PMCID: PMC10650955 DOI: 10.1039/d3md00286a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 07/31/2023] [Indexed: 12/01/2023] Open
Abstract
The upswing of antibiotic resistance is an escalating threat to human health. Resistance mediated by bacterial metallo-β-lactamases is of particular concern as these enzymes degrade β-lactams, our most frequently prescribed class of antibiotics. Inhibition of metallo-β-lactamases could allow the continued use of existing β-lactam antibiotics, such as penicillins, cephalosporins and carbapenems, whose applicability is becoming ever more limited. The design, synthesis, and NDM-1, VIM-2, and GIM-1 inhibitory activities (IC50 4.1-506 μM) of a series of novel non-cytotoxic α-aminophosphonate-based inhibitor candidates are presented herein. We disclose the solution NMR spectroscopic and computational investigation of their NDM-1 and VIM-2 binding sites and binding modes. Whereas the binding modes of the inhibitors are similar, VIM-2 showed a somewhat higher conformational flexibility, and complexed a larger number of inhibitor candidates in more varying binding modes than NDM-1. Phosphonate-type inhibitors may be potential candidates for development into therapeutics to combat metallo-β-lactamase resistant bacteria.
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Affiliation(s)
- Katarzyna Palica
- Department of Chemistry - BMC, Organic Chemistry, Uppsala University Husargatan 3 752 37 Uppsala Sweden
| | - Fritz Deufel
- Department of Chemistry - BMC, Organic Chemistry, Uppsala University Husargatan 3 752 37 Uppsala Sweden
| | - Susann Skagseth
- Department of Chemistry, Faculty of Science and Technology, UiT The Arctic University of Norway N-9037 Tromsø Norway
| | - Gabriela Paula Di Santo Metzler
- Department of Chemistry & Molecular Biology, University of Gothenburg Medicinaregatan 9C 413 90 Göteborg Sweden
- Center for Antibiotics Resistance Research (CARe) at University of Gothenburg 413 90 Göteborg Sweden
| | - Johannes Thoma
- Department of Chemistry & Molecular Biology, University of Gothenburg Medicinaregatan 9C 413 90 Göteborg Sweden
- Center for Antibiotics Resistance Research (CARe) at University of Gothenburg 413 90 Göteborg Sweden
| | - Anna Andersson Rasmussen
- Department of Chemistry - BMC, Organic Chemistry, Uppsala University Husargatan 3 752 37 Uppsala Sweden
| | - Arto Valkonen
- Department of Chemistry, University of Jyvaskyla Survontie 9B 40014 Finland
| | - Per Sunnerhagen
- Department of Chemistry & Molecular Biology, University of Gothenburg Medicinaregatan 9C 413 90 Göteborg Sweden
| | - Hanna-Kirsti S Leiros
- Department of Chemistry, Faculty of Science and Technology, UiT The Arctic University of Norway N-9037 Tromsø Norway
| | - Hanna Andersson
- Department of Chemistry - BMC, Organic Chemistry, Uppsala University Husargatan 3 752 37 Uppsala Sweden
| | - Mate Erdelyi
- Department of Chemistry - BMC, Organic Chemistry, Uppsala University Husargatan 3 752 37 Uppsala Sweden
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15
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Sun K, Xu P, Zhang Y, Yu P, Ju Y. Bibliometric insights into the most influential papers on antibiotic adjuvants: a comprehensive analysis. Front Pharmacol 2023; 14:1276018. [PMID: 38027012 PMCID: PMC10679448 DOI: 10.3389/fphar.2023.1276018] [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: 08/11/2023] [Accepted: 10/26/2023] [Indexed: 12/01/2023] Open
Abstract
Background: The utilization of antibiotic adjuvants presents a promising strategy for addressing bacterial resistance. Recently, the development of antibiotic adjuvants has attracted considerable attention from researchers in academia and industry. This study aimed to identify the most influential publications on antibiotic adjuvants and elucidate the hotspots and research trends in this field. Method: Original articles and reviews related to antibiotic adjuvants were retrieved from the Web of Science Core Collection database. The top 100 highly cited publications were selected and the visual analyses of publication outputs, countries, institutions, authors, journals, and keywords were conducted using Excel, VOSviewer, or CtieSpace software tools. Results: The top 100 cited publications concerning antibiotic adjuvants spanned the years 1977-2020, with citation counts ranging from 174 to 2,735. These publications encompassed 49 original articles and 51 reviews. The journal "Antimicrobial Agents and Chemotherapy" accounted for the highest number of publications (12%). The top 100 cited publications emanated from 39 countries, with the United States leading in production. Institutions in Canada and the United States exhibited the most substantial contributions to these highly cited publications. A total of 526 authors participated in these studies, with Robert E.W. Hancock, Laura J. V. Piddock, Xian-Zhi Li, Hiroshi Nikaido, and Olga Lomovskaya emerging as the most frequently nominated authors. The most common keywords included "E. coli", "P. aeruginosa", "S. aureus", "in-vitro activity", "antimicrobial peptide", "efflux pump inhibitor" "efflux pump", "MexAB-OprM" and "mechanism". These keywords underscored the hotspots of bacterial resistance mechanisms and the development of novel antibiotic adjuvants. Conclusion: Through the bibliometric analysis, this study identified the top 100 highly cited publications on antibiotic adjuvants. Moreover, the findings offered a comprehensive understanding of the characteristics and frontiers in this field.
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Affiliation(s)
- Ke Sun
- State Key Laboratory of Biotherapy and Cancer Center, Med-X Center for Manufacturing, Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Ping Xu
- Sichuan University Library, Sichuan University, Chengdu, China
| | - Yu Zhang
- Sichuan University Library, Sichuan University, Chengdu, China
| | - Pingjing Yu
- Sichuan University Library, Sichuan University, Chengdu, China
| | - Yuan Ju
- Sichuan University Library, Sichuan University, Chengdu, China
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16
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Bibi Z, Asghar I, Ashraf NM, Zeb I, Rashid U, Hamid A, Ali MK, Hatamleh AA, Al-Dosary MA, Ahmad R, Ali M. Prediction of Phytochemicals for Their Potential to Inhibit New Delhi Metallo β-Lactamase (NDM-1). Pharmaceuticals (Basel) 2023; 16:1404. [PMID: 37895875 PMCID: PMC10610165 DOI: 10.3390/ph16101404] [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: 08/09/2023] [Revised: 09/18/2023] [Accepted: 09/21/2023] [Indexed: 10/29/2023] Open
Abstract
The effectiveness of all antibiotics in the β-lactam group to cure bacterial infections has been impaired by the introduction of the New Delhi Metallo-β-lactamase (NDM-1) enzyme. Attempts have been made to discover a potent chemical as an inhibitor to this enzyme in order to restore the efficacy of antibiotics. However, it has been a challenging task to develop broad-spectrum inhibitors of metallo-β-lactamases. Lack of sequence homology across metallo-β-lactamases (MBLs), the rapidly evolving active site of the enzyme, and structural similarities between human enzymes and metallo-β-lactamases, are the primary causes for the difficulty in the development of these inhibitors. Therefore, it is imperative to concentrate on the discovery of an effective NDM-1 inhibitor. This study used various in silico approaches, including molecular docking and molecular dynamics simulations, to investigate the potential of phytochemicals to inhibit the NDM-1 enzyme. For this purpose, a library of about 59,000 phytochemicals was created from the literature and other databases, including FoodB, IMPPAT, and Phenol-Explorer. A physiochemical and pharmacokinetics analysis was performed to determine possible toxicity and mutagenicity of the ligands. Following the virtual screening, phytochemicals were assessed for their binding with NDM-1using docking scores, RMSD values, and other critical parameters. The docking score was determined by selecting the best conformation of the protein-ligand complex. Three phytochemicals, i.e., butein (polyphenol), monodemethylcurcumin (polyphenol), and rosmarinic acid (polyphenol) were identified as result of pharmacokinetics and molecular docking studies. Furthermore, molecular dynamics simulations were performed to determine structural stabilities of the protein-ligand complexes. Monodemethylcurcumin, butein, and rosmarinic acid were identified as potential inhibitors of NDM-1 based on their low RMSD, RMSF, hydrogen bond count, average Coulomb-Schrödinger interaction energy, and Lennard-Jones-Schrödinger interaction energy. The present investigation suggested that these phytochemicals might be promising candidates for future NDM-1 medication development to respond to antibiotic resistance.
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Affiliation(s)
- Zainab Bibi
- Department of Biotechnology, Abbottabad Campus, COMSATS University Islamabad, Abbottabad 22060, Pakistan (R.A.)
| | - Irfa Asghar
- Department of Biotechnology, Abbottabad Campus, COMSATS University Islamabad, Abbottabad 22060, Pakistan (R.A.)
| | - Naeem Mahmood Ashraf
- School of Biochemistry and Biotechnology, University of Punjab, Lahore P.O. Box 54590, Pakistan;
| | - Iftikhar Zeb
- Department of Biotechnology, Abbottabad Campus, COMSATS University Islamabad, Abbottabad 22060, Pakistan (R.A.)
| | - Umer Rashid
- Department of Chemistry, Abbottabad Campus, COMSATS University Islamabad, Abbottabad 22060, Pakistan;
| | - Arslan Hamid
- LIMES Institute, University of Bonn, D-53113 Bonn, Germany;
| | - Maria Kanwal Ali
- Institute of Nuclear Medicine, Oncology and Radiotherapy (INOR), Abbottabad 22060, Pakistan;
| | - Ashraf Atef Hatamleh
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia; (A.A.H.); (M.A.A.-D.)
| | - Munirah Abdullah Al-Dosary
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia; (A.A.H.); (M.A.A.-D.)
| | - Raza Ahmad
- Department of Biotechnology, Abbottabad Campus, COMSATS University Islamabad, Abbottabad 22060, Pakistan (R.A.)
| | - Muhammad Ali
- Department of Biotechnology, Abbottabad Campus, COMSATS University Islamabad, Abbottabad 22060, Pakistan (R.A.)
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17
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Lv H, Zhu Z, Qian C, Li T, Han Z, Zhang W, Si X, Wang J, Deng X, Li L, Fang T, Xia J, Wu S, Zhou Y. Discovery of isatin-β-methyldithiocarbazate derivatives as New Delhi metallo- β-lactamase-1 (NDM-1) inhibitors against NDM-1 producing clinical isolates. Biomed Pharmacother 2023; 166:115439. [PMID: 37673020 DOI: 10.1016/j.biopha.2023.115439] [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: 06/23/2023] [Revised: 08/20/2023] [Accepted: 08/31/2023] [Indexed: 09/08/2023] Open
Abstract
New Delhi metallo-β-lactamase-1 (NDM-1) poses a threat to public health due to its capability to hydrolyze nearly all β-lactam antibiotics, leaving limited treatment options for NDM-1 positive pathogens. Regrettably, there are presently no effective NDM-1 inhibitors in clinical use. This compels us to seek new compounds to combat multi-drug resistant bacterial infections (MDR). In our study, Zndm19 was identified as a new NDM-1 inhibitor through virtual screening and an NDM-1 enzyme activity inhibition assay. Subsequently, we employed the checkerboard method, time-killing assay, and combined disk test to investigate the synergistic bactericidal efficacy of Zndm19 in combination with meropenem (MEM). Meanwhile, molecular docking and site-directed mutagenesis were conducted to uncover the crucial amino acid residues engaged in Zndm19 binding. Finally, we established a mice peritonitis infection model to assess the synergistic effect of Zndm19 and MEM in vivo. Our findings demonstrated that 16 µg/mL of Zndm19 inhibited NDM-1 activity without affecting NDM-1 expression, restoring the bactericidal activity of MEM against NDM-1-positive Escherichia coli in vitro. Furthermore, MET-67, ASP-124, HIS-189, and HIS-250 amino acid residues constituted the active site of Zndm19 in NDM-1. Importantly, this combination therapy exhibited synergistic anti-infection activity in the mice peritonitis infection model, leading to an approximate 60% increase in survival rates and reduction of tissue bacterial load, effectively combating bacterial infection in vivo. In summary, our research validates that the synthetic novel NDM-1 inhibitor Zndm19 holds promise as a drug to treat drug-resistant bacterial infections, especially those harboring NDM-1.
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Affiliation(s)
- Hongfa Lv
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, China
| | - Zihao Zhu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Chenliang Qian
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China; School of Pharmacy, Jiangsu Ocean University, Lianyungang, China
| | - Tianlei Li
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zunsheng Han
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Wenxuan Zhang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xinxin Si
- School of Pharmacy, Jiangsu Ocean University, Lianyungang, China
| | - Jianfeng Wang
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, China
| | - Xuming Deng
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, China
| | - Li Li
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, China
| | - Tianqi Fang
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, China
| | - Jie Xia
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
| | - Song Wu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
| | - Yonglin Zhou
- Key Laboratory of Ministry of Education for Conservation and Utilization of Special Biological Resources in the Western China, School of Life Sciences, Ningxia University, Yinchuan, China; State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, China.
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18
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Dong X, Liu W, Dong Y, Wang K, Li K, Bian L. Metallo-β-lactamase SMB-1 evolves into a more efficient hydrolase under the selective pressure of meropenem. J Inorg Biochem 2023; 247:112323. [PMID: 37478781 DOI: 10.1016/j.jinorgbio.2023.112323] [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: 04/18/2023] [Revised: 06/27/2023] [Accepted: 07/06/2023] [Indexed: 07/23/2023]
Abstract
Metallo-β-lactamases (MβLs) are the primary mechanism of resistance to carbapenem antibiotics. To elucidate how MβLs have evolved with the introduction and use of antibiotics, the mutation and evolution of SMB-1 from Serratia marcescens were investigated in microbial evolution plates containing discontinuous meropenem (MEM) concentration gradients. The results revealed 2-point mutations, A242G and S257R; 1 double-site mutation, C240G/E258G; and 3 frameshift mutations, M5, M12, and M13, which are all missense mutations situated at the C-terminus. Compared with that of the wild-type (WT), the minimum inhibitory concentrations (MICs) of MEM for A242G, C240G/E258G, M5, M12, and M13 increased at least 120-fold, and that of S257R increased 8-fold. The catalytic efficiency kcat/Km increased by 365% and 647%, respectively. Concerning the structural changes, the structure at the active site changed from an ordered structure to an unordered conformation. Simultaneously, the flexibility of loop 1 was enhanced. These changes increased the volume of the active site cavity; thus, this was more conducive to exposing the Zn2+ site, facilitating substrate binding and conversion to products. In A242G, structural changes in Gly-242 can be transmitted to the active region via a network of interactions between the side chains of Gly-242 and the amino acid side chains near the active pocket. Together, these results pointed to the process of persistent drug tolerance and resistance, the SMB-1 enzyme evolved into a more exquisite structure with increased flexibility and stability, and stronger hydrolysis activity via genetic mutations and structural changes.
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Affiliation(s)
- Xiaoting Dong
- College of Life Science, Northwest University, Xi'an 710069, China
| | - Wenli Liu
- College of Life Science, Northwest University, Xi'an 710069, China
| | - Yuxuan Dong
- College of Life Science, Northwest University, Xi'an 710069, China
| | - Kun Wang
- College of Life Science, Northwest University, Xi'an 710069, China
| | - Kewei Li
- College of Life Science, Northwest University, Xi'an 710069, China
| | - Liujiao Bian
- College of Life Science, Northwest University, Xi'an 710069, China.
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19
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Jia Y, Schroeder B, Pfeifer Y, Fröhlich C, Deng L, Arkona C, Kuropka B, Sticht J, Ataka K, Bergemann S, Wolber G, Nitsche C, Mielke M, Leiros HKS, Werner G, Rademann J. Kinetics, Thermodynamics, and Structural Effects of Quinoline-2-Carboxylates, Zinc-Binding Inhibitors of New Delhi Metallo-β-lactamase-1 Re-sensitizing Multidrug-Resistant Bacteria for Carbapenems. J Med Chem 2023; 66:11761-11791. [PMID: 37585683 DOI: 10.1021/acs.jmedchem.3c00171] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/18/2023]
Abstract
Carbapenem resistance mediated by metallo-β-lactamases (MBL) such as New Delhi metallo-β-lactamase-1 (NDM-1) has become a major factor threatening the efficacy of essential β-lactam antibiotics. Starting from hit fragment dipicolinic acid (DPA), 8-hydroxy- and 8-sulfonamido-quinoline-2-carboxylic acids were developed as inhibitors of NDM-1 with highly improved inhibitory activity and binding affinity. The most active compounds formed reversibly inactive ternary protein-inhibitor complexes with two zinc ions as proven by native protein mass spectrometry and bio-layer interferometry. Modification of the NDM-1 structure with remarkable entropic gain was shown by isothermal titration calorimetry and NMR spectroscopy of isotopically labeled protein. The best compounds were potent inhibitors of NDM-1 and other representative MBL with no or little inhibition of human zinc-binding enzymes. These inhibitors significantly reduced the minimum inhibitory concentrations (MIC) of meropenem for multidrug-resistant bacteria recombinantly expressing blaNDM-1 as well as for several multidrug-resistant clinical strains at concentrations non-toxic to human cells.
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Affiliation(s)
- Yuwen Jia
- Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Str. 2+4, Berlin 14195, Germany
| | - Barbara Schroeder
- Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Str. 2+4, Berlin 14195, Germany
| | - Yvonne Pfeifer
- FG13 Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, Burgstraße 37, Wernigerode 38855, Germany
| | - Christopher Fröhlich
- Department of Chemistry, Faculty of Science and Technology, UiT The Arctic University of Norway, Tromsø 9037, Norway
| | - Lihua Deng
- Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Str. 2+4, Berlin 14195, Germany
| | - Christoph Arkona
- Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Str. 2+4, Berlin 14195, Germany
| | - Benno Kuropka
- Core Facility BioSupraMol, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Thielallee 63, Berlin 14195, Germany
| | - Jana Sticht
- Core Facility BioSupraMol, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Thielallee 63, Berlin 14195, Germany
| | - Kenichi Ataka
- Department of Physics, Freie Universität Berlin, Arnimallee 14, Berlin 14195, Germany
| | - Silke Bergemann
- Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Str. 2+4, Berlin 14195, Germany
| | - Gerhard Wolber
- Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Str. 2+4, Berlin 14195, Germany
| | - Christoph Nitsche
- Research School of Chemistry, Australian National University, Canberra 2601, Australian Capital Territory, Australia
| | - Martin Mielke
- Department of Infectious Diseases, Robert Koch Institute, Nordufer 20, Berlin 13353, Germany
| | - Hanna-Kirsti S Leiros
- Department of Chemistry, Faculty of Science and Technology, UiT The Arctic University of Norway, Tromsø 9037, Norway
| | - Guido Werner
- FG13 Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, Burgstraße 37, Wernigerode 38855, Germany
| | - Jörg Rademann
- Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Str. 2+4, Berlin 14195, Germany
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20
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S S, N H, Fasim A, More SS, Das Mitra S. Identification of a potential inhibitor for New Delhi metallo-β-lactamase 1 (NDM-1) from FDA approved chemical library- a drug repurposing approach to combat carbapenem resistance. J Biomol Struct Dyn 2023; 41:7700-7711. [PMID: 36165602 DOI: 10.1080/07391102.2022.2123402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 09/06/2022] [Indexed: 10/14/2022]
Abstract
Superbugs producing New Delhi metallo-β-lactamase 1 (NDM-1) enzyme is a growing crisis, that is adversely affecting the global health care system. NDM-1 empowers the bacteria to inactivate entire arsenal of β-lactam antibiotics including carbapenem (the last resort antibiotic) and remains ineffective to all the available β lactamase inhibitors used in the clinics. Limited therapeutic option available for rapidly disseminating NDM-1 producing bacteria makes it imperative to identify a potential inhibitor for NDM-1 enzyme. With drug repurposing approach, in this study, we used virtual screening of available Food and Drug Administration (FDA) approved chemical library (ZINC12 database) and captured 'adapalene' (FDA drug) as a potent inhibitor candidate for NDM-1 enzyme. Active site docking with NDM-1, showed adapalene with binding energy -9.21 kcal/mol and interacting with key amino acid residues (Asp124, His122, His189, His250, Cys208) in the active site of NDM-1. Further, molecular dynamic simulation of NDM-1 docked with the adapalene at 100 ns displayed a stable conformation dynamic, with relative RMSD and RMSF in the acceptable range. Subsequently, in vitro enzyme assays using recombinant NDM-1 protein demonstrated inhibition of NDM-1 by adapalene. Further, the combination of adapalene plus meropenem (carbapenem antibiotic) showed synergistic effect against the NDM-1 producing carbapenem (meropenem) resistant clinical isolates (Escherichia coli and Klebsiella pneumoniae). Overall, our data indicated that adapalene can be a potential inhibitor candidate for NDM-1 enzyme that can contribute to the development of a suitable adjuvant to save the activity of carbapenem antibiotic against infections caused by NDM-1 positive gram-negative bacteria. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shailaja S
- Department of Biological Sciences, School of Basic & Applied Sciences, Dayananda Sagar University, Bangalore, Karnataka, India
| | - Harshitha N
- Department of Biological Sciences, School of Basic & Applied Sciences, Dayananda Sagar University, Bangalore, Karnataka, India
| | - Aneesa Fasim
- Department of Biological Sciences, School of Basic & Applied Sciences, Dayananda Sagar University, Bangalore, Karnataka, India
| | - Sunil S More
- Department of Biological Sciences, School of Basic & Applied Sciences, Dayananda Sagar University, Bangalore, Karnataka, India
| | - Susweta Das Mitra
- Department of Biological Sciences, School of Basic & Applied Sciences, Dayananda Sagar University, Bangalore, Karnataka, India
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21
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Papastergiou T, Azé J, Bringay S, Louet M, Poncelet P, Rosales-Hurtado M, Vo-Hoang Y, Licznar-Fajardo P, Docquier JD, Gavara L. Discovering NDM-1 inhibitors using molecular substructure embeddings representations. J Integr Bioinform 2023; 0:jib-2022-0050. [PMID: 37498676 PMCID: PMC10389050 DOI: 10.1515/jib-2022-0050] [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: 10/24/2022] [Accepted: 06/12/2023] [Indexed: 07/29/2023] Open
Abstract
NDM-1 (New-Delhi-Metallo-β-lactamase-1) is an enzyme developed by bacteria that is implicated in bacteria resistance to almost all known antibiotics. In this study, we deliver a new, curated NDM-1 bioactivities database, along with a set of unifying rules for managing different activity properties and inconsistencies. We define the activity classification problem in terms of Multiple Instance Learning, employing embeddings corresponding to molecular substructures and present an ensemble ranking and classification framework, relaying on a k-fold Cross Validation method employing a per fold hyper-parameter optimization procedure, showing promising generalization ability. The MIL paradigm displayed an improvement up to 45.7 %, in terms of Balanced Accuracy, in comparison to the classical Machine Learning paradigm. Moreover, we investigate different compact molecular representations, based on atomic or bi-atomic substructures. Finally, we scanned the Drugbank for strongly active compounds and we present the top-15 ranked compounds.
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Affiliation(s)
- Thomas Papastergiou
- LIRMM, University of Montpellier, CNRS, 34095 Montpellier, France
- IBMM, CNRS, University of Montpellier, ENSCM, 34293 Montpellier, France
| | - Jérôme Azé
- LIRMM, University of Montpellier, CNRS, 34095 Montpellier, France
| | - Sandra Bringay
- LIRMM, University of Montpellier, CNRS, 34095 Montpellier, France
- AMIS, Paul Valery University, 34199 Montpellier, France
| | - Maxime Louet
- IBMM, CNRS, University of Montpellier, ENSCM, 34293 Montpellier, France
| | - Pascal Poncelet
- LIRMM, University of Montpellier, CNRS, 34095 Montpellier, France
| | | | - Yen Vo-Hoang
- IBMM, CNRS, University of Montpellier, ENSCM, 34293 Montpellier, France
| | | | - Jean-Denis Docquier
- Department of Medical Biotechnologies, University of Siena, I-53100 Siena, Italy
| | - Laurent Gavara
- IBMM, CNRS, University of Montpellier, ENSCM, 34293 Montpellier, France
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22
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Velema WA. Exploring antibiotic resistance with chemical tools. Chem Commun (Camb) 2023; 59:6148-6158. [PMID: 37039397 PMCID: PMC10194278 DOI: 10.1039/d3cc00759f] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 04/05/2023] [Indexed: 04/08/2023]
Abstract
Antibiotic resistance is an enormous problem that is accountable for over a million deaths annually, with numbers expected to significantly increase over the coming decades. Although some of the underlying causes leading up to antibiotic resistance are well understood, many of the molecular processes involved remain elusive. To better appreciate at a molecular level how resistance emerges, customized chemical biology tools can offer a solution. This Feature Article attempts to provide an overview of the wide variety of tools that have been developed over the last decade, by highlighting some of the more illustrative examples. These include the use of fluorescent, photoaffinity and activatable antibiotics and bacterial components to start to unravel the molecular mechanisms involved in resistance. The antibiotic crisis is an eminent global threat and requires the continuous development of creative chemical tools to dissect and ultimately counteract resistance.
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Affiliation(s)
- Willem A Velema
- Institute for Molecules and Materials, Radboud University Nijmegen, The Netherlands, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands.
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23
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Verma J, Jain D, Panda AP, Kant S, Kumar G, Ghosh AS. Involvement of the non-active site Residues in the Catalytic Activity of NDM-4 Metallo beta-lactamase. Protein J 2023:10.1007/s10930-023-10124-6. [PMID: 37170014 DOI: 10.1007/s10930-023-10124-6] [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] [Accepted: 05/07/2023] [Indexed: 05/13/2023]
Abstract
The rise of New Delhi metallo beta-lactamase (NDM) producing bacteria imposes a significant threat to the treatment of bacterial infections due to their broad spectrum against beta-lactams. The activity of metallo beta-lactamases is affected by active site residues as well as residues near the active site. Therefore, we aimed to identify the amino acid residues around the active site of NDM-4 which influence its function. To achieve that, seven substitution mutations (S191A, D192A, S213A, K216A, S217A, D223A and D225A) of NDM-4 were generated through site-directed mutagenesis. Out of these, expression of NDM-4_D192A and NDM-4_S217A in Escherichia coli cells increased the beta-lactam susceptibility as compared to NDM-4. Further, proteins were purified to assess the effect of substitution mutations on zinc content, in vitro catalytic efficiency, and stability of NDM-4. The catalytic efficiency was reduced for these mutants (D192A and S217A) towards beta-lactam substrates, while the thermal stability remained insubstantial as compared to NDM-4. However, the purified NDM-4_D192A exhibited altered zinc content. In silico studies reveal that these changes might be the outcomes of alterations in hydrogen bonding networks and substrate interactions. Taken together, we infer that the D192 and the S217 residues play a substantial role in the activity of NDM-4.
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Affiliation(s)
- Jyoti Verma
- Advanced Technology Development Centre, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, 721302, India
| | - Diamond Jain
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, 721302, India
| | - Aditya Prasad Panda
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, 721302, India
| | - Shri Kant
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, 721302, India
| | - Gaurav Kumar
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, 721302, India
| | - Anindya Sundar Ghosh
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal, 721302, India.
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24
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Dhanda G, Acharya Y, Haldar J. Antibiotic Adjuvants: A Versatile Approach to Combat Antibiotic Resistance. ACS OMEGA 2023; 8:10757-10783. [PMID: 37008128 PMCID: PMC10061514 DOI: 10.1021/acsomega.3c00312] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 02/21/2023] [Indexed: 06/13/2023]
Abstract
The problem of antibiotic resistance is on the rise, with multidrug-resistant strains emerging even to the last resort antibiotics. The drug discovery process is often stalled by stringent cut-offs required for effective drug design. In such a scenario, it is prudent to delve into the varying mechanisms of resistance to existing antibiotics and target them to improve antibiotic efficacy. Nonantibiotic compounds called antibiotic adjuvants which target bacterial resistance can be used in combination with obsolete drugs for an improved therapeutic regime. The field of "antibiotic adjuvants" has gained significant traction in recent years where mechanisms other than β-lactamase inhibition have been explored. This review discusses the multitude of acquired and inherent resistance mechanisms employed by bacteria to resist antibiotic action. The major focus of this review is how to target these resistance mechanisms by the use of antibiotic adjuvants. Different types of direct acting and indirect resistance breakers are discussed including enzyme inhibitors, efflux pump inhibitors, inhibitors of teichoic acid synthesis, and other cellular processes. The multifaceted class of membrane-targeting compounds with poly pharmacological effects and the potential of host immune-modulating compounds have also been reviewed. We conclude with providing insights about the existing challenges preventing clinical translation of different classes of adjuvants, especially membrane-perturbing compounds, and a framework about the possible directions which can be pursued to fill this gap. Antibiotic-adjuvant combinatorial therapy indeed has immense potential to be used as an upcoming orthogonal strategy to conventional antibiotic discovery.
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Affiliation(s)
- Geetika Dhanda
- Antimicrobial
Research Laboratory, New Chemistry Unit and School of Advanced
Materials, Jawaharlal Nehru Centre for Advanced
Scientific Research (JNCASR), Jakkur, Bengaluru 560064, Karnataka, India
| | - Yash Acharya
- Antimicrobial
Research Laboratory, New Chemistry Unit and School of Advanced
Materials, Jawaharlal Nehru Centre for Advanced
Scientific Research (JNCASR), Jakkur, Bengaluru 560064, Karnataka, India
| | - Jayanta Haldar
- Antimicrobial
Research Laboratory, New Chemistry Unit and School of Advanced
Materials, Jawaharlal Nehru Centre for Advanced
Scientific Research (JNCASR), Jakkur, Bengaluru 560064, Karnataka, India
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25
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Cheng K, Wu Q, Yao C, Chai Z, Jiang L, Liu M, Li C. Distinct Inhibition Modes of New Delhi Metallo-β-lactamase-1 Revealed by NMR Spectroscopy. JACS AU 2023; 3:849-859. [PMID: 37006760 PMCID: PMC10052233 DOI: 10.1021/jacsau.2c00651] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 02/13/2023] [Accepted: 02/14/2023] [Indexed: 06/19/2023]
Abstract
The wide spread of antibiotic-resistant "superbugs" containing New Delhi metallo-β-lactamase-1 (NDM-1) has become a threat to human health. However, clinically valid antibiotics to treat the superbugs' infection are not available now. Quick, simple, and reliable methods to assess the ligand-binding mode are key to developing and improving inhibitors against NDM-1. Herein, we report a straightforward NMR method to distinguish the NDM-1 ligand-binding mode using distinct NMR spectroscopy patterns of apo- and di-Zn-NDM-1 titrations with various inhibitors. Elucidating the inhibition mechanism will aid the development of efficient inhibitors for NDM-1.
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Affiliation(s)
- Kai Cheng
- Key
Laboratory of Magnetic Resonance in Biological Systems, State Key
Laboratory of Magnetic Resonance and Atomic and Molecular Physics,
National Center for Magnetic Resonance in Wuhan, Wuhan Institute of
Physics and Mathematics, Innovation Academy of Precision Measurement, Chinese Academy of Sciences, Wuhan 430071, China
| | - Qiong Wu
- Key
Laboratory of Magnetic Resonance in Biological Systems, State Key
Laboratory of Magnetic Resonance and Atomic and Molecular Physics,
National Center for Magnetic Resonance in Wuhan, Wuhan Institute of
Physics and Mathematics, Innovation Academy of Precision Measurement, Chinese Academy of Sciences, Wuhan 430071, China
| | - Chendie Yao
- Key
Laboratory of Magnetic Resonance in Biological Systems, State Key
Laboratory of Magnetic Resonance and Atomic and Molecular Physics,
National Center for Magnetic Resonance in Wuhan, Wuhan Institute of
Physics and Mathematics, Innovation Academy of Precision Measurement, Chinese Academy of Sciences, Wuhan 430071, China
| | - Zhaofei Chai
- Key
Laboratory of Magnetic Resonance in Biological Systems, State Key
Laboratory of Magnetic Resonance and Atomic and Molecular Physics,
National Center for Magnetic Resonance in Wuhan, Wuhan Institute of
Physics and Mathematics, Innovation Academy of Precision Measurement, Chinese Academy of Sciences, Wuhan 430071, China
| | - Ling Jiang
- Key
Laboratory of Magnetic Resonance in Biological Systems, State Key
Laboratory of Magnetic Resonance and Atomic and Molecular Physics,
National Center for Magnetic Resonance in Wuhan, Wuhan Institute of
Physics and Mathematics, Innovation Academy of Precision Measurement, Chinese Academy of Sciences, Wuhan 430071, China
- Wuhan
National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Maili Liu
- Key
Laboratory of Magnetic Resonance in Biological Systems, State Key
Laboratory of Magnetic Resonance and Atomic and Molecular Physics,
National Center for Magnetic Resonance in Wuhan, Wuhan Institute of
Physics and Mathematics, Innovation Academy of Precision Measurement, Chinese Academy of Sciences, Wuhan 430071, China
- Wuhan
National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Conggang Li
- Key
Laboratory of Magnetic Resonance in Biological Systems, State Key
Laboratory of Magnetic Resonance and Atomic and Molecular Physics,
National Center for Magnetic Resonance in Wuhan, Wuhan Institute of
Physics and Mathematics, Innovation Academy of Precision Measurement, Chinese Academy of Sciences, Wuhan 430071, China
- Wuhan
National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, China
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26
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Tolbatov I, Marrone A. Auranofin Targeting the NDM-1 Beta-Lactamase: Computational Insights into the Electronic Configuration and Quasi-Tetrahedral Coordination of Gold Ions. Pharmaceutics 2023; 15:pharmaceutics15030985. [PMID: 36986846 PMCID: PMC10057648 DOI: 10.3390/pharmaceutics15030985] [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: 02/27/2023] [Revised: 03/14/2023] [Accepted: 03/16/2023] [Indexed: 03/30/2023] Open
Abstract
Recently, the well-characterized metallodrug auranofin has been demonstrated to restore the penicillin and cephalosporin sensitivity in resistant bacterial strains via the inhibition of the NDM-1 beta-lactamase, which is operated via the Zn/Au substitution in its bimetallic core. The resulting unusual tetrahedral coordination of the two ions was investigated via the density functional theory calculations. By assessing several charge and multiplicity schemes, coupled with on/off constraining the positions of the coordinating residues, it was demonstrated that the experimental X-ray structure of the gold-bound NDM-1 is consistent with either Au(I)-Au(I) or Au(II)-Au(II) bimetallic moieties. The presented results suggest that the most probable mechanism for the auranofin-based Zn/Au exchange in NDM-1 includes the early formation of the Au(I)-Au(I) system, superseded by oxidation yielding the Au(II)-Au(II) species bearing the highest resemblance to the X-ray structure.
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Affiliation(s)
- Iogann Tolbatov
- Institute of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology, Av. Paisos Catalans 16, 43007 Tarragona, Spain
| | - Alessandro Marrone
- Dipartimento di Farmacia, Università degli Studi "G. D'Annunzio" Chieti-Pescara, Via dei Vestini 31, 66100 Chieti, Italy
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27
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The activity and mechanism of vidofludimus as a potent enzyme inhibitor against NDM-1-positive E. coli. Eur J Med Chem 2023; 250:115225. [PMID: 36870273 DOI: 10.1016/j.ejmech.2023.115225] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 02/11/2023] [Accepted: 02/20/2023] [Indexed: 03/03/2023]
Abstract
New Delhi metallo-β-lactamase-1 (NDM-1) is the most important and prevalent enzyme among all metallo-β-lactamases. NDM-1 can hydrolyze almost all-available β-lactam antibiotics including carbapenems, resulting in multidrug resistance, which poses an increasing clinical threat. However, there is no NDM-1 inhibitor approved for clinical treatment. Therefore, identifying a novel and potential enzyme inhibitor against NDM-1-mediated infections is an urgent need. In this study, vidofludimus was identified as a potential NDM-1 inhibitor by structure-based virtual screening and an enzyme activity inhibition assay. Vidofludimus significantly inhibited NDM-1 hydrolysis activity with a significant dose-dependent effect. When the vidofludimus concentration was 10 μg/ml, the inhibition rate and 50% inhibitory concentration were 93.3% and 13.8 ± 0.5 μM, respectively. In vitro, vidofludimus effectively restored the antibacterial activity of meropenem against NDM-1-positive Escherichia coli (E. coli), and the minimum inhibitory concentration of meropenem was decreased from 64 μg/ml to 4 μg/ml, a 16-fold reduction. The combination of vidofludimus and meropenem showed a significant synergistic effect with a fractional inhibitory concentration index of 0.125 and almost all the NDM-1-positive E. coli were killed within 12 h. Furthermore, the synergistic therapeutic effect of vidofludimus and meropenem in vivo was evaluated in mice infected with NDM-1 positive E. coli. Compared with the control treatment, vidofludimus combined with meropenem significantly improved the survival rate of mice infected with NDM-1-positive E. coli (P < 0.05), decreased the white blood cell count, the bacterial burden and inflammatory response induced by NDM-1-positive E. coli (P < 0.05), and alleviated histopathological damage in infected mice. It was demonstrated by molecular dynamic simulation, site-directed mutagenesis and biomolecular interaction that vidofludimus could interact directly with the key amino acids (Met67, His120, His122 and His250) and Zn2+ in the active site of NDM-1, thereby competitively inhibiting the hydrolysis activity of NDM-1 on meropenem. In summary, vidofludimus holds promise as anNDM-1 inhibitor, and the combination of vidofludimus and meropenem has potential as a therapeutic strategy for NDM-1-mediated infections.
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Fragment-Based Lead Discovery Strategies in Antimicrobial Drug Discovery. Antibiotics (Basel) 2023; 12:antibiotics12020315. [PMID: 36830226 PMCID: PMC9951956 DOI: 10.3390/antibiotics12020315] [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: 01/09/2023] [Revised: 01/30/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
Fragment-based lead discovery (FBLD) is a powerful application for developing ligands as modulators of disease targets. This approach strategy involves identification of interactions between low-molecular weight compounds (100-300 Da) and their putative targets, often with low affinity (KD ~0.1-1 mM) interactions. The focus of this screening methodology is to optimize and streamline identification of fragments with higher ligand efficiency (LE) than typical high-throughput screening. The focus of this review is on the last half decade of fragment-based drug discovery strategies that have been used for antimicrobial drug discovery.
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Heydarian N, Wouters CL, Neel A, Ferrell M, Panlilio H, Haight T, Gu T, Rice CV. Eradicating Biofilms of Carbapenem-Resistant Enterobacteriaceae by Simultaneously Dispersing the Biomass and Killing Planktonic Bacteria with PEGylated Branched Polyethyleneimine. ChemMedChem 2023; 18:e202200428. [PMID: 36542457 PMCID: PMC9899318 DOI: 10.1002/cmdc.202200428] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 11/21/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022]
Abstract
Carbapenem-resistant Enterobacteriaceae (CRE) are emerging pathogens that cause variety of severe infections. CRE evade antibiotic treatments because these bacteria produce enzymes that degrade a wide range of antibiotics including carbapenems and β-lactams. The formation of biofilms aggravates CRE infections, especially in a wound environment. These difficulties lead to persistent infection and non-healing wounds. This creates the need for new compounds to overcome CRE antimicrobial resistance and disrupt biofilms. Recent studies in our lab show that 600 Da branched polyethyleneimine (BPEI) and its derivative PEG350-BPEI can overcome antimicrobial resistance and eradicate biofilms in methicillin-resistant S. aureus, methicillin-resistant S. epidermidis, P. aeruginosa, and E. coli. In this study, the ability of 600 Da BPEI and PEG350-BPEI to eradicate carbapenem-resistant Enterobacteriaceae bacteria and their biofilms is demonstrated. We show that both BPEI and PEG350-BPEI have anti-biofilm efficacy against CRE strains expressing Klebsiella pneumoniae carbapenemases (KPCs) and metallo-β-lactamases (MBLs), such as New Delhi MBL (NDM-1). Furthermore, our results illustrate that BPEI affects planktonic CRE bacteria by increasing bacterial length and width from the inability to proceed with normal cell division processes. These data demonstrate the multi-functional properties of 600 Da BPEI and PEG350-BPEI to reduce biofilm formation and mitigate virulence in carbapenem-resistant Enterobacteriaceae.
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Affiliation(s)
- Neda Heydarian
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, OK 73019
| | - Cassandra L. Wouters
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, OK 73019
| | - Andrew Neel
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, OK 73019
| | - Maya Ferrell
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, OK 73019
| | - Hannah Panlilio
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, OK 73019
| | - Tristan Haight
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, OK 73019
| | - Tingting Gu
- Department of Biology, 730 Van Vleet Oval, Room 314, University of Oklahoma, Norman, OK 73019, USA
| | - Charles V. Rice
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, OK 73019
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Antibacterial Activity of Ebselen. Int J Mol Sci 2023; 24:ijms24021610. [PMID: 36675123 PMCID: PMC9864093 DOI: 10.3390/ijms24021610] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 01/02/2023] [Accepted: 01/09/2023] [Indexed: 01/15/2023] Open
Abstract
Ebselen is a low-molecular-weight organoselenium compound that has been broadly studied for its antioxidant, anti-inflammatory, and cytoprotective properties. These advantageous properties were initially associated with mimicking the activity of selenoprotein glutathione peroxidase, but the biomedical impact of this compound appear to be far more complex. Ebselen serves as a substrate or inhibitor with multiple protein/enzyme targets, whereas inhibition typically originates from the covalent modification of cysteine residues by opening the benzisoselenazolone ring and S-Se bond formation. The inhibition of enzymes of various classes and origins has been associated with substantial antimicrobial potential among other activities. In this contribution, we summarize the current state of the art regarding the antibacterial activity of ebselen. This activity, alone and in combination with commercial pharmaceuticals, against pathogens, including those resistant to drugs, is presented, together with the molecular mechanism behind the reactivity. The specific inactivation of thioredoxin reductase, bacterial toxins, and other resistance factors is considered to have certain therapeutic implications. Synergistic action and sensitization to common antibiotics assisted with the use of ebselen appear to be promising directions in the treatment of persistent infections.
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Li X, Wang Q, Zheng J, Guan Y, Liu C, Han J, Liu S, Liu T, Xiao C, Wang X, Liu Y. PHT427 as an effective New Delhi metallo-β-lactamase-1 (NDM-1) inhibitor restored the susceptibility of meropenem against Enterobacteriaceae producing NDM-1. Front Microbiol 2023; 14:1168052. [PMID: 37138606 PMCID: PMC10150926 DOI: 10.3389/fmicb.2023.1168052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 03/31/2023] [Indexed: 05/05/2023] Open
Abstract
Introduction With the increasingly serious problem of bacterial drug resistance caused by NDM-1, it is an important strategy to find effective inhibitors to assist β-lactam antibiotic treatment against NDM-1 resistant bacteria. In this study, PHT427 (4-dodecyl-N-1,3,4-thiadiazol-2-yl-benzenesulfonamide) was identified as a novel NDM-1 inhibitor and restored the susceptibility of meropenem against Enterobacteriaceae producing NDM-1. Methods We used a high throughput screening model to find NDM-1 inhibitor in the library of small molecular compounds. The interaction between the hit compound PHT427 and NDM-1 was analyzed by fluorescence quenching, surface plasmon resonance (SPR) assay, and molecular docking analysis. The efficacy of the compound in combination with meropenem was evaluated by determining the FICIs of Escherichia coli BL21(DE3)/pET30a(+)-bla NDM-1 and Klebsiella pneumoniae clinical strain C1928 (producing NDM-1). In addition, the mechanism of the inhibitory effect of PHT427 on NDM-1 was studied by site mutation, SPR, and zinc supplementation assays. Results PHT427 was identified as an inhibitor of NDM-1. It could significantly inhibit the activity of NDM-1 with an IC50 of 1.42 μmol/L, and restored the susceptibility of meropenem against E. coli BL21(DE3)/pET30a(+)-bla NDM-1 and K. pneumoniae clinical strain C1928 (producing NDM-1) in vitro. The mechanism study indicated that PHT427 could act on the zinc ions at the active site of NDM-1 and the catalytic key amino acid residues simultaneously. The mutation of Asn220 and Gln123 abolished the affinity of NDM-1 by PHT427 via SPR assay. Discussion This is the first report that PHT427 is a promising lead compound against carbapenem-resistant bacteria and it merits chemical optimization for drug development.
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Affiliation(s)
- Xiaohui Li
- National Laboratory for Screening New Microbial Drugs, Institute of Medicinal Biotechnology, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Qian Wang
- Key Laboratory of Marine Drugs, School of Medicine and Pharmacy, Ministry of Education, Ocean University of China, Qingdao, China
| | - Ji Zheng
- Institute of Medical Technology, Peking University Health Science Center, Beijing, China
- Department of Clinical Laboratory, Peking University People’s Hospital, Beijing, China
| | - Yan Guan
- National Laboratory for Screening New Microbial Drugs, Institute of Medicinal Biotechnology, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Chennan Liu
- Beijing Key Laboratory of Drug Resistance Tuberculosis Research, Beijing Chest Hospital, Beijing Tuberculosis and Thoracic Tumor Research Institute, Capital Medical University, Beijing, China
| | - Jiangxue Han
- National Laboratory for Screening New Microbial Drugs, Institute of Medicinal Biotechnology, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Sihan Liu
- National Laboratory for Screening New Microbial Drugs, Institute of Medicinal Biotechnology, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Tianjun Liu
- National Laboratory for Screening New Microbial Drugs, Institute of Medicinal Biotechnology, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Chunling Xiao
- National Laboratory for Screening New Microbial Drugs, Institute of Medicinal Biotechnology, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Xiao Wang
- National Laboratory for Screening New Microbial Drugs, Institute of Medicinal Biotechnology, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
- *Correspondence: Xiao Wang,
| | - Yishuang Liu
- National Laboratory for Screening New Microbial Drugs, Institute of Medicinal Biotechnology, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
- Yishuang Liu,
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Moreira JS, Galvão DS, Xavier CFC, Cunha S, Pita SSDR, Reis JN, Freitas HFD. Phenotypic and in silico studies for a series of synthetic thiosemicarbazones as New Delhi metallo-beta-lactamase carbapenemase inhibitors. J Biomol Struct Dyn 2022; 40:14223-14235. [PMID: 34766882 DOI: 10.1080/07391102.2021.2001379] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The past two decades have been marked by a global spread of bacterial resistance to β-lactam drugs and carbapenems derivatives are the ultimate treatment against multidrug-resistant bacteria. β-lactamase expression is related to resistance which demands the development of bacterial resistance blockers. Drug inhibitor combinations of serine-β-lactamase and β-lactam were successful employed in therapy despite their inactivity against New Delhi metallo-beta-lactamase (NDM). Until now, few compounds are active against NDM-producing bacteria and no specific inhibitors are available yet. The rational strategy for NDM inhibitors development starts with in vitro assays aiming to seek compounds that could act synergistically with β-lactam antibiotics. Thus, eight thiosemicarbazone derivatives were synthesized and investigated for their ability to reverse the resistant phenotype in NDM in Enterobacter cloacae. Phenotypic screening indicated that four isatin-beta-thiosemicarbazones showed Fractional Inhibitory Concentration (FIC) ≤ 250 µM in the presence of meropenem (4 µg/mL). The most promising compound (FIC= 31.25 µM) also presented synergistic effect (FICI = 0.34). Docking and molecular dynamics studies on NDM-thiosemicarbazone complex suggested that 2,3-dihydro-1H-indol-2-one subunit interacts with catalytic zinc and interacted through hydrogen bonds with Asp124 acting like a carboxylic acid bioisostere. Additionally, thiosemicarbazone tautomer with oxidized sulfur (thione) seems to act as a spacer rather than zinc chelator, and the aromatic moieties are stabilized by pi-pi and cation-pi interactions with His189 and Lys221 residues. Our results addressed some thiosemicarbazone structural changes to increase its biological activity against NDM and highlight its scaffold as promising alternatives to treat bacterial resistance.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Jonatham Souza Moreira
- Post-Graduation Program in Pharmacy, Pharmacy College, Federal University of Bahia, Salvador, Bahia, Brazil
| | | | | | - Silvio Cunha
- Chemistry Institute, Federal University of Bahia, Ondina, Salvador, Bahia, Brazil
| | - Samuel Silva da Rocha Pita
- Pharmacy College, Federal University of Bahia, Salvador, Bahia, Brazil.,Bioinformatics and Molecular Modeling Laboratory (LaBiMM), Federal University of Bahia, Salvador, Bahia, Brazil
| | - Joice Neves Reis
- Post-Graduation Program in Pharmacy, Pharmacy College, Federal University of Bahia, Salvador, Bahia, Brazil.,Pharmacy College, Federal University of Bahia, Salvador, Bahia, Brazil
| | - Humberto Fonseca de Freitas
- Post-Graduation Program in Pharmacy, Pharmacy College, Federal University of Bahia, Salvador, Bahia, Brazil.,Pharmacy College, Federal University of Bahia, Salvador, Bahia, Brazil.,Bioinformatics and Molecular Modeling Laboratory (LaBiMM), Federal University of Bahia, Salvador, Bahia, Brazil
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Legru A, Verdirosa F, Vo-Hoang Y, Tassone G, Vascon F, Thomas CA, Sannio F, Corsica G, Benvenuti M, Feller G, Coulon R, Marcoccia F, Devente SR, Bouajila E, Piveteau C, Leroux F, Deprez-Poulain R, Deprez B, Licznar-Fajardo P, Crowder MW, Cendron L, Pozzi C, Mangani S, Docquier JD, Hernandez JF, Gavara L. Optimization of 1,2,4-Triazole-3-thiones toward Broad-Spectrum Metallo-β-lactamase Inhibitors Showing Potent Synergistic Activity on VIM- and NDM-1-Producing Clinical Isolates. J Med Chem 2022; 65:16392-16419. [PMID: 36450011 DOI: 10.1021/acs.jmedchem.2c01257] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Metallo-β-lactamases (MBLs) contribute to the resistance of Gram-negative bacteria to carbapenems, last-resort antibiotics at hospital, and MBL inhibitors are urgently needed to preserve these important antibacterial drugs. Here, we describe a series of 1,2,4-triazole-3-thione-based inhibitors displaying an α-amino acid substituent, which amine was mono- or disubstituted by (hetero)aryl groups. Compounds disubstituted by certain nitrogen-containing heterocycles showed submicromolar activities against VIM-type enzymes and strong NDM-1 inhibition (Ki = 10-30 nM). Equilibrium dialysis, native mass spectrometry, isothermal calorimetry (ITC), and X-ray crystallography showed that the compounds inhibited both VIM-2 and NDM-1 at least partially by stripping the catalytic zinc ions. These inhibitors also displayed a very potent synergistic activity with meropenem (16- to 1000-fold minimum inhibitory concentration (MIC) reduction) against VIM-type- and NDM-1-producing ultraresistant clinical isolates, including Enterobacterales and Pseudomonas aeruginosa. Furthermore, selected compounds exhibited no or moderate toxicity toward HeLa cells, favorable absorption, distribution, metabolism, excretion (ADME) properties, and no or modest inhibition of several mammalian metalloenzymes.
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Affiliation(s)
- Alice Legru
- IBMM, CNRS, Univ Montpellier, ENSCM, 34000 Montpellier, France
| | - Federica Verdirosa
- Dipartimento di Biotecnologie Mediche, Università di Siena, 53100 Siena, Italy
| | - Yen Vo-Hoang
- IBMM, CNRS, Univ Montpellier, ENSCM, 34000 Montpellier, France
| | - Giusy Tassone
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università di Siena, 53100 Siena, Italy
| | - Filippo Vascon
- Laboratory of Structural Biology, Department of Biology, University of Padua, 35121 Padova, Italy
| | - Caitlyn A Thomas
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Filomena Sannio
- Dipartimento di Biotecnologie Mediche, Università di Siena, 53100 Siena, Italy
| | - Giuseppina Corsica
- Dipartimento di Biotecnologie Mediche, Università di Siena, 53100 Siena, Italy
| | - Manuela Benvenuti
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università di Siena, 53100 Siena, Italy
| | - Georges Feller
- Laboratoire de Biochimie, Centre d'Ingénierie des Protéines-InBioS, Université de Liège, Allée du 6 août B6, Sart-Tilman, B-4000 Liège, Belgium
| | - Rémi Coulon
- IBMM, CNRS, Univ Montpellier, ENSCM, 34000 Montpellier, France
| | - Francesca Marcoccia
- Dipartimento di Biotecnologie Mediche, Università di Siena, 53100 Siena, Italy
| | | | | | - Catherine Piveteau
- Drugs and Molecules for Living System, U1177, Inserm, Université de Lille, Faculté de Pharmacie, 59006 Lille, France
| | - Florence Leroux
- Drugs and Molecules for Living System, U1177, Inserm, Université de Lille, Faculté de Pharmacie, 59006 Lille, France
| | - Rebecca Deprez-Poulain
- Drugs and Molecules for Living System, U1177, Inserm, Université de Lille, Faculté de Pharmacie, 59006 Lille, France
| | - Benoît Deprez
- Drugs and Molecules for Living System, U1177, Inserm, Université de Lille, Faculté de Pharmacie, 59006 Lille, France
| | - Patricia Licznar-Fajardo
- HydroSciences Montpellier, UMR5151, Univ Montpellier, CNRS, IRD, CHU Montpellier, 34000 Montpellier, France
| | - Michael W Crowder
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Laura Cendron
- Laboratory of Structural Biology, Department of Biology, University of Padua, 35121 Padova, Italy
| | - Cecilia Pozzi
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università di Siena, 53100 Siena, Italy
| | - Stefano Mangani
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università di Siena, 53100 Siena, Italy
| | - Jean-Denis Docquier
- Dipartimento di Biotecnologie Mediche, Università di Siena, 53100 Siena, Italy.,Centre d'Ingénierie des Protéines-InBioS, Université de Liège, B-4000 Liège, Belgium
| | | | - Laurent Gavara
- IBMM, CNRS, Univ Montpellier, ENSCM, 34000 Montpellier, France
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Ma Y, Liang Y, Guo M, Min D, Zheng L, Tang Y, Sun X. Strategic design of lysine-targeted irreversible covalent NDM-1 inhibitors. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2022.108072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Ma J, Tang B, Lin J, Ed-Dra A, Lin H, Wu J, Dong Y, Yang H, Yue M. Genome Assessment of Carbapenem- and Colistin-Resistant Escherichia coli from Patients in a Sentinel Hospital in China. Cells 2022; 11:3480. [PMID: 36359876 PMCID: PMC9653657 DOI: 10.3390/cells11213480] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 10/31/2022] [Accepted: 11/01/2022] [Indexed: 07/30/2023] Open
Abstract
Antimicrobial-resistant (AMR) pathogens are a significant threat to public health worldwide. However, the primary carrier of AMR genes, particularly against last-resort antibiotics, is still only partially studied in Chinese hospitals. In a sentinel hospital in China, we collected 157 E. coli strains from patients between January and July 2021. One blaNDM-1-, nine blaNDM-5-, and one mcr-1-positive E. coli recovered from inpatients were identified as resistant to meropenem and colistin. There are 37 virulence genes discovered in the 11 strains, including astA in strain EC21Z-147 (O128: H4), which belongs to the enteroaggregative E. coli (EAEC). The blaNDM gene is distributed into distinct ST types, including ST48, ST616, ST410, ST711, and ST2003, while the mcr-1 gene was identified in ST117. The conjugative plasmids IncX3, IncI1-I, and IncI2 mediated the blaNDM-5 and mcr-1 genes detected among inpatients. Notably, the youngest age at which mcr-1-positive E. coli has been reported was at one day old, in a child in which the strain is closely related to strains with animal origins. Hospitals are major environments for the spread and dissemination of critical virulence and AMR genes, which requires active monitoring systems at the genome level to surveil the spread of virulence and AMR.
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Affiliation(s)
- Jiangang Ma
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products & Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Biao Tang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products & Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Jiahui Lin
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products & Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | | | - Hui Lin
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products & Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Jing Wu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products & Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Yuzhi Dong
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products & Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Hua Yang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products & Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Min Yue
- Hainan Institute of Zhejiang University, Sanya 572025, China
- Institute of Preventive Veterinary Sciences and Department of Veterinary Medicine, Zhejiang University College of Animal Sciences, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Hangzhou 310058, China
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310058, China
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A Cephalosporin-Tripodalamine Conjugate Inhibits Metallo-β-Lactamase with High Efficacy and Low Toxicity. Antimicrob Agents Chemother 2022; 66:e0035222. [PMID: 36094199 PMCID: PMC9578398 DOI: 10.1128/aac.00352-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The wide spread of metallo-β-lactamase (MBL)-expressing bacteria has greatly threatened human health, and there is an urgent need for inhibitors against MBLs. Herein, we present a cephalosporin-tripodalamine conjugate (DPASC) as a potent MBL inhibitor with a block-release design. The cephalosporin tag blocks the ligand binding site to reduce toxicity and is cleaved by MBLs to release active ligands to inhibit MBLs in situ. The screening of MBL-expressing pathogenic strains with 16 μg/mL DPASC showed a decrease of the minimum inhibitory concentration of meropenem (MEM) by 16 to 512-fold, and its toxicity was minimal to human HepG2 cells, with an IC50 exceeding 512 μg/mL. An in vivo infection model with Galleria mellonella larvae showed an increased 3-day survival rate of 87% with the coadministration of DPASC and MEM, compared to 50% with MEM alone and no toxicity at a dose of 256 mg/kg of DPASC. Our findings with DPASC demonstrate that it is an effective MBL inhibitor and that the block-release strategy could be useful for the development of new MBL inhibitors.
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Cole MS, Hegde PV, Aldrich CC. β-Lactamase-Mediated Fragmentation: Historical Perspectives and Recent Advances in Diagnostics, Imaging, and Antibacterial Design. ACS Infect Dis 2022; 8:1992-2018. [PMID: 36048623 DOI: 10.1021/acsinfecdis.2c00315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The discovery of β-lactam (BL) antibiotics in the early 20th century represented a remarkable advancement in human medicine, allowing for the widespread treatment of infectious diseases that had plagued humanity throughout history. Yet, this triumph was followed closely by the emergence of β-lactamase (BLase), a bacterial weapon to destroy BLs. BLase production is a primary mechanism of resistance to BL antibiotics, and the spread of new homologues with expanded hydrolytic activity represents a pressing threat to global health. Nonetheless, researchers have developed strategies that take advantage of this defense mechanism, exploiting BLase activity in the creation of probes, diagnostic tools, and even novel antibiotics selective for resistant organisms. Early discoveries in the 1960s and 1970s demonstrating that certain BLs expel a leaving group upon BLase cleavage have spawned an entire field dedicated to employing this selective release mechanism, termed BLase-mediated fragmentation. Chemical probes have been developed for imaging and studying BLase-expressing organisms in the laboratory and diagnosing BL-resistant infections in the clinic. Perhaps most promising, new antibiotics have been developed that use BLase-mediated fragmentation to selectively release cytotoxic chemical "warheads" at the site of infection, reducing off-target effects and allowing for the repurposing of putative antibiotics against resistant organisms. This Review will provide some historical background to the emergence of this field and highlight some exciting recent reports that demonstrate the promise of this unique release mechanism.
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Affiliation(s)
- Malcolm S Cole
- Department of Medicinal Chemistry, University of Minnesota, 308 Harvard St SE, Minneapolis, Minnesota 55455, United States
| | - Pooja V Hegde
- Department of Medicinal Chemistry, University of Minnesota, 308 Harvard St SE, Minneapolis, Minnesota 55455, United States
| | - Courtney C Aldrich
- Department of Medicinal Chemistry, University of Minnesota, 308 Harvard St SE, Minneapolis, Minnesota 55455, United States
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Identification of a Potential Inhibitor (MCULE-8777613195-0-12) of New Delhi Metallo-β-Lactamase-1 (NDM-1) Using In Silico and In Vitro Approaches. Molecules 2022; 27:molecules27185930. [PMID: 36144666 PMCID: PMC9504514 DOI: 10.3390/molecules27185930] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 08/04/2022] [Accepted: 08/08/2022] [Indexed: 11/17/2022] Open
Abstract
New Delhi metallo-β-lactamase-1 (NDM-1), expressed in different Gram-negative bacteria, is a versatile enzyme capable of hydrolyzing β-lactam rings containing antibiotics such as penicillins, cephalosporins, and even carbapenems. Multidrug resistance in bacteria mediated by NDM-1 is an emerging threat to the public health, with an enormous economic burden. There is a scarcity in the availability of specific NDM-1 inhibitors, and also a lag in the development of new inhibitors in pharmaceutical industries. In order to identify novel inhibitors of NDM-1, we screened a library of more than 20 million compounds, available at the MCULE purchasable database. Virtual screening led to the identification of six potential inhibitors, namely, MCULE-1996250788-0-2, MCULE-8777613195-0-12, MCULE-2896881895-0-14, MCULE-5843881524-0-3, MCULE-4937132985-0-1, and MCULE-7157846117-0-1. Furthermore, analyses by molecular docking and ADME properties showed that MCULE-8777613195-0-12 was the most suitable inhibitor against NDM-1. An analysis of the binding pose revealed that MCULE-8777613195-0-12 formed four hydrogen bonds with the catalytic residues of NDM-1 (His120, His122, His189, and Cys208) and interacted with other key residues. Molecular dynamics simulation and principal component analysis confirmed the stability of the NDM-1 and MCULE-8777613195-0-12 complex. The in vitro enzyme kinetics showed that the catalytic efficiency (i.e., kcat/Km) of NDM-1 on various antibiotics decreased significantly in the presence of MCULE-8777613195-0-12, due to poor catalytic proficiency (kcat) and affinity (Km). The IC50 value of MCULE-8777613195-0-12 (54.2 µM) was comparable to that of a known inhibitor, i.e., D-captopril (10.3 µM). In sum, MCULE-8777613195-0-12 may serve as a scaffold to further design/develop more potent inhibitors of NDM-1 and other β-lactamases.
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Yue K, Xu C, Wang Z, Liu W, Liu C, Xu X, Xing Y, Chen S, Li X, Wan S. 1,2-Isoselenazol-3(2H)-one derivatives as NDM-1 inhibitors displaying synergistic antimicrobial effects with meropenem on NDM-1 producing clinical isolates. Bioorg Chem 2022; 129:106153. [DOI: 10.1016/j.bioorg.2022.106153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 08/16/2022] [Accepted: 09/12/2022] [Indexed: 11/30/2022]
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A fragment-based drug discovery strategy applied to the identification of NDM-1 β-lactamase inhibitors. Eur J Med Chem 2022; 240:114599. [PMID: 35841882 DOI: 10.1016/j.ejmech.2022.114599] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 06/26/2022] [Accepted: 07/07/2022] [Indexed: 11/23/2022]
Abstract
Hydrolysis of β-lactam drugs, a major class of antibiotics, by serine or metallo-β-lactamases (SBL or MBL) is one of the main mechanisms for antibiotic resistance. New Delhi Metallo-β-lactamase-1 (NDM-1), an acquired metallo-carbapenemase first reported in 2009, is currently considered one of the most clinically relevant targets for the development of β-lactam-β-lactamase inhibitor combinations active on NDM-producing clinical isolates. Identification of scaffolds that could be further rationally pharmacomodulated to design new and efficient NDM-1 inhibitors is thus urgently needed. Fragment-based drug discovery (FBDD) has become of great interest for the development of new drugs for the past few years and combination of several FBDD strategies, such as virtual and NMR screening, can reduce the drawbacks of each of them independently. Our methodology starting from a high throughput virtual screening on NDM-1 of a large library (more than 700,000 compounds) allowed, after slicing the hit molecules into fragments, to build a targeted library. These hit fragments were included in an in-house untargeted library fragments that was screened by Saturation Transfer Difference (STD) Nuclear Magnetic Resonance (NMR). 37 fragments were finally identified and used to establish a pharmacophore. 10 molecules based on these hit fragments were synthesized to validate our strategy. Indenone 89 that combined two identified fragments shows an inhibitory activity on NDM-1 with a Ki value of 4 μM.
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Aromatic Schiff bases confer inhibitory efficacy against New Delhi metallo-β-lactamase-1 (NDM-1). Bioorg Chem 2022; 126:105910. [PMID: 35653899 DOI: 10.1016/j.bioorg.2022.105910] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 05/10/2022] [Accepted: 05/23/2022] [Indexed: 12/24/2022]
Abstract
The irregular use of antibiotics has created a natural selection pressure for bacteria to adapt resistance. Bacterial resistance caused by metallo-β-lactamases (MβLs) has been the most prevalent in terms of posing a threat to human health. The New Delhi metallo-β-lactamase-1 (NDM-1) has been shown to be capable of hydrolyzing almost all β-lactams. In this work, eight aromatic Schiff bases 1-8 were prepared and identified by enzyme kinetic assays to be the potent inhibitors of NDM-1 (except 4). These molecules exhibited a more than 95 % inhibition, and an IC50 value in the range of 0.13-19 μM on the target enzyme, and 3 was found to be the most effective inhibitor (IC50 = 130 nM). Analysis of structure-activity relationship revealed that the o-hydroxy phenyl improved the inhibitory activity of Schiff bases on NDM-1. The inhibition mode assays including isothermal titration calorimetry (ITC) disclosed that both compounds 3 and 5 exhibited a reversibly mixed inhibition on NDM-1, with a Ki value of 1.9 and 10.8 μM, respectively. Antibacterial activity tests indicated that a dose of 64 μg·mL-1 Schiff bases resulted in 2-128-fold reduction in MICs of cefazolin on E. coli producing NDM-1 (except 4). Cytotoxicity assays showed that both Schiff bases 3 and 5 have low cytotoxicity on the mouse fibroblast (L929) cells at a concentration of up to 400 μM. Docking studies suggested that the hydroxyl group interacts with Gln123 and Glu152 of NDM-1, and the amino groups interact with the backbone amide groups of Glu152 and Asp223. This study provided a novel scaffold for the development of NDM-1 inhibitors.
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Dhanda G, Mukherjee R, Basak D, Haldar J. Small-Molecular Adjuvants with Weak Membrane Perturbation Potentiate Antibiotics against Gram-Negative Superbugs. ACS Infect Dis 2022; 8:1086-1097. [PMID: 35404568 DOI: 10.1021/acsinfecdis.2c00092] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Combination therapy with membrane-targeting compounds is at the forefront because the bacterial membrane is an attractive target considering its role in various multidrug-resistant elements. However, this strategy is crippled by the toxicity associated with these agents. The structural requirements for optimum membrane perturbation and minimum toxicity have not been explored for membrane-targeting antibiotic potentiators or adjuvants. Here, we report the structural influence of different chemical moieties on membrane perturbation, activity, toxicity, and potentiating ability in norspermidine derivatives. It has been shown in this report that weak membrane perturbation, achieved by the incorporation of cyclic hydrophobic moieties, is an effective strategy to design antibiotic adjuvants with negligible in vitro toxicity and activity but good potentiating ability. Aryl or adamantane functionalized derivatives were found to be better resorts as opposed to the acyclic analogues, exhibiting as high as 4096-fold potentiation of multiple classes of antibiotics toward critical Gram-negative superbugs. The mechanism of potentiation was nonspecific, consisting of weak outer-membrane permeabilization, membrane depolarization, and efflux inhibition. This unique concept of "weakly perturbing the membrane" by incorporating cyclic hydrophobic moieties in a chemical design with free amine groups serves as a breakthrough for nontoxic membrane-perturbing adjuvants and has the potential to revitalize the effect of obsolete antibiotics to treat complicated Gram-negative bacterial infections.
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Affiliation(s)
- Geetika Dhanda
- Antimicrobial Research Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, Bengaluru 560064, Karnataka, India
| | - Riya Mukherjee
- Antimicrobial Research Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, Bengaluru 560064, Karnataka, India
| | - Debajyoti Basak
- Antimicrobial Research Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, Bengaluru 560064, Karnataka, India
| | - Jayanta Haldar
- Antimicrobial Research Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, Bengaluru 560064, Karnataka, India
- School of Advanced Materials, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, Bengaluru 560064, Karnataka, India
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The development of New Delhi metallo-β-lactamase-1 inhibitors since 2018. Microbiol Res 2022; 261:127079. [DOI: 10.1016/j.micres.2022.127079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 04/22/2022] [Accepted: 05/23/2022] [Indexed: 11/21/2022]
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Dou WT, Han HH, Sedgwick AC, Zhu GB, Zang Y, Yang XR, Yoon J, James TD, Li J, He XP. Fluorescent probes for the detection of disease-associated biomarkers. Sci Bull (Beijing) 2022; 67:853-878. [PMID: 36546238 DOI: 10.1016/j.scib.2022.01.014] [Citation(s) in RCA: 57] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 12/30/2021] [Accepted: 01/04/2022] [Indexed: 01/10/2023]
Abstract
Fluorescent probes have emerged as indispensable chemical tools to the field of chemical biology and medicine. The ability to detect intracellular species and monitor physiological processes has not only advanced our knowledge in biology but has provided new approaches towards disease diagnosis. In this review, we detail the design criteria and strategies for some recently reported fluorescent probes that can detect a wide range of biologically important species in cells and in vivo. In doing so, we highlight the importance of each biological species and their role in biological systems and for disease progression. We then discuss the current problems and challenges of existing technologies and provide our perspective on the future directions of the research area. Overall, we hope this review will provide inspiration for researchers and prove as useful guide for the development of the next generation of fluorescent probes.
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Affiliation(s)
- Wei-Tao Dou
- Key Laboratory for Advanced Materials and Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, Frontiers Center for Materiobiology and Dynamic Chemistry, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Hai-Hao Han
- Key Laboratory for Advanced Materials and Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, Frontiers Center for Materiobiology and Dynamic Chemistry, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Adam C Sedgwick
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712-1224, USA
| | - Guo-Biao Zhu
- Key Laboratory for Advanced Materials and Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, Frontiers Center for Materiobiology and Dynamic Chemistry, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Yi Zang
- National Center for Drug Screening, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Xin-Rong Yang
- Department of Liver Surgery & Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Shanghai 200032, China.
| | - Juyoung Yoon
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea.
| | - Tony D James
- Department of Chemistry, University of Bath, Bath BA2 7AY, UK; School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang 453007, China.
| | - Jia Li
- National Center for Drug Screening, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.
| | - Xiao-Peng He
- Key Laboratory for Advanced Materials and Joint International Research Laboratory of Precision Chemistry and Molecular Engineering, Feringa Nobel Prize Scientist Joint Research Center, Frontiers Center for Materiobiology and Dynamic Chemistry, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, China.
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Chen C, Oelschlaeger P, Wang D, Xu H, Wang Q, Wang C, Zhao A, Yang KW. Structure and Mechanism-Guided Design of Dual Serine/Metallo-Carbapenemase Inhibitors. J Med Chem 2022; 65:5954-5974. [PMID: 35420040 DOI: 10.1021/acs.jmedchem.2c00213] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Serine/metallo-carbapenemase-coproducing pathogens, often referred to as "superbugs", are a significant clinical problem. They hydrolyze nearly all available β-lactam antibiotics, especially carbapenems considered as last-resort antibiotics, seriously endangering efficacious antibacterial treatment. Despite the continuous global spread of carbapenem resistance, no dual-action inhibitors are available in therapy. This Perspective is the first systematic investigation of all chemotypes, modes of inhibition, and crystal structures of dual serine/metallo-carbapenemase inhibitors. An overview of the key strategy for designing dual serine/metallo-carbapenemase inhibitors and their mechanism of action is provided, as guiding rules for the development of clinically available dual inhibitors, coadministrated with carbapenems, to overcome the carbapenem resistance issue.
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Affiliation(s)
- Cheng Chen
- College of Forestry, Northwest A&F University, Yangling 712100, Shaanxi, P. R. China
| | - Peter Oelschlaeger
- Department of Pharmaceutical Sciences, College of Pharmacy, Western University of Health Sciences, 309 East Second Street, Pomona 91766, California, United States
| | - Dongmei Wang
- College of Forestry, Northwest A&F University, Yangling 712100, Shaanxi, P. R. China
| | - Hao Xu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310030, P. R. China
| | - Qian Wang
- Department of Clinical Laboratory, The First Affiliated Hospital of Henan University of Chinese Medicine, Jinshui District 450046, Zhengzhou, P. R. China
| | - Cheng Wang
- College of Forestry, Northwest A&F University, Yangling 712100, Shaanxi, P. R. China
| | - Aiguo Zhao
- College of Forestry, Northwest A&F University, Yangling 712100, Shaanxi, P. R. China
| | - Ke-Wu Yang
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an 710127, P. R. China
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Thomas PW, Cho EJ, Bethel CR, Smisek T, Ahn YC, Schroeder JM, Thomas CA, Dalby KN, Beckham JT, Crowder MW, Bonomo RA, Fast W. Discovery of an Effective Small-Molecule Allosteric Inhibitor of New Delhi Metallo-β-lactamase (NDM). ACS Infect Dis 2022; 8:811-824. [PMID: 35353502 DOI: 10.1021/acsinfecdis.1c00577] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
To identify novel inhibitors of the carbapenemase New Delhi metallo-β-lactamase (NDM) as possible therapeutic compounds, we conducted a high-throughput screen of a 43,358-compound library. One of these compounds, a 2-quinazolinone linked through a diacylhydrazine to a phenyl ring (QDP-1) (IC50 = 7.9 ± 0.5 μM), was characterized as a slow-binding reversible inhibitor (Kiapp = 4 ± 2 μM) with a noncompetitive mode of inhibition in which substrate and inhibitor enhance each other's binding affinity. These studies, along with differential scanning fluorimetry, zinc quantitation, and selectivity studies, support an allosteric mechanism of inhibition. Cotreatment with QDP-1 effectively lowers minimum inhibitory concentrations of carbapenems for a panel of resistant Escherichia coli and Klebsiella pneumoniae clinical isolates expressing NDM-1 but not for those expressing only serine carbapenemases. QDP-1 represents a novel allosteric approach for NDM drug development for potential use alone or with other NDM inhibitors to counter carbapenem resistance in enterobacterales.
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Affiliation(s)
- Pei W. Thomas
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, Texas 78712, United States
| | - Eun Jeong Cho
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, Texas 78712, United States
- Targeted Therapeutic Drug Discovery and Development Program, College of Pharmacy, University of Texas, Austin, Texas 78712, United States
| | - Christopher R. Bethel
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio 44106, United States
| | - Thomas Smisek
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, Texas 78712, United States
| | - Yeong-Chan Ahn
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, Texas 78712, United States
| | - John M. Schroeder
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, Texas 78712, United States
| | - Caitlyn A. Thomas
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Kevin N. Dalby
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, Texas 78712, United States
- Targeted Therapeutic Drug Discovery and Development Program, College of Pharmacy, University of Texas, Austin, Texas 78712, United States
| | - Josh T. Beckham
- Texas Institute for Discovery Education in Science, University of Texas, Austin, Texas 78712, United States
| | - Michael W. Crowder
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - Robert A. Bonomo
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio 44106, United States
- Department of Biochemistry, Case Western Reserve University, Cleveland, Ohio 44106, United States
- Department of Medicine, Case Western Reserve University, Cleveland, Ohio 44106, United States
- Departments of Pharmacology, Molecular Biology & Microbiology, and Proteomics & Bioinformatics, Case Western Reserve University, Cleveland, Ohio 44106, United States
- CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), Cleveland, Ohio 44106, United States
| | - Walter Fast
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, Texas 78712, United States
- LaMontagne Center for Infectious Disease, University of Texas, Austin, Texas 78712, United States
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Methimazole and α-lipoic acid as metallo-β-lactamases inhibitors. J Antibiot (Tokyo) 2022; 75:282-286. [PMID: 35197545 DOI: 10.1038/s41429-022-00513-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 01/26/2022] [Accepted: 01/30/2022] [Indexed: 11/08/2022]
Abstract
The emergence of bacterial resistance poses a serious threat to public health. One of the most important resistance mechanisms against β-lactam antibiotics is the production of metallo-β-lactamases (MBLs). In this study, α-lipoic acid (LA) and methimazole (MMI), which have been used in clinical practice as non-antibacterial drugs and as a supplement, were chosen to explore their potential to be metallo-β-lactamases inhibitors (MBLIs). Enzyme inhibition assays showed that LA and MMI had moderate inhibitory activity against NDM-1 but no activity against VIM-2 and IMP-7. Antibacterial assays to determine synergy, demonstrated that the combination of LA or MMI with meropenem (MER) reduced the MIC value of MER against NDM-1 producing E. coli 16 times and 4 times, respectively, lower than that of MER alone. The fractional inhibitory concentration index (FICI) values were calculated to be less than 0.5, indicating that both LA and MMI had synergistic antibacterial effects with MER against all three MBLs expressing E. coli strains. The time-kill studies also suggested that LA and MMI were effective in restoring the antibacterial effect of MER. These findings revealed that LA and MMI are potential carbapenem enhancers, and provide a starting point for the development of potent MBLIs.
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Risedronate and Methotrexate Are High-Affinity Inhibitors of New Delhi Metallo-β-Lactamase-1 (NDM-1): A Drug Repurposing Approach. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27041283. [PMID: 35209073 PMCID: PMC8878330 DOI: 10.3390/molecules27041283] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 02/01/2022] [Accepted: 02/08/2022] [Indexed: 01/01/2023]
Abstract
Bacteria expressing New Delhi metallo-β-lactamase-1 (NDM-1) can hydrolyze β-lactam antibiotics (penicillins, cephalosporins, and carbapenems) and, thus, mediate multidrug resistance. The worldwide dissemination of NDM-1 poses a serious threat to public health, imposing a huge economic burden in the development of new antibiotics. Thus, there is an urgent need for the identification of novel NDM-1 inhibitors from a pool of already-known drug molecules. Here, we screened a library of FDA-approved drugs to identify novel non-β-lactam ring-containing inhibitors of NDM-1 by applying computational as well as in vitro experimental approaches. Different steps of high-throughput virtual screening, molecular docking, molecular dynamics simulation, and enzyme kinetics were performed to identify risedronate and methotrexate as the inhibitors with the most potential. The molecular mechanics/generalized Born surface area (MM/GBSA) and molecular dynamics (MD) simulations showed that both of the compounds (risedronate and methotrexate) formed a stable complex with NDM-1. Furthermore, analyses of the binding pose revealed that risedronate formed two hydrogen bonds and three electrostatic interactions with the catalytic residues of NDM-1. Similarly, methotrexate formed four hydrogen bonds and one electrostatic interaction with NDM-1’s active site residues. The docking scores of risedronate and methotrexate for NDM-1 were –10.543 kcal mol−1 and −10.189 kcal mol−1, respectively. Steady-state enzyme kinetics in the presence of risedronate and methotrexate showed a decreased catalytic efficiency (i.e., kcat/Km) of NDM-1 on various antibiotics, owing to poor catalytic proficiency and affinity. The results were further validated by determining the MICs of imipenem and meropenem in the presence of risedronate and methotrexate. The IC50 values of the identified inhibitors were in the micromolar range. The findings of this study should be helpful in further characterizing the potential of risedronate and methotrexate to treat bacterial infections.
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A Natural Novel Mutation in the blaNDM-5 Promoter Reducing Carbapenems Resistance in a Clinical Escherichia coli Strain. Microbiol Spectr 2022; 10:e0118321. [PMID: 35138141 PMCID: PMC8826935 DOI: 10.1128/spectrum.01183-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Acharya Y, Dhanda G, Sarkar P, Haldar J. Pursuit of next-generation glycopeptides: a journey with vancomycin. Chem Commun (Camb) 2022; 58:1881-1897. [PMID: 35043130 DOI: 10.1039/d1cc06635h] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Vancomycin, a blockbuster antibiotic of the glycopeptide class, has been a life-saving therapeutic against multidrug-resistant Gram-positive infections. The emergence of glycopeptide resistance has however enunciated the need to develop credible alternatives with potent activity against vancomycin-resistant bacteria. Medicinal chemistry has responded to this challenge through various strategies, one of them being the development of semisynthetic analogues. Many groups, including ours, have been contributing towards the development of semisynthetic vancomycin analogues to tackle vancomycin-resistant bacteria. In this feature article, we have discussed our research contribution to the field of glycopeptides, which includes our strategies and designs of vancomycin analogues incorporating multimodal mechanisms of action. The strategies discussed here, such as conferring membrane activity, enhanced binding to target, multivalency, etc. involve semisynthetic modifications to vancomycin at the carboxy terminal and the amino group of the vancosamine sugar of vancomycin, to develop novel analogues. These analogues have demonstrated their superior efficacy in tackling the inherited forms of vancomycin resistance in Gram-positive and Gram-negative bacteria, including highly drug-resistant strains. More importantly, these analogues also possess the ability to tackle various non-inherited forms of bacterial resistance, such as metabolically dormant stationary-phase and persister cells, bacterial biofilms, and intracellular pathogens. Our derivatives also display superior pharmacokinetics, and less propensity for resistance development, owing to their different modes of action. Through this feature article, we present to the reader a concise picture of the multitude of approaches that can be used to tackle different types of resistance through semisynthetic modifications to vancomycin. We have also highlighted the challenges and lacunae in the field, and potential directions which future research can explore.
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Affiliation(s)
- Yash Acharya
- Antimicrobial Research Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, Bengaluru 560064, Karnataka, India.
| | - Geetika Dhanda
- Antimicrobial Research Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, Bengaluru 560064, Karnataka, India.
| | - Paramita Sarkar
- Antimicrobial Research Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, Bengaluru 560064, Karnataka, India.
| | - Jayanta Haldar
- Antimicrobial Research Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, Bengaluru 560064, Karnataka, India. .,School of Advanced Materials, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, Bengaluru 560064, Karnataka, India
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