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Mansour B, El-Sherbeny MA, Al-Omary FAM, Saber S, Ramadan HA, El-Baz AM, Mourad AAE, Abdel-Aziz NI. New Pyrazole-Clubbed Pyrimidine or Pyrazoline Hybrids as Anti-Methicillin-Resistant Staphylococcus aureus Agents: Design, Synthesis, In Vitro and In Vivo Evaluation, and Molecular Modeling Simulation. ACS OMEGA 2023; 8:44250-44264. [PMID: 38027391 PMCID: PMC10666275 DOI: 10.1021/acsomega.3c06936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 10/18/2023] [Accepted: 10/20/2023] [Indexed: 12/01/2023]
Abstract
Two hybrid series of pyrazole-clubbed pyrimidines 5a-c and pyrazole-clubbed pyrazoline compounds 6a,b and 7 were designed as attractive scaffolds to be investigated in vitro and in vivo for antibacterial activity against methicillin-resistant Staphylococcus aureus (MRSA) and Pseudomonas aeruginosa. From the results of the in vitro antibacterial screening, compound 5c showed excellent activity (minimal inhibitory concentration, MIC = 521 μM) when compared with that of the reference antibiotic levofloxacin (MIC = 346 μM). The inhibition of the target dihydrofolate reductase (DHFR) enzyme by compounds 4 and 5a-c (IC50 = 5.00 ± 0.23, 4.20 ± 0.20, 4.10 ± 0.19, and 4.00 ± 0.18 μM, respectively) was found to be better than the reference drug trimethoprim (IC50 = 5.54 ± 0.28 μM). Molecular modeling simulation results have justified the order of activity of all the newly synthesized compounds as DHFR enzyme inhibitors, and compound 5c exhibited the best binding profile (-13.6169386 kcal/mol). Hence, the most potent inhibitor of the DHFR enzyme, 5c, was chosen to be evaluated in vivo for its activity in treating MRSA-induced keratitis in rats and that, in turn, significantly (P < 0.0001) reduced infection in rats when compared to MRSA-treated group results.
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Affiliation(s)
- Basem Mansour
- Department
of Pharmaceutical Chemistry, Faculty of Pharmacy, Delta University for Science and Technology, Gamasa 11152, Dakahlia, Egypt
| | - Magda A. El-Sherbeny
- Department
of Pharmaceutical Chemistry, Faculty of Pharmacy, Delta University for Science and Technology, Gamasa 11152, Dakahlia, Egypt
- Department
of Medicinal Chemistry, Faculty of Pharmacy, University of Mansoura, Mansoura 35516, Egypt
| | - Fatmah A. M. Al-Omary
- Department
of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Sameh Saber
- Department
of Pharmacology, Faculty of Pharmacy, Delta
University for Science and Technology, Gamasa 11152, Dakahlia, Egypt
| | - Heba A. Ramadan
- Department
of Microbiology and Immunology Faculty of Pharmacy, Delta University for Science and Technology, Gamasa 11152, Dakahlia, Egypt
| | - Ahmed M. El-Baz
- Department
of Microbiology and Immunology Faculty of Pharmacy, Delta University for Science and Technology, Gamasa 11152, Dakahlia, Egypt
| | - Ahmed A. E. Mourad
- Department
of Pharmacology and Toxicology, Faculty of Pharmacy, Port Said University, Port Said 42511, Egypt
| | - Naglaa I. Abdel-Aziz
- Department
of Pharmaceutical Chemistry, Faculty of Pharmacy, Delta University for Science and Technology, Gamasa 11152, Dakahlia, Egypt
- Department
of Medicinal Chemistry, Faculty of Pharmacy, University of Mansoura, Mansoura 35516, Egypt
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2
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Quazi S, Rashid MT, Malik JA, Gavas S. The Discovery of Novel Antimicrobial Agents through the Application of Isocyanide-Based Multicomponent Reactions. Antibiotics (Basel) 2023; 12:antibiotics12050849. [PMID: 37237752 DOI: 10.3390/antibiotics12050849] [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: 11/01/2022] [Revised: 04/26/2023] [Accepted: 04/28/2023] [Indexed: 05/28/2023] Open
Abstract
Multicomponent reactions (MCR) have been used to synthesize a wide range of analogs from several classes of heterocyclic compounds, with multifaceted medicinal uses. The synthesis of highly functionalized molecules in a single pot is a unique property of MCR, allowing researchers to quickly assemble libraries of compounds of biological interest and uncover novel leads as possible therapeutic agents. Isocyanide-based multicomponent reactions have proven to be extremely effective at swiftly specifying members of compound libraries, particularly in the discovery of drugs. The understanding of structure-activity correlations that drive the development of new goods and technology requires structural variety in these libraries. In today's world, antibiotic resistance is a major ongoing problem that poses risks to public health. The implementation of isocyanide-based multicomponent reactions upholds a significant potential in this regard. By utilizing such reactions, new antimicrobial compounds can be discovered and subsequently used to fight against such concerns. This study discusses the recent developments in antimicrobial medication discovery using isocyanide-based multicomponent reactions (IMCRs). Furthermore, the article emphasizes the potential of IMCRs (Isocyanide-based multicomponent based reactions) in the near future.
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Affiliation(s)
- Sameer Quazi
- GenLab Biosolutions Private Limited, Bangalore 560043, Karnataka, India
- Department of Biomedical Sciences, School of Life Sciences, Anglia Ruskin University, Cambridge CB1 1PT, UK
- School of Health Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M13 9PL, UK
- SCAMT Institute, ITMO University, St. Petersburg 197101, Russia
| | | | - Javid Ahmad Malik
- Department of Zoology, Guru Ghasidas University, Bilaspur 495009, Chhattisgarh, India
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3
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The Broad-Spectrum Antitrypanosomal Inhibitory Efficiency of the Antimetabolite/Anticancer Drug Raltitrexed. Processes (Basel) 2022. [DOI: 10.3390/pr10112158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Raltitrexed is a classical antifolate drug with antimetabolite and anticancer properties. In this research, we provide its detailed antitrypanosomal inhibition against six Trypanosoma species and investigate its potential mode of action. Molecular dynamics (MD) simulations and in silico analyses were used to track the binding strength and stability. Raltitrexed showed broad-spectrum trypanocidal actions against Trypanosoma brucei brucei GUTat3.1, T. b. rhodesiense IL1501, T. b. gambiense IL1922, T. evansi Tansui, T. equiperdum IVM-t1 and T. congolense IL3000. The estimated IC50 was found to be in the range of 5.18–24.13 µg/mL, indicating inhibition of Trypanosoma in the low micromolar range. Although the co-crystallized ligand had robust hydrogen bonding and lipophilic characteristics, its docking score was only −4.6 compared to raltitrexed’s −7.78, indicating strong binding with T. brucei dihydrofolate reductase-thymidylate synthase (TbDHFR-TS). MD simulations support the strong binding of raltitrexed with TbDHFR-TS evidenced by low root mean square deviation (RMSD), low residues fluctuations, a tight radius of gyration (ROG) and an average of 3.38 ± 1.3 hydrogen bonds during 50 ns MD simulation. The prospective extended spectrum of raltitrexed against Trypanosoma species grants further research for the synthesis of raltitrexed derivatives and repurposing against other protozoa.
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Brenig C, Mestizo PD, Zelder F. Functionalisation of vitamin B 12 derivatives with a cobalt β-phenyl ligand boosters antimetabolite activity in bacteria. RSC Adv 2022; 12:28553-28559. [PMID: 36320527 PMCID: PMC9541496 DOI: 10.1039/d2ra05748d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 09/27/2022] [Indexed: 11/06/2022] Open
Abstract
This study describes the syntheses of four singly- and two doubly-modified vitamin B12 derivatives for generating antimetabolites of Lactobacillus delbrueckii (L. delbrueckii). The two most potent antagonists, a Coβ-phenyl-cobalamin-c,8-lactam and a 10-bromo-Coβ-phenylcobalamin combine a c-lactam or 10-bromo modification at the “eastern” site of the corrin ring with an artificial organometallic phenyl group instead of a cyano ligand at the β-site of the cobalt center. These two doubly-modified B12 antagonists (10 nM) inhibit fully B12-dependent (0.1 nM) growth of L. delbrueckii. In contrast to potent 10-bromo-Coβ-phenylcobalamin, single modified 10-bromo-Coβ-cyanocobalamin lacking the artificial organometallic phenyl ligand does not show any inhibitory effect. These results suggest, that the organometallic β-phenyl ligand at the Co center ultimately steers the metabolic effect of the 10-bromo-analogue. This study describes the syntheses of four singly- and two doubly-modified vitamin B12 derivatives for generating antimetabolites of Lactobacillus delbrueckii (L. delbrueckii).![]()
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Affiliation(s)
- Christopher Brenig
- Department of Chemistry, University of ZurichWinterthurerstrasse 190CH 8057 ZurichSwitzerlandhttps://www.felix-zelder.net+41 44 635 6803
| | - Paula Daniela Mestizo
- Department of Chemistry, University of ZurichWinterthurerstrasse 190CH 8057 ZurichSwitzerlandhttps://www.felix-zelder.net+41 44 635 6803
| | - Felix Zelder
- Department of Chemistry, University of ZurichWinterthurerstrasse 190CH 8057 ZurichSwitzerlandhttps://www.felix-zelder.net+41 44 635 6803
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5
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Laczi D, Johnstone MD, Fleming CL. Photoresponsive Small Molecule Inhibitors for the Remote Control of Enzyme Activity. Chem Asian J 2022; 17:e202200200. [PMID: 35446477 PMCID: PMC9322446 DOI: 10.1002/asia.202200200] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/01/2022] [Indexed: 12/14/2022]
Abstract
The development of new and effective therapeutics is reliant on the ability to study the underlying mechanisms of potential drug targets in live cells and multicellular systems. A persistent challenge in many drug development programmes is poor selectivity, which can obscure the mechanisms involved and lead to poorly understood modes of action. In efforts to improve our understanding of these complex processes, small molecule inhibitors have been developed in which their OFF/ON therapeutic activity can be toggled using light. Photopharmacology is devoted to using light to modulate drugs. Herein, we highlight the recent progress made towards the development of light‐responsive small molecule inhibitors of selected enzymatic targets. Given the size of this field, literature from 2015 onwards has been reviewed.
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Affiliation(s)
- Dóra Laczi
- Centre for Biomedical and Chemical Sciences, School of Science, Auckland University of Technology, Private Bag 92006, Auckland, 1142, New Zealand
| | - Mark D Johnstone
- Centre for Biomedical and Chemical Sciences, School of Science, Auckland University of Technology, Private Bag 92006, Auckland, 1142, New Zealand
| | - Cassandra L Fleming
- Centre for Biomedical and Chemical Sciences, School of Science, Auckland University of Technology, Private Bag 92006, Auckland, 1142, New Zealand
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6
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Pedrola M, Jorba M, Jardas E, Jardi F, Ghashghaei O, Viñas M, Lavilla R. Multicomponent Reactions Upon the Known Drug Trimethoprim as a Source of Novel Antimicrobial Agents. Front Chem 2019; 7:475. [PMID: 31334221 PMCID: PMC6621506 DOI: 10.3389/fchem.2019.00475] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 06/20/2019] [Indexed: 01/02/2023] Open
Abstract
Novel antibiotic compounds have been prepared through a selective multicomponent reaction upon the known drug Trimethoprim. The Groebke-Blackburn-Bienaymé reaction involving this α-aminoazine, with a range of aldehydes and isocyanides afforded the desired adducts in one-step. The analogs display meaningful structural features of the initial drug together with relevant modifications at several points, keeping antibiotic potency and showing satisfactory antimicrobial profile (good activity levels and reduced growth rates), especially against methicillin-resistant Staphylococcus aureus. The new products may open new possibilities to fight bacterial infections.
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Affiliation(s)
- Marina Pedrola
- Laboratory of Medicinal Chemistry, Faculty of Pharmacy and Food Sciences and Institute of Biomedicine (IBUB), University of Barcelona, Barcelona, Spain
| | - Marta Jorba
- Laboratory of Molecular Microbiology & Antimicrobials, Department of Pathology & Experimental Therapeutics, Medical School, Hospitalet de Llobregat, University of Barcelona, Barcelona, Spain.,Bellvitge Institute for Biomedical Research (IDIBELL), Barcelona, Spain
| | - Eda Jardas
- Laboratory of Medicinal Chemistry, Faculty of Pharmacy and Food Sciences and Institute of Biomedicine (IBUB), University of Barcelona, Barcelona, Spain
| | - Ferran Jardi
- Laboratory of Medicinal Chemistry, Faculty of Pharmacy and Food Sciences and Institute of Biomedicine (IBUB), University of Barcelona, Barcelona, Spain
| | - Ouldouz Ghashghaei
- Laboratory of Medicinal Chemistry, Faculty of Pharmacy and Food Sciences and Institute of Biomedicine (IBUB), University of Barcelona, Barcelona, Spain
| | - Miguel Viñas
- Laboratory of Molecular Microbiology & Antimicrobials, Department of Pathology & Experimental Therapeutics, Medical School, Hospitalet de Llobregat, University of Barcelona, Barcelona, Spain.,Bellvitge Institute for Biomedical Research (IDIBELL), Barcelona, Spain
| | - Rodolfo Lavilla
- Laboratory of Medicinal Chemistry, Faculty of Pharmacy and Food Sciences and Institute of Biomedicine (IBUB), University of Barcelona, Barcelona, Spain
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7
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Carey PR, Whitmer GR, Yoon MJ, Lombardo MN, Pusztai-Carey M, Heidari-Torkabadi H, Che T. Measuring Drug-Induced Changes in Metabolite Populations of Live Bacteria: Real Time Analysis by Raman Spectroscopy. J Phys Chem B 2018; 122:6377-6385. [PMID: 29792435 DOI: 10.1021/acs.jpcb.8b03279] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Raman difference spectroscopy is shown to provide a wealth of molecular detail on changes within bacterial cells caused by infusion of antibiotics or hydrogen peroxide. Escherichia coli strains paired with chloramphenicol, dihydrofolate reductase propargyl-based inhibitors, meropenem, or hydrogen peroxide provide details of the depletion of protein and nucleic acid populations in real time. Additionally, other reproducible Raman features appear and are attributed to changes in cell metabolite populations. An initial candidate for one of the metabolites involves population increases of citrate, an intermediate within the tricarboxyclic acid cycle. This is supported by the observation that a strain of E. coli without the ability to synthesize citrate, gltA, lacks an intense feature in the Raman difference spectrum that has been ascribed to citrate. The methodology for obtaining the Raman data involves infusing the drug into live cells, then washing, freezing, and finally lyophilizing the cells. The freeze-dried cells are then examined under a Raman microscope. The difference spectra [cells treated with drug] - [cells without treatment] are time-dependent and can yield population kinetics for intracellular species in vivo. There is a strong resemblance between the Raman difference spectra of E. coli cells treated with meropenem and those treated with hydrogen peroxide.
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Affiliation(s)
- Paul R Carey
- Department of Biochemistry , Case Western Reserve University School of Medicine , 10900 Euclid Avenue , Cleveland Ohio 44106 , United States
| | - Grant R Whitmer
- Department of Biochemistry , Case Western Reserve University School of Medicine , 10900 Euclid Avenue , Cleveland Ohio 44106 , United States
| | - Michael J Yoon
- Department of Biochemistry , Case Western Reserve University School of Medicine , 10900 Euclid Avenue , Cleveland Ohio 44106 , United States
| | - Michael N Lombardo
- Department of Pharmaceutical Sciences , University of Connecticut , 69 North Eagleville Road , Storrs Connecticut 06269 , United States
| | - Marianne Pusztai-Carey
- Department of Biochemistry , Case Western Reserve University School of Medicine , 10900 Euclid Avenue , Cleveland Ohio 44106 , United States
| | - Hossein Heidari-Torkabadi
- Department of Biochemistry , Case Western Reserve University School of Medicine , 10900 Euclid Avenue , Cleveland Ohio 44106 , United States
| | - Tao Che
- Department of Biochemistry , Case Western Reserve University School of Medicine , 10900 Euclid Avenue , Cleveland Ohio 44106 , United States
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8
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Review on Abyssomicins: Inhibitors of the Chorismate Pathway and Folate Biosynthesis. Molecules 2018; 23:molecules23061371. [PMID: 29882815 PMCID: PMC6100094 DOI: 10.3390/molecules23061371] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Revised: 05/30/2018] [Accepted: 06/04/2018] [Indexed: 11/16/2022] Open
Abstract
Antifolates targeting folate biosynthesis within the shikimate-chorismate-folate metabolic pathway are ideal and selective antimicrobials, since higher eukaryotes lack this pathway and rely on an exogenous source of folate. Resistance to the available antifolates, inhibiting the folate pathway, underlines the need for novel antibiotic scaffolds and molecular targets. While para-aminobenzoic acid synthesis within the chorismate pathway constitutes a novel molecular target for antifolates, abyssomicins are its first known natural inhibitors. This review describes the abyssomicin family, a novel spirotetronate polyketide Class I antimicrobial. It summarizes synthetic and biological studies, structural, biosynthetic, and biological properties of the abyssomicin family members. This paper aims to explain their molecular target, mechanism of action, structure⁻activity relationship, and to explore their biological and pharmacological potential. Thirty-two natural abyssomicins and numerous synthetic analogues have been reported. The biological activity of abyssomicins includes their antimicrobial activity against Gram-positive bacteria and mycobacteria, antitumor properties, latent human immunodeficiency virus (HIV) reactivator, anti-HIV and HIV replication inducer properties. Their antimalarial properties have not been explored yet. Future analoging programs using the structure⁻activity relationship data and synthetic approaches may provide a novel abyssomicin structure that is active and devoid of cytotoxicity. Abyssomicin J and atrop-o-benzyl-desmethylabyssomicin C constitute promising candidates for such programs.
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9
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Wegener M, Hansen MJ, Driessen AJM, Szymanski W, Feringa BL. Photocontrol of Antibacterial Activity: Shifting from UV to Red Light Activation. J Am Chem Soc 2017; 139:17979-17986. [PMID: 29136373 PMCID: PMC5730949 DOI: 10.1021/jacs.7b09281] [Citation(s) in RCA: 190] [Impact Index Per Article: 27.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Indexed: 12/24/2022]
Abstract
The field of photopharmacology aims to introduce smart drugs that, through the incorporation of molecular photoswitches, allow for the remote spatial and temporal control of bioactivity by light. This concept could be particularly beneficial in the treatment of bacterial infections, by reducing the systemic and environmental side effects of antibiotics. A major concern in the realization of such light-responsive drugs is the wavelength of the light that is applied. Studies on the photocontrol of biologically active agents mostly rely on UV light, which is cytotoxic and poorly suited for tissue penetration. In our efforts to develop photoswitchable antibiotics, we introduce here antibacterial agents whose activity can be controlled by visible light, while getting into the therapeutic window. For that purpose, a UV-light-responsive core structure based on diaminopyrimidines with suitable antibacterial properties was identified. Subsequent modification of an azobenzene photoswitch moiety led to structures that allowed us to control their activity against Escherichia coli in both directions with light in the visible region. For the first time, full in situ photocontrol of antibacterial activity in the presence of bacteria was attained with green and violet light. Most remarkably, one of the diaminopyrimidines revealed an at least 8-fold difference in activity before and after irradiation with red light at 652 nm, showcasing the effective "activation" of a biological agent otherwise inactive within the investigated concentration range, and doing so with red light in the therapeutic window.
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Affiliation(s)
- Michael Wegener
- Centre
for Systems Chemistry, Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747
AG Groningen, The Netherlands
| | - Mickel J. Hansen
- Centre
for Systems Chemistry, Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747
AG Groningen, The Netherlands
| | - Arnold J. M. Driessen
- Molecular
Microbiology, Groningen Biomolecular Sciences
and Biotechnology Institute, Nijenborgh 7 9747 AG Groningen, The Netherlands
| | - Wiktor Szymanski
- Centre
for Systems Chemistry, Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747
AG Groningen, The Netherlands
- Department
of Radiology, University of Groningen, University
Medical Centre Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - Ben L. Feringa
- Centre
for Systems Chemistry, Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747
AG Groningen, The Netherlands
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10
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1,3,5-triazaspiro[5.5]undeca-2,4-dienes as selective Mycobacterium tuberculosis dihydrofolate reductase inhibitors with potent whole cell activity. Eur J Med Chem 2017; 144:262-276. [PMID: 29274493 DOI: 10.1016/j.ejmech.2017.12.017] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 11/17/2017] [Accepted: 12/05/2017] [Indexed: 11/23/2022]
Abstract
The emergence of multi- and extensively-drug resistant tubercular (MDR- and XDR-TB) strains of mycobacteria has limited the use of existing therapies, therefore new drugs are needed. Dihydrofolate reductase (DHFR) has recently attracted much attention as a target for the development of anti-TB agents. This study aimed to develop selective M. tuberculosis DHFR inhibitors using rationale scaffolding design and synthesis, phenotype-oriented screening, enzymatic inhibitory study, whole cell on-target validation, molecular modeling, and in vitro DMPK determination to derive new anti-TB agents. 2,4-diamino-1-phenyl-1,3,5-triazaspiro[5.5]undeca-2,4-dienes 20b and 20c were identified as selective M. tuberculosis DHFR inhibitors, showing promising antimycobacterial activities (MIC50: 0.01 μM and MIC90: 0.025 μM on M. tuberculosis H37Rv). This study provided compelling evidence that compound 20b and 20c exerted whole cell antimycobacterial activity through DHFR inhibition. In addition, these two compounds exhibited low cytotoxicity and low hemolytic activity. The in vitro DMPK and physiochemical properties suggested their potential in vivo efficacy.
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11
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Alotaibi M, Reyes BD, Le T, Luong P, Valafar F, Metzger RP, Fogel GB, Hecht D. Structure-based analysis of Bacilli and plasmid dihydrofolate reductase evolution. J Mol Graph Model 2017; 71:135-153. [PMID: 27914300 PMCID: PMC5203806 DOI: 10.1016/j.jmgm.2016.10.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 10/04/2016] [Accepted: 10/10/2016] [Indexed: 12/15/2022]
Abstract
Dihydrofolate reductase (DHFR), a key enzyme in tetrahydrofolate-mediated biosynthetic pathways, has a structural motif known to be highly conserved over a wide range of organisms. Given its critical role in purine and amino acid synthesis, DHFR is a well established therapeutic target for treating a wide range of prokaryotic and eukaryotic infections as well as certain types of cancer. Here we present a structural-based computer analysis of bacterial (Bacilli) and plasmid DHFR evolution. We generated a structure-based sequence alignment using 7 wild-type DHFR x-ray crystal structures obtained from the RCSB Protein Data Bank and 350 chromosomal and plasmid homology models we generated from sequences obtained from the NCBI Protein Database. We used these alignments to compare active site and non-active site conservation in terms of amino acid residues, secondary structure and amino acid residue class. With respect to amino acid sequences and residue classes, active-site positions in both plasmid and chromosomal DHFR are significantly more conserved than non-active site positions. Secondary structure conservation was similar for active site and non-active site positions. Plasmid-encoded DHFR proteins have greater degree of sequence and residue class conservation, particularly in sequence positions associated with a network of concerted protein motions, than chromosomal-encoded DHFR proteins. These structure-based were used to build DHFR specific phylogenetic trees from which evidence for horizontal gene transfer was identified.
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Affiliation(s)
- Mona Alotaibi
- Department of Chemistry and Biochemistry, San Diego State University, San Diego, CA 92182-1030, USA; King Saud University, P.O. Box 245714, Riyadh 11312, Saudi Arabia.
| | - Ben Delos Reyes
- Department of Chemistry and Biochemistry, San Diego State University, San Diego, CA 92182-1030, USA
| | - Tin Le
- Department of Chemistry and Biochemistry, San Diego State University, San Diego, CA 92182-1030, USA
| | - Phuong Luong
- Department of Chemistry and Biochemistry, San Diego State University, San Diego, CA 92182-1030, USA
| | - Faramarz Valafar
- Bioinformatics and Medical Informatics Research Center, San Diego State University, San Diego, CA 92182-7720, USA.
| | - Robert P Metzger
- Department of Chemistry and Biochemistry, San Diego State University, San Diego, CA 92182-1030, USA.
| | - Gary B Fogel
- Natural Selection, Inc., 6480 Weathers Place, Suite 350, San Diego, CA 92121, USA.
| | - David Hecht
- Department of Chemistry and Biochemistry, San Diego State University, San Diego, CA 92182-1030, USA; Department of Chemistry, Southwestern College, 900 Otay Lakes Rd., Chula Vista, CA 91910, USA.
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12
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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: 1.5] [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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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: 3.5] [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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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: 18] [Impact Index Per Article: 2.3] [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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Abstract
The practice of medicine was profoundly transformed by the introduction of the antibiotics (compounds isolated from Nature) and the antibacterials (compounds prepared by synthesis) for the control of bacterial infection. As a result of the extraordinary success of these compounds over decades of time, a timeless biological activity for these compounds has been presumed. This presumption is no longer. The inexorable acquisition of resistance mechanisms by bacteria is retransforming medical practice. Credible answers to this dilemma are far better recognized than they are being implemented. In this perspective we examine (and in key respects, reiterate) the chemical and biological strategies being used to address the challenge of bacterial resistance.
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Affiliation(s)
- Jed F. Fisher
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame IN 46556–5670, USA
| | - Shahriar Mobashery
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame IN 46556–5670, USA
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16
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Guo Y, Ji SZ, Chen C, Liu HW, Zhao JH, Zheng YL, Ji YF. A ligand-free, powerful, and practical method for methoxylation of unactivated aryl bromides by use of the CuCl/HCOOMe/MeONa/MeOH system. RESEARCH ON CHEMICAL INTERMEDIATES 2015. [DOI: 10.1007/s11164-014-1917-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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17
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Carey PR, Heidari-Torkabadi H. New techniques in antibiotic discovery and resistance: Raman spectroscopy. Ann N Y Acad Sci 2015; 1354:67-81. [PMID: 26275225 DOI: 10.1111/nyas.12847] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Revised: 06/15/2015] [Accepted: 06/18/2015] [Indexed: 11/29/2022]
Abstract
Raman spectroscopy can play a role in both antibiotic discovery and understanding the molecular basis of resistance. A major challenge in drug development is to measure the population of the drug molecules inside a cell line and to follow the chemistry of their reactions with intracellular targets. Recently, a protocol based on Raman microscopy has been developed that achieves these goals. Drug candidates are soaked into live bacterial cells and subsequently the cells are frozen and freeze-dried. The samples yield exemplary (nonresonance) Raman data that provide a measure of the number of drug molecules within each cell, as well as details of drug-target interactions. Results are discussed for two classes of compounds inhibiting either β-lactamase or dihydrofolate reductase enzymes in a number of Gram-positive or Gram-negative cell lines. The advantages of the present protocol are that it does not use labels and it can measure the kinetics of cell-compound uptake on the time scale of minutes. Spectroscopic interpretation is supported by in vitro Raman experiments. Studying drug-target interactions in aqueous solution and in single crystals can provide molecular level insights into drug-target interactions, which, in turn, provide the underpinnings of our understanding of data from bacterial cells. Thus, the applicability of X-ray crystallographic-derived data to in-cell chemistry can be tested.
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Affiliation(s)
- Paul R Carey
- Department of Biochemistry.,Department of Chemistry, Case Western Reserve University, Cleveland, Ohio
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18
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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: 25] [Impact Index Per Article: 2.8] [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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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: 2.3] [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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Abstract
INTRODUCTION The folate biosynthetic pathway, responsible for the de novo synthesis of thymidine and other key cellular components, is essential in all life forms and is especially critical in rapidly proliferating cells. As such, druggable targets along this pathway offer opportunities to impact many disease states such as cancer, infectious disease and autoimmune disease. In this article, recent progress on the development of antifolate compounds is reviewed. AREAS COVERED The evaluation of the patent literature during the period 2010 - 2013 focused on any compounds inhibiting recognized targets on the folate biosynthetic pathway. EXPERT OPINION The folate pathway constitutes a well-validated and well-characterized set of targets; this pathway continues to elicit considerable enthusiasm for new drug discovery from both academic and industrial pharmaceutical research groups. Within the pathway, the enzymes dihydrofolate reductase and thymidylate synthase persist as the most attractive targets for new drug discovery for the treatment of cancer and infectious disease. Importantly, new potential targets for antifolates such as those on the purine biosynthetic pathway have been recently explored. The use of structure-based drug design is a major aspect in modern approaches to these drug targets.
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Affiliation(s)
- Amy C Anderson
- University of Connecticut, Department of Pharmaceutical Sciences , 69 N. Eagleville Road, Storrs, CT 06269 , USA
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