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Sonawane NG, Thakur A, Pillai AKS, Sharma A, Gunjal AP, Sharma K. Recent Cutting-Edge Designing Strategies for Mtb-DHFR Inhibitors as Antitubercular Agents. Chem Biol Drug Des 2024; 104:e70027. [PMID: 39660864 DOI: 10.1111/cbdd.70027] [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: 07/25/2024] [Revised: 10/03/2024] [Accepted: 11/25/2024] [Indexed: 12/12/2024]
Abstract
Tuberculosis (TB) is an obstinate and infectious disease requiring a relatively longer treatment duration than other bacterial infections. The current treatment regime is prolonged and cumbersome, with adverse effects, often leading to nonadherence. The upsurge in TB's multidrug-resistant and extensively drug-resistant strains with evolved resistance to existing drugs has compounded the problems. The last two decades witnessed unprecedented progress in developing TB drugs with better efficacy and reduced toxicity. Of late, inhibitors targeting the dihydrofolate reductase (DHFR) enzyme were being explored and developed as antitubercular drugs. A plethora of diverse molecular cores, such as pteridines, diamino heterocycles, diamino triazoles, and nontraditional cores, were developed recently as Mtb-DHFR targets. Besides the characteristic binding pockets of Mtb-DHFR, an extended hydrophilic binding pocket was also studied for intermolecular interactions with the designed compounds to assess the enzyme specificity. In this study, prominent DHFR inhibitors developed in the last two decades were reported. Key features of the designed compounds, such as the structural similarities with existing pharmacophores, interactions with binding pockets, enzyme selectivity and specificity, and percentage of inhibition, were evaluated. The authors hope the study will help streamline the pharmacological pipeline of Mtb-DHFR inhibitors and bring the investigators one step closer to success.
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Affiliation(s)
- Nitin Govind Sonawane
- Department of Chemistry, School of Engineering, Amrita Vidyapeetham, Bengaluru, India
| | - Amrita Thakur
- Department of Chemistry, School of Engineering, Amrita Vidyapeetham, Bengaluru, India
| | | | - Ajay Sharma
- Department of Pharmacognosy, SPS, DPSRU, New Delhi, India
| | - Amol Pandurang Gunjal
- Department of Chemistry, School of Engineering, Amrita Vidyapeetham, Bengaluru, India
| | - Kalicharan Sharma
- Department of Pharmaceutical Chemistry, ISF College of Pharmacy, Moga, Punjab, India
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2
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Leonidou N, Xia Y, Friedrich L, Schütz MS, Dräger A. Exploring the metabolic profile of A. baumannii for antimicrobial development using genome-scale modeling. PLoS Pathog 2024; 20:e1012528. [PMID: 39312576 PMCID: PMC11463759 DOI: 10.1371/journal.ppat.1012528] [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] [Received: 02/08/2024] [Revised: 10/09/2024] [Accepted: 08/26/2024] [Indexed: 09/25/2024] Open
Abstract
With the emergence of multidrug-resistant bacteria, the World Health Organization published a catalog of microorganisms urgently needing new antibiotics, with the carbapenem-resistant Acinetobacter baumannii designated as "critical". Such isolates, frequently detected in healthcare settings, pose a global pandemic threat. One way to facilitate a systemic view of bacterial metabolism and allow the development of new therapeutics is to apply constraint-based modeling. Here, we developed a versatile workflow to build high-quality and simulation-ready genome-scale metabolic models. We applied our workflow to create a metabolic model for A. baumannii and validated its predictive capabilities using experimental nutrient utilization and gene essentiality data. Our analysis showed that our model iACB23LX could recapitulate cellular metabolic phenotypes observed during in vitro experiments, while positive biomass production rates were observed and experimentally validated in various growth media. We further defined a minimal set of compounds that increase A. baumannii's cellular biomass and identified putative essential genes with no human counterparts, offering new candidates for future antimicrobial development. Finally, we assembled and curated the first collection of metabolic reconstructions for distinct A. baumannii strains and analyzed their growth characteristics. The presented models are in a standardized and well-curated format, enhancing their usability for multi-strain network reconstruction.
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Affiliation(s)
- Nantia Leonidou
- Computational Systems Biology of Infections and Antimicrobial-Resistant Pathogens, Institute for Bioinformatics and Medical Informatics (IBMI), Eberhard Karl University of Tübingen, Tübingen, Germany
- Department of Computer Science, Eberhard Karl University of Tübingen, Tübingen, Germany
- Cluster of Excellence ‘Controlling Microbes to Fight Infections’, Eberhard Karl University of Tübingen, Tübingen, Germany
- German Center for Infection Research (DZIF), partner site Tübingen, Germany
- Quantitative Biology Center (QBiC), Eberhard Karl University of Tübingen, Tübingen, Germany
| | - Yufan Xia
- Department of Computer Science, Eberhard Karl University of Tübingen, Tübingen, Germany
| | - Lea Friedrich
- Interfaculty Institute for Microbiology and Infection Medicine, Institute for Medical Microbiology and Hygiene, University Hospital Tübingen, Tübingen, Germany
| | - Monika S. Schütz
- German Center for Infection Research (DZIF), partner site Tübingen, Germany
- Interfaculty Institute for Microbiology and Infection Medicine, Institute for Medical Microbiology and Hygiene, University Hospital Tübingen, Tübingen, Germany
| | - Andreas Dräger
- Computational Systems Biology of Infections and Antimicrobial-Resistant Pathogens, Institute for Bioinformatics and Medical Informatics (IBMI), Eberhard Karl University of Tübingen, Tübingen, Germany
- German Center for Infection Research (DZIF), partner site Tübingen, Germany
- Quantitative Biology Center (QBiC), Eberhard Karl University of Tübingen, Tübingen, Germany
- Data Analytics and Bioinformatics, Institute of Computer Science, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
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3
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dos Santos BR, Ramos ABDSB, de Menezes RPB, Scotti MT, Colombo FA, Marques MJ, Reimão JQ. Anti- Toxoplasma gondii screening of MMV pandemic response box and evaluation of RWJ-67657 efficacy in chronically infected mice. Parasitology 2023; 150:1226-1235. [PMID: 37859414 PMCID: PMC10941209 DOI: 10.1017/s0031182023000999] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 10/07/2023] [Accepted: 10/09/2023] [Indexed: 10/21/2023]
Abstract
Toxoplasmosis is a significant public health concern with limited therapeutic options. The medicines for malaria venture (MMV) developed the pandemic response box (PRB) containing 400 drug-like molecules with broad pathogen activity. The aim of this work is to evaluate PRB compounds for their anti-Toxoplasma gondii activity and identify promising candidates for further evaluation. Screening identified 42 selective compounds with half effective concentration (EC50) ranging from 2.4 to 913.1 nm and half cytotoxic concentration (CC50) ranging from 6 μm to >50 μm. Selectivity index (SI) values (CC50/EC50) ranged from 11 to 17 708. Based on its in silico and in vitro profile and its commercial availability, RWJ-67657 was selected for further studies. Molecular docking analysis showed RWJ-67657 is predicted to bind to T. gondii p38 mitogen-activated protein kinase (TgMAPK). Oral administration of RWJ-67657 (20 mg kg day−1/10 days) significantly reduced parasite burden in chronically infected mice compared to mock-treated group (P < 0.01). These findings highlight the PRB as a promising source for anti-T. gondii compounds, with several showing favourable drug properties, including MMV1634492, MMV002731, MMV1634491, MMV1581551, MMV011565, MMV1581558, MMV1578577, MMV233495 and MMV1580482, firstly described here as anti-T. gondii agents. RWJ-67657 emerges as a valuable drug candidate for experimental chronic cerebral toxoplasmosis therapy.
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Affiliation(s)
- Bruna Ramos dos Santos
- Departamento de Morfologia e Patologia Básica, Faculdade de Medicina de Jundiaí, Laboratory of Preclinical Assays and Research of Alternative Sources of Innovative Therapy for Toxoplasmosis and Other Sicknesses (PARASITTOS), Jundiaí, Brazil
| | | | - Renata Priscila Barros de Menezes
- Programa de Pós-graduação em Produtos Naturais e Sintéticos Bioativos (PgPNSB), Instituto de Pesquisa em Fármacos e Medicamentos (IPeFarM), Universidade Federal da Paraíba, Campus I, Cidade Universitária, João Pessoa, Brazil
| | - Marcus Tullius Scotti
- Programa de Pós-graduação em Produtos Naturais e Sintéticos Bioativos (PgPNSB), Instituto de Pesquisa em Fármacos e Medicamentos (IPeFarM), Universidade Federal da Paraíba, Campus I, Cidade Universitária, João Pessoa, Brazil
| | - Fábio Antônio Colombo
- Departamento de Análises Clínicas e Toxicológicas, Faculdade de Ciências Farmacêuticas, Universidade Federal de Alfenas, Alfenas, Brazil
| | - Marcos José Marques
- Departamento de Análises Clínicas e Toxicológicas, Faculdade de Ciências Farmacêuticas, Universidade Federal de Alfenas, Alfenas, Brazil
| | - Juliana Quero Reimão
- Departamento de Morfologia e Patologia Básica, Faculdade de Medicina de Jundiaí, Laboratory of Preclinical Assays and Research of Alternative Sources of Innovative Therapy for Toxoplasmosis and Other Sicknesses (PARASITTOS), Jundiaí, Brazil
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Promising Antifungal Molecules against Mucormycosis Agents Identified from Pandemic Response Box ®: In Vitro and In Silico Analyses. J Fungi (Basel) 2023; 9:jof9020187. [PMID: 36836302 PMCID: PMC9959553 DOI: 10.3390/jof9020187] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 01/25/2023] [Accepted: 01/27/2023] [Indexed: 02/04/2023] Open
Abstract
Mucormycosis is considered concerning invasive fungal infections due to its high mortality rates, difficult diagnosis and limited treatment approaches. Mucorales species are highly resistant to many antifungal agents and the search for alternatives is an urgent need. In the present study, a library with 400 compounds called the Pandemic Response Box® was used and four compounds were identified: alexidine and three non-commercial molecules. These compounds showed anti-biofilm activity, as well as alterations in fungal morphology and cell wall and plasma membrane structure. They also induced oxidative stress and mitochondrial membrane depolarization. In silico analysis revealed promising pharmacological parameters. These results suggest that these four compounds are potent candidates to be considered in future studies for the development of new approaches to treat mucormycosis.
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Multistage and transmission-blocking targeted antimalarials discovered from the open-source MMV Pandemic Response Box. Nat Commun 2021; 12:269. [PMID: 33431834 PMCID: PMC7801607 DOI: 10.1038/s41467-020-20629-8] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 12/10/2020] [Indexed: 12/30/2022] Open
Abstract
Chemical matter is needed to target the divergent biology associated with the different life cycle stages of Plasmodium. Here, we report the parallel de novo screening of the Medicines for Malaria Venture (MMV) Pandemic Response Box against Plasmodium asexual and liver stage parasites, stage IV/V gametocytes, gametes, oocysts and as endectocides. Unique chemotypes were identified with both multistage activity or stage-specific activity, including structurally diverse gametocyte-targeted compounds with potent transmission-blocking activity, such as the JmjC inhibitor ML324 and the antitubercular clinical candidate SQ109. Mechanistic investigations prove that ML324 prevents histone demethylation, resulting in aberrant gene expression and death in gametocytes. Moreover, the selection of parasites resistant to SQ109 implicates the druggable V-type H+-ATPase for the reduced sensitivity. Our data therefore provides an expansive dataset of compounds that could be redirected for antimalarial development and also point towards proteins that can be targeted in multiple parasite life cycle stages. Here, Reader et al. screen the Medicines for Malaria Venture Pandemic Response Box in parallel against Plasmodiumasexual and liver stage parasites, stage IV/V gametocytes, gametes, oocysts and as endectocides. They identify two potent transmission-blocking drugs: a histone demethylase inhibitor ML324 and the antitubercular SQ109.
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Fowler PW. How quickly can we predict trimethoprim resistance using alchemical free energy methods? Interface Focus 2020; 10:20190141. [PMID: 33178416 PMCID: PMC7653339 DOI: 10.1098/rsfs.2019.0141] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/11/2020] [Indexed: 12/15/2022] Open
Abstract
The emergence of antimicrobial resistance threatens modern medicine and necessitates more personalized treatment of bacterial infections. Sequencing the whole genome of the pathogen(s) in a clinical sample offers one way to improve clinical microbiology diagnostic services, and has already been adopted for tuberculosis in some countries. A key weakness of a genetics clinical microbiology is it cannot return a result for rare or novel genetic variants and therefore predictive methods are required. Non-synonymous mutations in the S. aureus dfrB gene can be successfully classified as either conferring resistance (or not) by calculating their effect on the binding free energy of the antibiotic, trimethoprim. The underlying approach, alchemical free energy methods, requires large numbers of molecular dynamics simulations to be run. We show that a large number (N = 15) of binding free energies calculated from a series of very short (50 ps) molecular dynamics simulations are able to satisfactorily classify all seven mutations in our clinically derived testset. A result for a single mutation could therefore be returned in less than an hour, thereby demonstrating that this or similar methods are now sufficiently fast and reproducible for clinical use.
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Affiliation(s)
- Philip W. Fowler
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DU, UK
- National Institute of Health Research Oxford Biomedical Research Centre, John Radcliffe Hospital, Headley Way, Oxford OX3 9DU, UK
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7
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Tang B, Gong T, Cui Y, Wang L, He C, Lu M, Chen J, Jing M, Zhang A, Li Y. Characteristics of oral methicillin-resistant Staphylococcus epidermidis isolated from dental plaque. Int J Oral Sci 2020; 12:15. [PMID: 32385260 PMCID: PMC7210960 DOI: 10.1038/s41368-020-0079-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 01/29/2020] [Accepted: 03/30/2020] [Indexed: 02/05/2023] Open
Abstract
The oral microbial community is widely regarded as a latent reservoir of antibiotic resistance genes. This study assessed the molecular epidemiology, susceptibility profile, and resistance mechanisms of 35 methicillin-resistant Staphylococcus epidermidis (MRSE) strains isolated from the dental plaque of a healthy human population. Broth microdilution minimum inhibitory concentrations (MICs) revealed that all the isolates were nonsusceptible to oxacillin and penicillin G. Most of them were also resistant to trimethoprim (65.7%) and erythromycin (54.3%). The resistance to multiple antibiotics was found to be largely due to the acquisition of plasmid-borne genes. The mecA and dfrA genes were found in all the isolates, mostly dfrG (80%), aacA-aphD (20%), aadD (28.6%), aphA3 (22.9%), msrA (5.7%), and the ermC gene (14.3%). Classical mutational mechanisms found in these isolates were mainly efflux pumps such as qacA (31.4%), qacC (25.7%), tetK (17.1%), and norA (8.6%). Multilocus sequence type analysis revealed that sequence type 59 (ST59) strains comprised 71.43% of the typed isolates, and the eBURST algorithm clustered STs into the clonal complex 2-II(CC2-II). The staphyloccoccal cassette chromosome mec (SCCmec) type results showed that 25 (71.43%) were assigned to type IV. Moreover, 88.66% of the isolates were found to harbor six or more biofilm-associated genes. The aap, atlE, embp, sdrF, and IS256 genes were detected in all 35 isolates. This research demonstrates that biofilm-positive multiple-antibiotic-resistant ST59-SCCmec IV S. epidermidis strains exist in the dental plaque of healthy people and may be a potential risk for the transmission of antibiotic resistance.
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Affiliation(s)
- Boyu Tang
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Tao Gong
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Yujia Cui
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Lingyun Wang
- Division of Infectious Diseases, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Chao He
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Miao Lu
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Jiamin Chen
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Meiling Jing
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Anqi Zhang
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Yuqing Li
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases & West China Hospital of Stomatology, Sichuan University, Chengdu, China.
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Fowler PW, Cole K, Gordon NC, Kearns AM, Llewelyn MJ, Peto TEA, Crook DW, Walker AS. Robust Prediction of Resistance to Trimethoprim in Staphylococcus aureus. Cell Chem Biol 2018; 25:339-349.e4. [PMID: 29307840 DOI: 10.1016/j.chembiol.2017.12.009] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 10/24/2017] [Accepted: 12/08/2017] [Indexed: 01/28/2023]
Abstract
The rise of antibiotic resistance threatens modern medicine; to combat it new diagnostic methods are required. Sequencing the whole genome of a pathogen offers the potential to accurately determine which antibiotics will be effective to treat a patient. A key limitation of this approach is that it cannot classify rare or previously unseen mutations. Here we demonstrate that alchemical free energy methods, a well-established class of methods from computational chemistry, can successfully predict whether mutations in Staphylococcus aureus dihydrofolate reductase confer resistance to trimethoprim. We also show that the method is quantitatively accurate by calculating how much the most common resistance-conferring mutation, F99Y, reduces the binding free energy of trimethoprim and comparing predicted and experimentally measured minimum inhibitory concentrations for seven different mutations. Finally, by considering up to 32 free energy calculations for each mutation, we estimate its specificity and sensitivity.
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Affiliation(s)
- Philip W Fowler
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Headley Way, Oxford OX3 9DU, UK.
| | - Kevin Cole
- Department of Infectious Diseases and Microbiology, Royal Sussex County Hospital, Brighton, Brighton and Sussex Medical School, Brighton BN1 9PS, UK
| | - N Claire Gordon
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Headley Way, Oxford OX3 9DU, UK
| | - Angela M Kearns
- Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, Public Health England, Colindale NW9 5EQ, UK
| | - Martin J Llewelyn
- Department of Infectious Diseases and Microbiology, Royal Sussex County Hospital, Brighton, Brighton and Sussex Medical School, Brighton BN1 9PS, UK
| | - Tim E A Peto
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Headley Way, Oxford OX3 9DU, UK
| | - Derrick W Crook
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Headley Way, Oxford OX3 9DU, UK
| | - A Sarah Walker
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Headley Way, Oxford OX3 9DU, UK
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Ojewole A, Lowegard A, Gainza P, Reeve SM, Georgiev I, Anderson AC, Donald BR. OSPREY Predicts Resistance Mutations Using Positive and Negative Computational Protein Design. Methods Mol Biol 2017; 1529:291-306. [PMID: 27914058 PMCID: PMC5192561 DOI: 10.1007/978-1-4939-6637-0_15] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Drug resistance in protein targets is an increasingly common phenomenon that reduces the efficacy of both existing and new antibiotics. However, knowledge of future resistance mutations during pre-clinical phases of drug development would enable the design of novel antibiotics that are robust against not only known resistant mutants, but also against those that have not yet been clinically observed. Computational structure-based protein design (CSPD) is a transformative field that enables the prediction of protein sequences with desired biochemical properties such as binding affinity and specificity to a target. The use of CSPD to predict previously unseen resistance mutations represents one of the frontiers of computational protein design. In a recent study (Reeve et al. Proc Natl Acad Sci U S A 112(3):749-754, 2015), we used our OSPREY (Open Source Protein REdesign for You) suite of CSPD algorithms to prospectively predict resistance mutations that arise in the active site of the dihydrofolate reductase enzyme from methicillin-resistant Staphylococcus aureus (SaDHFR) in response to selective pressure from an experimental competitive inhibitor. We demonstrated that our top predicted candidates are indeed viable resistant mutants. Since that study, we have significantly enhanced the capabilities of OSPREY with not only improved modeling of backbone flexibility, but also efficient multi-state design, fast sparse approximations, partitioned continuous rotamers for more accurate energy bounds, and a computationally efficient representation of molecular-mechanics and quantum-mechanical energy functions. Here, using SaDHFR as an example, we present a protocol for resistance prediction using the latest version of OSPREY. Specifically, we show how to use a combination of positive and negative design to predict active site escape mutations that maintain the enzyme's catalytic function but selectively ablate binding of an inhibitor.
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Affiliation(s)
- Adegoke Ojewole
- Program in Computational Biology and Bioinformatics, Duke University, Durham, NC, 27708, USA
| | - Anna Lowegard
- Program in Computational Biology and Bioinformatics, Duke University, Durham, NC, 27708, USA
| | - Pablo Gainza
- Department of Computer Science, Duke University, Durham, NC, 27708, USA
| | - Stephanie M Reeve
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT, 06269, USA
| | - Ivelin Georgiev
- Department of Computer Science, Duke University, Durham, NC, 27708, USA
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, Bethesda, MD, 20892, USA
| | - Amy C Anderson
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT, 06269, USA
| | - Bruce R Donald
- Department of Computer Science, Duke University, Durham, NC, 27708, USA.
- Department of Biochemistry, Duke University, Durham, NC, 27708, USA.
- Department of Chemistry, Duke University, Durham, NC, 27708, USA.
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10
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Reeve SM, Scocchera EW, G-Dayanadan N, Keshipeddy S, Krucinska J, Hajian B, Ferreira J, Nailor M, Aeschlimann J, Wright DL, Anderson AC. MRSA Isolates from United States Hospitals Carry dfrG and dfrK Resistance Genes and Succumb to Propargyl-Linked Antifolates. Cell Chem Biol 2016; 23:1458-1467. [PMID: 27939900 DOI: 10.1016/j.chembiol.2016.11.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2016] [Revised: 09/15/2016] [Accepted: 11/14/2016] [Indexed: 10/20/2022]
Abstract
Antibiotic resistance is a rapidly evolving health concern that requires a sustained effort to understand mechanisms of resistance and to develop new agents that overcome those mechanisms. The dihydrofolate reductase (DHFR) inhibitor, trimethoprim (TMP), remains one of the most important orally administered antibiotics. However, resistance through chromosomal mutations and mobile, plasmid-encoded insensitive DHFRs threatens the continued use of this agent. We are pursuing the development of new propargyl-linked antifolate (PLA) DHFR inhibitors designed to evade these mechanisms. While analyzing contemporary TMP-resistant clinical isolates of methicillin-resistant and sensitive Staphylococcus aureus, we discovered two mobile resistance elements, dfrG and dfrK. This is the first identification of these resistance mechanisms in the United States. These resistant organisms were isolated from a variety of infection sites, show clonal diversity, and each contain distinct resistance genotypes for common antibiotics. Several PLAs showed significant activity against these resistant strains by direct inhibition of the TMP resistance elements.
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Affiliation(s)
- Stephanie M Reeve
- Department of Pharmaceutical Sciences, University of Connecticut, 69 North Eagleville Road, Storrs, CT 06269, USA
| | - Eric W Scocchera
- Department of Pharmaceutical Sciences, University of Connecticut, 69 North Eagleville Road, Storrs, CT 06269, USA
| | - Narendran G-Dayanadan
- Department of Pharmaceutical Sciences, University of Connecticut, 69 North Eagleville Road, Storrs, CT 06269, USA
| | - Santosh Keshipeddy
- Department of Pharmaceutical Sciences, University of Connecticut, 69 North Eagleville Road, Storrs, CT 06269, USA
| | - Jolanta Krucinska
- Department of Pharmaceutical Sciences, University of Connecticut, 69 North Eagleville Road, Storrs, CT 06269, USA
| | - Behnoush Hajian
- Department of Pharmaceutical Sciences, University of Connecticut, 69 North Eagleville Road, Storrs, CT 06269, USA
| | - Jacob Ferreira
- Department of Pharmaceutical Sciences, University of Connecticut, 69 North Eagleville Road, Storrs, CT 06269, USA
| | - Michael Nailor
- Department of Pharmacy Practice, University of Connecticut, 69 North Eagleville Road, Storrs, CT 06269, USA; Department of Pharmacy Services, Hartford Hospital, 80 Seymour Street, Hartford, CT 06102, USA
| | - Jeffrey Aeschlimann
- Department of Pharmacy Practice, University of Connecticut, 69 North Eagleville Road, Storrs, CT 06269, USA; Division of Infectious Diseases and Department of Pharmacy Services, UConn Health/John Dempsey Hospital, 263 Farmington Avenue, Farmington, CT 06030, USA
| | - Dennis L Wright
- Department of Pharmaceutical Sciences, University of Connecticut, 69 North Eagleville Road, Storrs, CT 06269, USA.
| | - Amy C Anderson
- Department of Pharmaceutical Sciences, University of Connecticut, 69 North Eagleville Road, Storrs, CT 06269, USA
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11
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Hajian B, Scocchera E, Keshipeddy S, G-Dayanandan N, Shoen C, Krucinska J, Reeve S, Cynamon M, Anderson AC, Wright DL. Propargyl-Linked Antifolates Are Potent Inhibitors of Drug-Sensitive and Drug-Resistant Mycobacterium tuberculosis. PLoS One 2016; 11:e0161740. [PMID: 27580226 PMCID: PMC5006990 DOI: 10.1371/journal.pone.0161740] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 08/10/2016] [Indexed: 12/24/2022] Open
Abstract
Mycobacterium tuberculosis continues to cause widespread, life-threatening disease. In the last decade, this threat has grown dramatically as multi- and extensively-drug resistant (MDR and XDR) bacteria have spread globally and the number of agents that effectively treat these infections is significantly reduced. We have been developing the propargyl-linked antifolates (PLAs) as potent inhibitors of the essential enzyme dihydrofolate reductase (DHFR) from bacteria and recently found that charged PLAs with partial zwitterionic character showed improved mycobacterial cell permeability. Building on a hypothesis that these PLAs may penetrate the outer membrane of M. tuberculosis and inhibit the essential cytoplasmic DHFR, we screened a group of PLAs for antitubercular activity. In this work, we identified several PLAs as potent inhibitors of the growth of M. tuberculosis with several of the compounds exhibiting minimum inhibition concentrations equal to or less than 1 μg/mL. Furthermore, two of the compounds were very potent inhibitors of MDR and XDR strains. A high resolution crystal structure of one PLA bound to DHFR from M. tuberculosis reveals the interactions of the ligands with the target enzyme.
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Affiliation(s)
- Behnoush Hajian
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, Connecticut, United States of America
| | - Eric Scocchera
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, Connecticut, United States of America
| | - Santosh Keshipeddy
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, Connecticut, United States of America
| | - Narendran G-Dayanandan
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, Connecticut, United States of America
| | - Carolyn Shoen
- Veterans Affairs Medical Center, Syracuse, New York, United States of America
| | - Jolanta Krucinska
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, Connecticut, United States of America
| | - Stephanie Reeve
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, Connecticut, United States of America
| | - Michael Cynamon
- Veterans Affairs Medical Center, Syracuse, New York, United States of America
| | - Amy C. Anderson
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, Connecticut, United States of America
- * E-mail: (ACA); (DLW)
| | - Dennis L. Wright
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, Connecticut, United States of America
- * E-mail: (ACA); (DLW)
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12
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Estrada A, Wright DL, Anderson AC. Antibacterial Antifolates: From Development through Resistance to the Next Generation. Cold Spring Harb Perspect Med 2016; 6:a028324. [PMID: 27352799 PMCID: PMC4968165 DOI: 10.1101/cshperspect.a028324] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The folate cycle is one of the key metabolic pathways used by bacteria to synthesize vital building blocks required for proliferation. Therapeutic agents targeting enzymes in this cycle, such as trimethoprim and sulfamethoxazole, are among some of the most important and continually used antibacterials to treat both Gram-positive and Gram-negative pathogens. As with all antibacterial agents, the emergence of resistance threatens the continued clinical use of these life-saving drugs. In this article, we describe and analyze resistance mechanisms that have been clinically observed and review newer generations of preclinical compounds designed to overcome the molecular basis of the resistance.
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Affiliation(s)
- Alexavier Estrada
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, Connecticut 06269
| | - Dennis L Wright
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, Connecticut 06269
| | - Amy C Anderson
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, Connecticut 06269
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13
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Scocchera E, Reeve SM, Keshipeddy S, Lombardo MN, Hajian B, Sochia AE, Alverson JB, Priestley ND, Anderson AC, Wright DL. Charged Nonclassical Antifolates with Activity Against Gram-Positive and Gram-Negative Pathogens. ACS Med Chem Lett 2016; 7:692-6. [PMID: 27437079 DOI: 10.1021/acsmedchemlett.6b00120] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 05/05/2016] [Indexed: 01/08/2023] Open
Abstract
Although classical, negatively charged antifolates such as methotrexate possess high affinity for the dihydrofolate reductase (DHFR) enzyme, they are unable to penetrate the bacterial cell wall, rendering them poor antibacterial agents. Herein, we report a new class of charged propargyl-linked antifolates that capture some of the key contacts common to the classical antifolates while maintaining the ability to passively diffuse across the bacterial cell wall. Eight synthesized compounds exhibit extraordinary potency against Gram-positive S. aureus with limited toxicity against mammalian cells and good metabolic profile. High resolution crystal structures of two of the compounds reveal extensive interactions between the carboxylate and active site residues through a highly organized water network.
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Affiliation(s)
- Eric Scocchera
- Department
of Pharmaceutical Sciences, University of Connecticut, 69 North
Eagleville Road, Storrs, Connecticut 06268, United States
| | - Stephanie M. Reeve
- Department
of Pharmaceutical Sciences, University of Connecticut, 69 North
Eagleville Road, Storrs, Connecticut 06268, United States
| | - Santosh Keshipeddy
- Department
of Pharmaceutical Sciences, University of Connecticut, 69 North
Eagleville Road, Storrs, Connecticut 06268, United States
| | - Michael N. Lombardo
- Department
of Pharmaceutical Sciences, University of Connecticut, 69 North
Eagleville Road, Storrs, Connecticut 06268, United States
| | - Behnoush Hajian
- Department
of Pharmaceutical Sciences, University of Connecticut, 69 North
Eagleville Road, Storrs, Connecticut 06268, United States
| | - Adrienne E. Sochia
- Deptartment
of Chemistry, University of Montana, Missoula, Montana 59812, United States
| | - Jeremy B. Alverson
- Deptartment
of Chemistry, University of Montana, Missoula, Montana 59812, United States
| | - Nigel D. Priestley
- Deptartment
of Chemistry, University of Montana, Missoula, Montana 59812, United States
| | - Amy C. Anderson
- Department
of Pharmaceutical Sciences, University of Connecticut, 69 North
Eagleville Road, Storrs, Connecticut 06268, United States
| | - Dennis L. Wright
- Department
of Pharmaceutical Sciences, University of Connecticut, 69 North
Eagleville Road, Storrs, Connecticut 06268, United States
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14
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Reeve SM, Scocchera E, Ferreira JJ, G-Dayanandan N, Keshipeddy S, Wright DL, Anderson AC. Charged Propargyl-Linked Antifolates Reveal Mechanisms of Antifolate Resistance and Inhibit Trimethoprim-Resistant MRSA Strains Possessing Clinically Relevant Mutations. J Med Chem 2016; 59:6493-500. [PMID: 27308944 DOI: 10.1021/acs.jmedchem.6b00688] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Drug-resistant enzymes must balance catalytic function with inhibitor destabilization to provide a fitness advantage. This sensitive balance, often involving very subtle structural changes, must be achieved through a selection process involving a minimal number of eligible point mutations. As part of a program to design propargyl-linked antifolates (PLAs) against trimethoprim-resistant dihydrofolate reductase (DHFR) from Staphylococcus aureus, we have conducted a thorough study of several clinically observed chromosomal mutations in the enzyme at the cellular, biochemical, and structural levels. Through this work, we have identified a promising lead series that displays significantly greater activity against these mutant enzymes and strains than TMP. The best inhibitors have enzyme inhibition and MIC values near or below that of trimethoprim against wild-type S. aureus. Moreover, these studies employ a series of crystal structures of several mutant enzymes bound to the same inhibitor; analysis of the structures reveals a more detailed molecular understanding of drug resistance in this important enzyme.
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Affiliation(s)
- Stephanie M Reeve
- Department of Pharmaceutical Sciences, University of Connecticut , 69 North Eagleville Road, Storrs, Connecticut 06269, United States
| | - Eric Scocchera
- Department of Pharmaceutical Sciences, University of Connecticut , 69 North Eagleville Road, Storrs, Connecticut 06269, United States
| | - Jacob J Ferreira
- Department of Pharmaceutical Sciences, University of Connecticut , 69 North Eagleville Road, Storrs, Connecticut 06269, United States
| | - Narendran G-Dayanandan
- Department of Pharmaceutical Sciences, University of Connecticut , 69 North Eagleville Road, Storrs, Connecticut 06269, United States
| | - Santosh Keshipeddy
- Department of Pharmaceutical Sciences, University of Connecticut , 69 North Eagleville Road, Storrs, Connecticut 06269, United States
| | - Dennis L Wright
- Department of Pharmaceutical Sciences, University of Connecticut , 69 North Eagleville Road, Storrs, Connecticut 06269, United States
| | - Amy C Anderson
- Department of Pharmaceutical Sciences, University of Connecticut , 69 North Eagleville Road, Storrs, Connecticut 06269, United States
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15
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Nyíri K, Vértessy BG. Perturbation of genome integrity to fight pathogenic microorganisms. Biochim Biophys Acta Gen Subj 2016; 1861:3593-3612. [PMID: 27217086 DOI: 10.1016/j.bbagen.2016.05.024] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 05/05/2016] [Accepted: 05/18/2016] [Indexed: 10/21/2022]
Abstract
BACKGROUND Resistance against antibiotics is unfortunately still a major biomedical challenge for a wide range of pathogens responsible for potentially fatal diseases. SCOPE OF REVIEW In this study, we aim at providing a critical assessment of the recent advances in design and use of drugs targeting genome integrity by perturbation of thymidylate biosynthesis. MAJOR CONCLUSION We find that research efforts from several independent laboratories resulted in chemically highly distinct classes of inhibitors of key enzymes within the routes of thymidylate biosynthesis. The present article covers numerous studies describing perturbation of this metabolic pathway in some of the most challenging pathogens like Mycobacterium tuberculosis, Plasmodium falciparum, and Staphylococcus aureus. GENERAL SIGNIFICANCE Our comparative analysis allows a thorough summary of the current approaches to target thymidylate biosynthesis enzymes and also include an outlook suggesting novel ways of inhibitory strategies. This article is part of a Special Issue entitled "Science for Life" Guest Editor: Dr. Austen Angell, Dr. Salvatore Magazù and Dr. Federica Migliardo.
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Affiliation(s)
- Kinga Nyíri
- Dept. Biotechnology, Budapest University of Technology and Economics, 4 Szent Gellért tér, Budapest HU 1111, Hungary; Institute of Enzymology, RCNS, Hungarian Academy of Sciences, 2 Magyar tudósok körútja, Budapest HU 1117, Hungary.
| | - Beáta G Vértessy
- Dept. Biotechnology, Budapest University of Technology and Economics, 4 Szent Gellért tér, Budapest HU 1111, Hungary; Institute of Enzymology, RCNS, Hungarian Academy of Sciences, 2 Magyar tudósok körútja, Budapest HU 1117, Hungary.
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16
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Lombardo MN, G-Dayanandan N, Wright DL, Anderson AC. Crystal Structures of Trimethoprim-Resistant DfrA1 Rationalize Potent Inhibition by Propargyl-Linked Antifolates. ACS Infect Dis 2016; 2:149-56. [PMID: 27624966 DOI: 10.1021/acsinfecdis.5b00129] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Multidrug-resistant Enterobacteriaceae, notably Escherichia coli and Klebsiella pneumoniae, have become major health concerns worldwide. Resistance to effective therapeutics is often carried by class I and II integrons that can confer insensitivity to carbapenems, extended spectrum β-lactamases, the antifolate trimethoprim, fluoroquinolones, and aminoglycosides. Specifically of interest to the study here, a prevalent gene (dfrA1) coding for an insensitive dihydrofolate reductase (DHFR) confers 190- or 1000-fold resistance to trimethoprim for K. pneumoniae and E. coli, respectively. Attaining inhibition of both the wild-type and resistant forms of the enzyme is critical for new antifolates. For several years, we have been developing the propargyl-linked antifolates (PLAs) as effective inhibitors against trimethoprim-resistant DHFR enzymes. Here, we show that the PLAs are active against both the wild-type and DfrA1 DHFR proteins. We report two high-resolution crystal structures of DfrA1 bound to potent PLAs. The structure-activity relationships and crystal structures will be critical in driving the design of broadly active inhibitors against wild-type and resistant DHFR.
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Affiliation(s)
- Michael N. Lombardo
- Department
of Pharmaceutical Sciences, University of Connecticut, 69 North
Eagleville Road, Storrs, Connecticut 06269, United States
| | - Narendran G-Dayanandan
- Department
of Pharmaceutical Sciences, University of Connecticut, 69 North
Eagleville Road, Storrs, Connecticut 06269, United States
| | - Dennis L. Wright
- Department
of Pharmaceutical Sciences, University of Connecticut, 69 North
Eagleville Road, Storrs, Connecticut 06269, United States
| | - Amy C. Anderson
- Department
of Pharmaceutical Sciences, University of Connecticut, 69 North
Eagleville Road, Storrs, Connecticut 06269, United States
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17
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Keshipeddy S, Reeve SM, Anderson AC, Wright DL. Nonracemic Antifolates Stereoselectively Recruit Alternate Cofactors and Overcome Resistance in S. aureus. J Am Chem Soc 2015; 137:8983-90. [PMID: 26098608 PMCID: PMC4733634 DOI: 10.1021/jacs.5b01442] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
While antifolates such as Bactrim (trimethoprim-sulfamethoxazole; TMP-SMX) continue to play an important role in treating community-acquired methicillin-resistant Staphylococcus aureus (CA-MRSA), resistance-conferring mutations, specifically F98Y of dihydrofolate reductase (DHFR), have arisen and compromise continued use. In an attempt to extend the lifetime of this important class, we have developed a class of propargyl-linked antifolates (PLAs) that exhibit potent inhibition of the enzyme and bacterial strains. Probing the role of the configuration at the single propargylic stereocenter in these inhibitors required us to develop a new approach to nonracemic 3-aryl-1-butyne building blocks by the pairwise use of asymmetric conjugate addition and aldehyde dehydration protocols. Using this new route, a series of nonracemic PLA inhibitors was prepared and shown to possess potent enzyme inhibition (IC50 values <50 nM), antibacterial effects (several with MIC values <1 μg/mL) and to form stable ternary complexes with both wild-type and resistant mutants. Unexpectedly, crystal structures of a pair of individual enantiomers in the wild-type DHFR revealed that the single change in configuration of the stereocenter drove the selection of an alternative NADPH cofactor, with the minor α-anomer appearing with R-27. Remarkably, this cofactor switching becomes much more prevalent when the F98Y mutation is present. The observation of cofactor site plasticity leads to a postulate for the structural basis of TMP resistance in DHFR and also suggests design strategies that can be used to target these resistant enzymes.
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Affiliation(s)
| | | | - Amy C. Anderson
- Department of Pharmaceutical Sciences, University of Connecticut, 69 N. Eagleville Rd., Storrs, CT 06269
| | - Dennis L. Wright
- Department of Pharmaceutical Sciences, University of Connecticut, 69 N. Eagleville Rd., Storrs, CT 06269
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18
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Protein design algorithms predict viable resistance to an experimental antifolate. Proc Natl Acad Sci U S A 2014; 112:749-54. [PMID: 25552560 DOI: 10.1073/pnas.1411548112] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Methods to accurately predict potential drug target mutations in response to early-stage leads could drive the design of more resilient first generation drug candidates. In this study, a structure-based protein design algorithm (K* in the OSPREY suite) was used to prospectively identify single-nucleotide polymorphisms that confer resistance to an experimental inhibitor effective against dihydrofolate reductase (DHFR) from Staphylococcus aureus. Four of the top-ranked mutations in DHFR were found to be catalytically competent and resistant to the inhibitor. Selection of resistant bacteria in vitro reveals that two of the predicted mutations arise in the background of a compensatory mutation. Using enzyme kinetics, microbiology, and crystal structures of the complexes, we determined the fitness of the mutant enzymes and strains, the structural basis of resistance, and the compensatory relationship of the mutations. To our knowledge, this work illustrates the first application of protein design algorithms to prospectively predict viable resistance mutations that arise in bacteria under antibiotic pressure.
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19
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Crystal structures of Klebsiella pneumoniae dihydrofolate reductase bound to propargyl-linked antifolates reveal features for potency and selectivity. Antimicrob Agents Chemother 2014; 58:7484-91. [PMID: 25288083 DOI: 10.1128/aac.03555-14] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Resistance to the antibacterial antifolate trimethoprim (TMP) is increasing in members of the family Enterobacteriaceae, driving the design of next-generation antifolates effective against these Gram-negative pathogens. The propargyl-linked antifolates are potent inhibitors of dihydrofolate reductases (DHFR) from several TMP-sensitive and -resistant species, including Klebsiella pneumoniae. Recently, we have determined that these antifolates inhibit the growth of strains of K. pneumoniae, some with MIC values of 1 μg/ml. In order to further the design of potent and selective antifolates against members of the Enterobacteriaceae, we determined the first crystal structures of K. pneumoniae DHFR bound to two of the propargyl-linked antifolates. These structures highlight that interactions with Leu 28, Ile 50, Ile 94, and Leu 54 are necessary for potency; comparison with structures of human DHFR bound to the same inhibitors reveal differences in residues (N64E, P61G, F31L, and V115I) and loop conformations (residues 49 to 53) that may be exploited for selectivity.
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20
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Nurjadi D, Olalekan AO, Layer F, Shittu AO, Alabi A, Ghebremedhin B, Schaumburg F, Hofmann-Eifler J, Van Genderen PJJ, Caumes E, Fleck R, Mockenhaupt FP, Herrmann M, Kern WV, Abdulla S, Grobusch MP, Kremsner PG, Wolz C, Zanger P. Emergence of trimethoprim resistance gene dfrG in Staphylococcus aureus causing human infection and colonization in sub-Saharan Africa and its import to Europe. J Antimicrob Chemother 2014; 69:2361-8. [PMID: 24855123 DOI: 10.1093/jac/dku174] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
OBJECTIVES Co-trimoxazole (trimethoprim/sulfamethoxazole) is clinically valuable in treating skin and soft tissue infections (SSTIs) caused by community-associated methicillin-resistant Staphylococcus aureus (MRSA). The genetic basis of emerging trimethoprim/sulfamethoxazole resistance in S. aureus from Africa is unknown. Such knowledge is essential to anticipate its further spread. We investigated the molecular epidemiology of trimethoprim resistance in S. aureus collected in and imported from Africa. METHODS Five hundred and ninety-eight human S. aureus isolates collected at five locations across sub-Saharan Africa [Gabon, Namibia, Nigeria (two) and Tanzania] and 47 isolates from travellers treated at six clinics in Europe because of SSTIs on return from Africa were tested for susceptibility to trimethoprim, sulfamethoxazole and trimethoprim/sulfamethoxazole, screened for genes mediating trimethoprim resistance in staphylococci [dfrA (dfrS1), dfrB, dfrG and dfrK] and assigned to spa genotypes and clonal complexes. RESULTS In 313 clinical and 285 colonizing S. aureus from Africa, 54% of isolates were resistant to trimethoprim, 21% to sulfamethoxazole and 19% to trimethoprim/sulfamethoxazole. We found that 94% of trimethoprim resistance was mediated by the dfrG gene. Of the 47 S. aureus isolates from travellers with SSTIs, 27 (57%) were trimethoprim resistant and carried dfrG. Markers of trimethoprim resistance other than dfrG were rare. The presence of dfrG genes in S. aureus was neither geographically nor clonally restricted. CONCLUSIONS dfrG, previously perceived to be an uncommon cause of trimethoprim resistance in human S. aureus, is widespread in Africa and abundant in imported S. aureus from ill returning travellers. These findings may foreshadow the loss of trimethoprim/sulfamethoxazole for the empirical treatment of SSTIs caused by community-associated MRSA.
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Affiliation(s)
- Dennis Nurjadi
- Deutsches Zentrum für Infektionsforschung (DZIF), Institut für Tropenmedizin, Universitätsklinikum, Wilhelmstraße 27, 72074 Tübingen, Germany Deutsches Zentrum für Infektionsforschung (DZIF), Institut für Medizinische Mikrobiologie und Hygiene, Universitätsklinikum, Elfriede-Aulhorn-Straße 6, 72076 Tübingen, Germany
| | - Adesola O Olalekan
- Deutsches Zentrum für Infektionsforschung (DZIF), Institut für Tropenmedizin, Universitätsklinikum, Wilhelmstraße 27, 72074 Tübingen, Germany Department of Medical Microbiology and Parasitology, Ladoke Akintola University of Technology, PO Box 4000, Ogbomoso, Nigeria
| | - Franziska Layer
- Nationales Referenzzentrum für Staphylokokken und Enterokokken, Robert Koch Institut, Burgstraße 37, 38855 Wernigerode, Germany
| | - Adebayo O Shittu
- Department of Microbiology, Obafemi Awolowo University, Ile-Ife 22005, Nigeria
| | - Abraham Alabi
- Centre de Recherches Médicales de Lambaréné (CERMEL), B.P. 118, Lambaréné, Gabon
| | - Beniam Ghebremedhin
- Institut für Medizinische Mikrobiologie, Universitätsklinikum, Leipziger Straße 44, 39120 Magdeburg, Germany/Department Humanmedizin, Universität Witten/Herdecke, Alfred-Herrhausen-Straße 50, 58448 Witten, Germany/Helios Clinic, Heusnerstraße 40, 42283 Wuppertal, Germany
| | - Frieder Schaumburg
- Institut für Medizinische Mikrobiologie, Universitätsklinikum Münster, Domagkstraße 10, 48149 Münster, Germany
| | - Jonas Hofmann-Eifler
- Bagamoyo Research and Training Center, Ifakara Health Institute, PO Box 74, Bagamoyo, Tanzania Universitätsklinikum Freiburg, Abteilung Infektiologie, Hugstetter Straße 55, 79106 Freiburg, Germany
| | - Perry J J Van Genderen
- Instituut voor Tropische Ziekten, Havenziekenhuis, Haringvliet 72, 3011 TG Rotterdam, The Netherlands
| | - Eric Caumes
- Service de Maladies Infectieuses et Tropicales, groupe hospitalier Pitié-Salpêtrière, 47-83 boulevard de l'Hôpital, 75651 Paris cedex 13, France/Sorbonne Universités, UPMC Univ Paris 06, F-75005, Paris, France
| | - Ralf Fleck
- Tropenklinik, Paul-Lechler-Krankenhaus, 72076 Tübingen, Germany
| | - Frank P Mockenhaupt
- Institut für Tropenmedizin und Internationale Gesundheit, Charité-Universitätsmedizin Berlin, Spandauer Damm 130, 14050 Berlin, Germany
| | - Mathias Herrmann
- Institut für Medizinische Mikrobiologie und Hygiene, Universitätsklinikum des Saarlandes, Kirrberger Straße, 66421 Homburg/Saar, Germany
| | - Winfried V Kern
- Universitätsklinikum Freiburg, Abteilung Infektiologie, Hugstetter Straße 55, 79106 Freiburg, Germany
| | - Salim Abdulla
- Bagamoyo Research and Training Center, Ifakara Health Institute, PO Box 74, Bagamoyo, Tanzania
| | - Martin P Grobusch
- Centre de Recherches Médicales de Lambaréné (CERMEL), B.P. 118, Lambaréné, Gabon Center of Tropical Medicine and Travel Medicine, Department of Infectious Diseases, Academic Medical Center, University of Amsterdam, Meibergdreef 9, 1105 Amsterdam, The Netherlands
| | - Peter G Kremsner
- Deutsches Zentrum für Infektionsforschung (DZIF), Institut für Tropenmedizin, Universitätsklinikum, Wilhelmstraße 27, 72074 Tübingen, Germany Centre de Recherches Médicales de Lambaréné (CERMEL), B.P. 118, Lambaréné, Gabon
| | - Christiane Wolz
- Deutsches Zentrum für Infektionsforschung (DZIF), Institut für Medizinische Mikrobiologie und Hygiene, Universitätsklinikum, Elfriede-Aulhorn-Straße 6, 72076 Tübingen, Germany
| | - Philipp Zanger
- Deutsches Zentrum für Infektionsforschung (DZIF), Institut für Tropenmedizin, Universitätsklinikum, Wilhelmstraße 27, 72074 Tübingen, Germany
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21
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Silver LL. Antibacterial Discovery: Problems and Possibilities. Antibiotics (Basel) 2013. [DOI: 10.1002/9783527659685.ch2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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22
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Lamb KM, G-Dayanandan N, Wright DL, Anderson AC. Elucidating features that drive the design of selective antifolates using crystal structures of human dihydrofolate reductase. Biochemistry 2013; 52:7318-26. [PMID: 24053334 DOI: 10.1021/bi400852h] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The pursuit of antimicrobial drugs that target dihydrofolate reductase (DHFR) exploits differences in sequence and dynamics between the pathogenic and human enzymes. Here, we present five crystal structures of human DHFR bound to a new class of antimicrobial agents, the propargyl-linked antifolates (PLAs), with a range of potency (IC50 values of 0.045-1.07 μM) for human DHFR. These structures reveal that interactions between the ligands and Asn 64, Phe 31, and Phe 34 are important for increased affinity for human DHFR and that loop residues 58-64 undergo ligand-induced conformational changes. The utility of these structural studies was demonstrated through the design of three new ligands that reduce the number of contacts with Asn 64, Phe 31, and Phe 34. Synthesis and evaluation show that one of the designed inhibitors exhibits the lowest affinity for human DHFR of any of the PLAs (2.64 μM). Comparisons of structures of human and Staphylococcus aureus DHFR bound to the same PLA reveal a conformational change in the ligand that enhances interactions with residues Phe 92 (Val 115 in huDHFR) and Ile 50 (Ile 60 in huDHFR) in S. aureus DHFR, yielding selectivity. Likewise, comparisons of human and Candida glabrata DHFR bound to the same ligand show that hydrophobic interactions with residues Ile 121 and Phe 66 (Val 115 and Asn 64 in human DHFR) yield selective inhibitors. The identification of residue substitutions that are important for selectivity and the observation of active site flexibility will help guide antimicrobial antifolate development for the inhibition of pathogenic species.
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Affiliation(s)
- Kristen M Lamb
- Department of Pharmaceutical Sciences, University of Connecticut , 69 North Eagleville Road, Storrs, Connecticut 06269, United States
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23
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Zhou W, Scocchera EW, Wright DL, Anderson AC. Antifolates as effective antimicrobial agents: new generations of trimethoprim analogs. MEDCHEMCOMM 2013. [DOI: 10.1039/c3md00104k] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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Abstract
The synthesis of the bacterial peptidoglycan has been recognized for over 50 years as fertile ground for antibacterial discovery. Initially, empirical screening of natural products for inhibition of bacterial growth detected many chemical classes of antibiotics whose specific mechanisms of action were eventually dissected and defined. Of the nontoxic antibiotics discovered, most were found to be inhibitors of either protein synthesis or cell wall synthesis, which led to more directed screening for inhibitors of these pathways. Directed screening and design programs for cell wall inhibitors have been undertaken since the 1960s. In that time it has become clear that, while certain steps and intermediates have yielded selective inhibitors and are established targets, other potential targets have not yielded inhibitors whose antibacterial activity is proven to be solely due to that inhibition. Why has this search been so problematic? Are the established targets still worth pursuing? This review will attempt to answer these and other questions and evaluate the viability of targets related to peptidoglycan synthesis.
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Affiliation(s)
- Lynn L Silver
- LL Silver Consulting, LLC, Springfield, New Jersey 07081, USA.
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