1
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Reens AL, Crooks AL, Su CC, Nagy TA, Reens DL, Podoll JD, Edwards ME, Yu EW, Detweiler CS. A cell-based infection assay identifies efflux pump modulators that reduce bacterial intracellular load. PLoS Pathog 2018; 14:e1007115. [PMID: 29879224 PMCID: PMC6007937 DOI: 10.1371/journal.ppat.1007115] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 06/19/2018] [Accepted: 05/21/2018] [Indexed: 12/20/2022] Open
Abstract
Bacterial efflux pumps transport small molecules from the cytoplasm or periplasm outside the cell. Efflux pump activity is typically increased in multi-drug resistant (MDR) pathogens; chemicals that inhibit efflux pumps may have potential for antibiotic development. Using an in-cell screen, we identified three efflux pump modulators (EPMs) from a drug diversity library. The screening platform uses macrophages infected with the human Gram-negative pathogen Salmonella enterica (Salmonella) to identify small molecules that prevent bacterial replication or survival within the host environment. A secondary screen for hit compounds that increase the accumulation of an efflux pump substrate, Hoechst 33342, identified three small molecules with activity comparable to the known efflux pump inhibitor PAβN (Phe-Arg β-naphthylamide). The three putative EPMs demonstrated significant antibacterial activity against Salmonella within primary and cell culture macrophages and within a human epithelial cell line. Unlike traditional antibiotics, the three compounds did not inhibit bacterial growth in standard microbiological media. The three compounds prevented energy-dependent efflux pump activity in Salmonella and bound the AcrB subunit of the AcrAB-TolC efflux system with KDs in the micromolar range. Moreover, the EPMs display antibacterial synergy with antimicrobial peptides, a class of host innate immune defense molecules present in body fluids and cells. The EPMs also had synergistic activity with antibiotics exported by AcrAB-TolC in broth and in macrophages and inhibited efflux pump activity in MDR Gram-negative ESKAPE clinical isolates. Thus, an in-cell screening approach identified EPMs that synergize with innate immunity to kill bacteria and have potential for development as adjuvants to antibiotics.
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Affiliation(s)
- Abigail L. Reens
- Department of Molecular, Cellular, & Developmental Biology, University of Colorado Boulder, Boulder, CO, United States of America
| | - Amy L. Crooks
- Department of Molecular, Cellular, & Developmental Biology, University of Colorado Boulder, Boulder, CO, United States of America
| | - Chih-Chia Su
- Department of Pharmacology, Case Western Reserve, Cleveland OH, United States of America
| | - Toni A. Nagy
- Department of Molecular, Cellular, & Developmental Biology, University of Colorado Boulder, Boulder, CO, United States of America
| | - David L. Reens
- Department of Physics, University of Colorado Boulder, Boulder, CO, United States of America
- JILA, National Institutes of Standards and Technology and University of Colorado Boulder, Boulder, CO, United States of America
| | - Jessica D. Podoll
- Department of Molecular, Cellular, & Developmental Biology, University of Colorado Boulder, Boulder, CO, United States of America
| | - Madeline E. Edwards
- Department of Molecular, Cellular, & Developmental Biology, University of Colorado Boulder, Boulder, CO, United States of America
| | - Edward W. Yu
- Department of Pharmacology, Case Western Reserve, Cleveland OH, United States of America
| | - Corrella S. Detweiler
- Department of Molecular, Cellular, & Developmental Biology, University of Colorado Boulder, Boulder, CO, United States of America
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2
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Hajiebrahimi A, Ghasemi Y, Sakhteman A. FLIP: An assisting software in structure based drug design using fingerprint of protein-ligand interaction profiles. J Mol Graph Model 2017; 78:234-244. [PMID: 29121561 DOI: 10.1016/j.jmgm.2017.10.021] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 10/29/2017] [Accepted: 10/30/2017] [Indexed: 11/29/2022]
Abstract
With the growing number of labor-intensive data in the pharmaceutical industries and public domain for protein-ligand complexes, a significant challenge is still remaining in managing and leveraging this vast information. Here, a standalone application is presented for analysis, organization, and illustration of structural data and molecular interactions for exploiting 3D-structures into simple 1D fingerprints. The utility of the approach was shown in unraveling a feasible solution for post-processing of docking results in parallel with providing fruitful analysis for users in order to investigate molecular interactions. Remarkably, all interaction possibilities including (hydrogen bond, water-bridged, electrostatic, and hydrophobic as well as π- π and cation-π interactions) are supported both in the form of fingerprints and compelling reports. These investigations are mainly considered based on right orientation, location, and geometry of the interacting pairs rather than the acquisition of the energy terms. The reasonable efficiency of our application in different models was comparable to recent methods It is clearly presented that FLIP provides a faster way to generate usable fingerprints for ligand and protein binding modes. FLIP is free for academic use and is available at: http://zistrayan.com/development/download/flip/package.zip.
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Affiliation(s)
- Ali Hajiebrahimi
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran; Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.
| | - Younes Ghasemi
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran; Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.
| | - Amirhossein Sakhteman
- Department of Medicinal Chemistry, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran.
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3
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Wong LH, Sinha S, Bergeron JR, Mellor JC, Giaever G, Flaherty P, Nislow C. Reverse Chemical Genetics: Comprehensive Fitness Profiling Reveals the Spectrum of Drug Target Interactions. PLoS Genet 2016; 12:e1006275. [PMID: 27588687 PMCID: PMC5010250 DOI: 10.1371/journal.pgen.1006275] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 08/03/2016] [Indexed: 01/22/2023] Open
Abstract
The emergence and prevalence of drug resistance demands streamlined strategies to identify drug resistant variants in a fast, systematic and cost-effective way. Methods commonly used to understand and predict drug resistance rely on limited clinical studies from patients who are refractory to drugs or on laborious evolution experiments with poor coverage of the gene variants. Here, we report an integrative functional variomics methodology combining deep sequencing and a Bayesian statistical model to provide a comprehensive list of drug resistance alleles from complex variant populations. Dihydrofolate reductase, the target of methotrexate chemotherapy drug, was used as a model to identify functional mutant alleles correlated with methotrexate resistance. This systematic approach identified previously reported resistance mutations, as well as novel point mutations that were validated in vivo. Use of this systematic strategy as a routine diagnostics tool widens the scope of successful drug research and development. One of the most profound outcomes of fast, reliable genome sequencing is the ability to tailor drug therapy to an individual’s genotype. This ‘personalized’ or ‘precision medicine’ is the realization of a decades-long effort to maximize drug effect and limit unwanted side effects. An undesirable consequence of such targeted therapies, however, is the emergence of drug resistance. This outcome is the result of an evolutionary process where mutations in the drug target render the drug perturbation allow such mutant cells to proliferate. Because of the unbiased, and stochastic nature of the emergence of drug resistance, it is impossible to predict. We developed a test where hundreds of thousands of mutant cells are exposed to a drug simultaneously and those cells that modulate resistance survive. This method is innovative because it partners a high-throughput experimental protocol with a tailored statistical model to identify all mutations that modulate resistance. Finally, we used synthetic biology to re-create these mutations and demonstrate that they were, in fact, bona fide drug-resistant variants. These mutations were further extended and confirmed to also be resistant in the human orthologue. This combined biological-computational approach allows one to identify drug’s degree of resistance to both guide treatments and future drug discovery.
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Affiliation(s)
- Lai H. Wong
- Department of Pharmaceutical Sciences, University of British Columbia, Vancouver, Canada
| | - Sunita Sinha
- Department of Pharmaceutical Sciences, University of British Columbia, Vancouver, Canada
| | - Julien R. Bergeron
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
| | | | - Guri Giaever
- Department of Pharmaceutical Sciences, University of British Columbia, Vancouver, Canada
| | - Patrick Flaherty
- Department of Mathematics and Statistics, University of Massachusetts, Amherst, Massachusetts, United States of America
- * E-mail: (PF); (CN)
| | - Corey Nislow
- Department of Pharmaceutical Sciences, University of British Columbia, Vancouver, Canada
- * E-mail: (PF); (CN)
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4
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Bourne CR, Wakeham N, Webb N, Nammalwar B, Bunce RA, Berlin KD, Barrow WW. The structure and competitive substrate inhibition of dihydrofolate reductase from Enterococcus faecalis reveal restrictions to cofactor docking. Biochemistry 2014; 53:1228-38. [PMID: 24495113 PMCID: PMC3985486 DOI: 10.1021/bi401104t] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
![]()
We
are addressing bacterial resistance to antibiotics by repurposing
a well-established classic antimicrobial target, the dihydrofolate
reductase (DHFR) enzyme. In this work, we have focused on Enterococcus faecalis, a nosocomial pathogen that frequently
harbors antibiotic resistance determinants leading to complicated
and difficult-to-treat infections. An inhibitor series with a hydrophobic
dihydrophthalazine heterocycle was designed from the anti-folate trimethoprim.
We have examined the potency of this inhibitor series based on inhibition
of DHFR enzyme activity and bacterial growth, including in the presence
of the exogenous product analogue folinic acid. The resulting preferences
were rationalized using a cocrystal structure of the DHFR from this
organism with a propyl-bearing series member (RAB-propyl). In a companion
apo structure, we identify four buried waters that act as placeholders
for a conserved hydrogen-bonding network to the substrate and indicate
an important role in protein stability during catalytic cycling. In
these structures, the nicotinamide of the nicotinamide adenine dinucleotide
phosphate cofactor is visualized outside of its binding pocket, which
is exacerbated by RAB-propyl binding. Finally, homology models of
the TMPR sequences dfrK and dfrF were constructed. While the dfrK-encoded protein
shows clear sequence changes that would be detrimental to inhibitor
binding, the dfrF-encoded protein model suggests
the protein would be relatively unstable. These data suggest a utility
for anti-DHFR compounds for treating infections arising from E. faecalis. They also highlight a role for water in stabilizing
the DHFR substrate pocket and for competitive substrate inhibitors
that may gain advantages in potency by the perturbation of cofactor
dynamics.
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Affiliation(s)
- Christina R Bourne
- Department of Veterinary Pathobiology, Oklahoma State University , Stillwater, Oklahoma 74078, United States
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5
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Then RL. Antimicrobial Dihydrofolate Reductase Inhibitors - Achievements and Future Options: Review. J Chemother 2013; 16:3-12. [PMID: 15077993 DOI: 10.1179/joc.2004.16.1.3] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
Abstract
Despite all progress made in the fight against infections caused by bacteria, fungi, protozoa or viruses, there is a need for more and new active agents. Intensive efforts are currently directed against many new and attractive targets, and are hoped to result in new useful agents. The opportunities offered by some known and validated targets are, however, by far not exhausted. Dihydrofolate reductase (DHFR, EC 1.5.1.3) attracted much attention over several decades, which yielded several useful agents. There are excellent chances for new drugs in this field, and they are thought to increase by limiting the spectrum of activity. Whereas trimethoprim seems to present the optimum which can be achieved for a broad spectrum antibacterial agent, specific agents could probably be designed for well defined groups or specific organisms, such as staphylococci among the bacteria, or for a number of parasites, such as Plasmodium falciparum, the fungus Pneumocystis carinii, and several protozoa, such as Trypanosoma, Toxoplasma, and others. This would even extend to herbicides or specific plant pathogens. Achievements and current efforts directed against new DHFR-inhibitors are reviewed, considering only the most recent literature.
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Affiliation(s)
- R L Then
- Morphochem AG, Microbiology, CH-4058 Basel, Switzerland.
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6
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Dihydrofolate reductase as a therapeutic target for infectious diseases: opportunities and challenges. Future Med Chem 2012; 4:1335-65. [DOI: 10.4155/fmc.12.68] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Infectious diseases caused by parasites continue to take a massive toll on human health in the poor regions of the world. Filling the anti-infective drug-discovery pipeline has never been as challenging as it is now. The organisms responsible for these diseases have interesting biology with many potential biochemical targets. Inhibition of metabolic enzymes has been established as an attractive strategy for anti-infectious drug development. In this field, dihydrofolate reductase (DHFR) is an important enzyme in nucleic and amino acid synthesis and an extensively studied drug target over the past 50 years. The challenges for novel DHFR inhibition-based chemotherapeutics for the treatment of infectious diseases are now focused on overcoming the resistance problem as well as cost–effectiveness. Each year, the large number of literature citations attest the continued popularity of DHFR. It becomes truly the ‘enzyme of choice for all seasons and almost all reasons’. Herein, we summarize the opportunities and challenges in developing novel lead based on this target.
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7
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Chao B, Tong XK, Tang W, Li DW, He PL, Garcia JM, Zeng LM, Gao AH, Yang L, Li J, Nan FJ, Jacobs M, Altmeyer R, Zuo JP, Hu YH. Discovery and optimization of 2,4-diaminoquinazoline derivatives as a new class of potent dengue virus inhibitors. J Med Chem 2012; 55:3135-43. [PMID: 22448770 DOI: 10.1021/jm2015952] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The results of a high-throughput screening assay using the DENV-2 replicon showed that the 2,4-diaminoquinazoline derivative 4a has a high dengue virus inhibitory activity (EC(50) = 0.15 μM). A series of 2,4-diaminoquinazoline derivatives based on 4a as a lead compound were synthesized and subjected to structure-antidengue activity relationship studies. Among the series of 2,4-diaminoquinazoline derivative probed, 4o was observed to display both the highest antiviral potency (EC(50) = 2.8 nM, SI > 1000) and an excellent pharmacokinetic profile.
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Affiliation(s)
- Bo Chao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
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8
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Paulsen JL, Bendel SD, Anderson AC. Crystal structures of Candida albicans dihydrofolate reductase bound to propargyl-linked antifolates reveal the flexibility of active site loop residues critical for ligand potency and selectivity. Chem Biol Drug Des 2011; 78:505-12. [PMID: 21726415 PMCID: PMC3171590 DOI: 10.1111/j.1747-0285.2011.01169.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Candida albicans and Candida glabrata cause fungal bloodstream infections that are associated with significant mortality. As part of an effort to develop potent and selective antifolates that target dihydrofolate reductase (DHFR) from Candida species, we report three ternary crystal structures of C. albicans DHFR (CaDHFR) bound to novel propargyl-linked analogs. Consistent with earlier modeling results, these structures show that hydrophobic pockets in the binding site may be exploited to increase ligand potency. The crystal structures also confirm that loop residues Thr 58- Phe 66, which flank the active site and influence ligand potency and selectivity, adopt multiple conformations. To aid the development of a dual Candida spp. inhibitor, three new crystal structures of C. glabrata DHFR (CgDHFR) bound to similar ligands as those bound in the ternary structures of CaDHFR are also reported here. Loop residues 58-66 in CgDHFR and human DHFR are 1 and 3 Å closer to the folate binding site, respectively, than loop residues in CaDHFR, suggesting that a properly size ligand could be a potent and selective dual inhibitor of CaDHFR and CgDHFR.
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Affiliation(s)
| | | | - Amy C. Anderson
- Corresponding author: Amy C. Anderson, Dept. of Pharmaceutical Sciences, University of Connecticut, 69 N. Eagleville Rd., Storrs, CT 06269, , phone: (860)486-6145, fax: (860)486-6857
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9
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Carroll MJ, Gromova AV, Miller KR, Tang H, Wang XS, Tripathy A, Singleton SF, Collins EJ, Lee AL. Direct detection of structurally resolved dynamics in a multiconformation receptor-ligand complex. J Am Chem Soc 2011; 133:6422-8. [PMID: 21469679 DOI: 10.1021/ja2005253] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Structure-based drug design relies on static protein structures despite significant evidence for the need to include protein dynamics as a serious consideration. In practice, dynamic motions are neglected because they are not understood well enough to model, a situation resulting from a lack of explicit experimental examples of dynamic receptor-ligand complexes. Here, we report high-resolution details of pronounced ~1 ms time scale motions of a receptor-small molecule complex using a combination of NMR and X-ray crystallography. Large conformational dynamics in Escherichia coli dihydrofolate reductase are driven by internal switching motions of the drug-like, nanomolar-affinity inhibitor. Carr-Purcell-Meiboom-Gill relaxation dispersion experiments and NOEs revealed the crystal structure to contain critical elements of the high energy protein-ligand conformation. The availability of accurate, structurally resolved dynamics in a protein-ligand complex should serve as a valuable benchmark for modeling dynamics in other receptor-ligand complexes and prediction of binding affinities.
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Affiliation(s)
- Mary J Carroll
- Division of Medicinal Chemistry and Natural Products, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
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10
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Paulsen JL, Liu J, Bolstad DB, Smith A, Priestley ND, Wright DL, Anderson AC. In vitro biological activity and structural analysis of 2,4-diamino-5-(2'-arylpropargyl)pyrimidine inhibitors of Candida albicans. Bioorg Med Chem 2009; 17:4866-72. [PMID: 19560363 PMCID: PMC2724765 DOI: 10.1016/j.bmc.2009.06.021] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2009] [Revised: 06/10/2009] [Accepted: 06/12/2009] [Indexed: 11/28/2022]
Abstract
In order to develop new antifungal agents effective against two species of Candida, we have designed a series of dihydrofolate reductase (DHFR) inhibitors. Here, we explore the structure-activity relationships of these inhibitors toward Candida albicans DHFR by evaluating enzyme inhibition, antifungal activity and toxicity to mammalian cells. Analysis of docked complexes of the enzyme and inhibitors yields the structural basis of relative potency. The meta-biphenyl series of this class exhibits the greatest enzyme inhibition, selectivity and antifungal activity.
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Affiliation(s)
- Janet L. Paulsen
- Dept. of Pharmaceutical Sciences, University of Connecticut, 69 N. Eagleville Rd., Storrs, CT 06269
| | - Jieying Liu
- Dept. of Pharmaceutical Sciences, University of Connecticut, 69 N. Eagleville Rd., Storrs, CT 06269
| | - David B. Bolstad
- Dept. of Pharmaceutical Sciences, University of Connecticut, 69 N. Eagleville Rd., Storrs, CT 06269
| | - Adrienne Smith
- Dept. of Chemistry, University of Montana, Missoula, MT 59812
| | | | - Dennis L. Wright
- Dept. of Pharmaceutical Sciences, University of Connecticut, 69 N. Eagleville Rd., Storrs, CT 06269
| | - Amy C. Anderson
- Dept. of Pharmaceutical Sciences, University of Connecticut, 69 N. Eagleville Rd., Storrs, CT 06269
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11
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Bourne CR, Bunce RA, Bourne PC, Berlin KD, Barrow EW, Barrow WW. Crystal structure of Bacillus anthracis dihydrofolate reductase with the dihydrophthalazine-based trimethoprim derivative RAB1 provides a structural explanation of potency and selectivity. Antimicrob Agents Chemother 2009; 53:3065-73. [PMID: 19364848 PMCID: PMC2704665 DOI: 10.1128/aac.01666-08] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2008] [Revised: 02/03/2009] [Accepted: 04/06/2009] [Indexed: 11/20/2022] Open
Abstract
Bacillus anthracis possesses an innate resistance to the antibiotic trimethoprim due to poor binding to dihydrofolate reductase (DHFR); currently, there are no commercial antibacterials that target this enzyme in B. anthracis. We have previously reported a series of dihydrophthalazine-based trimethoprim derivatives that are inhibitors for this target. In the present work, we have synthesized one compound (RAB1) displaying favorable 50% inhibitory concentration (54 nM) and MIC (< or =12.8 microg/ml) values. RAB1 was cocrystallized with the B. anthracis DHFR in the space group P2(1)2(1)2(1), and X-ray diffraction data were collected to a 2.3-A resolution. Binding of RAB1 causes a conformational change of the side chain of Arg58 and Met37 to accommodate the dihydrophthalazine moiety. Unlike the natural substrate or trimethoprim, the dihydrophthalazine group provides a large hydrophobic anchor that embeds within the DHFR active site and accounts for its selective inhibitory activity against B. anthracis.
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Affiliation(s)
- Christina R Bourne
- Department of Veterinary Pathobiology, Oklahoma State University, Stillwater, OK 74078, USA.
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12
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Liu J, Bolstad DB, Smith AE, Priestley ND, Wright DL, Anderson AC. Structure-guided development of efficacious antifungal agents targeting Candida glabrata dihydrofolate reductase. CHEMISTRY & BIOLOGY 2008; 15:990-6. [PMID: 18804036 PMCID: PMC2610858 DOI: 10.1016/j.chembiol.2008.07.013] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2008] [Revised: 07/03/2008] [Accepted: 07/23/2008] [Indexed: 01/07/2023]
Abstract
Candida glabrata is a lethal fungal pathogen resistant to many antifungal agents and has emerged as a critical target for drug discovery. Over the past several years, we have been developing a class of propargyl-linked antifolates as antimicrobials and hypothesized that these compounds could be effective inhibitors of dihydrofolate reductase (DHFR) from C. glabrata. We initially screened a small collection of these inhibitors and found modest levels of potency. Subsequently, we determined the crystal structure of C. glabrata DHFR bound to a representative inhibitor with data to 1.6 A resolution. Using this structure, we designed and synthesized second-generation inhibitors. These inhibitors bind the C. glabrata DHFR enzyme with subnanomolar potency, display greater than 2000-fold levels of selectivity over the human enzyme, and inhibit the growth of C. glabrata at levels observed with clinically employed therapeutics.
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Affiliation(s)
- Jieying Liu
- Dept. of Pharmaceutical Sciences, University of Connecticut, 69 N. Eagleville Rd., Storrs, CT 06269
| | - David B. Bolstad
- Dept. of Pharmaceutical Sciences, University of Connecticut, 69 N. Eagleville Rd., Storrs, CT 06269
| | - Adrienne E. Smith
- Promiliad Biopharma Inc., 950 West Fork Petty Creek Rd., Alberton, MT 59820
| | - Nigel D. Priestley
- Promiliad Biopharma Inc., 950 West Fork Petty Creek Rd., Alberton, MT 59820
| | - Dennis L. Wright
- Dept. of Pharmaceutical Sciences, University of Connecticut, 69 N. Eagleville Rd., Storrs, CT 06269,Corresponding authors: Amy C. Anderson and Dennis L. Wright ; ; phone: (860)486-6145 or (860)486-1556, fax: (860)486-6857
| | - Amy C. Anderson
- Dept. of Pharmaceutical Sciences, University of Connecticut, 69 N. Eagleville Rd., Storrs, CT 06269,Corresponding authors: Amy C. Anderson and Dennis L. Wright ; ; phone: (860)486-6145 or (860)486-1556, fax: (860)486-6857
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13
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Henrich S, Richter S, Wade RC. On the use of PIPSA to guide target-selective drug design. ChemMedChem 2008; 3:413-7. [PMID: 18061917 DOI: 10.1002/cmdc.200700154] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Stefan Henrich
- EML Research GmbH, Schloss-Wolfsbrunnenweg 33, 69118 Heidelberg, Germany.
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14
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Ramar S, Bag S, Tawari N, Degani M. 3-D-QSAR Analysis of 2-(Oxalylamino) benzoic acid Class of Protein Tyrosine Phosphatase 1B Inhibitors by CoMFA and Cerius2.GA. ACTA ACUST UNITED AC 2007. [DOI: 10.1002/qsar.200630090] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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15
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Hartshorn MJ, Verdonk ML, Chessari G, Brewerton SC, Mooij WTM, Mortenson PN, Murray CW. Diverse, high-quality test set for the validation of protein-ligand docking performance. J Med Chem 2007; 50:726-41. [PMID: 17300160 DOI: 10.1021/jm061277y] [Citation(s) in RCA: 447] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
A procedure for analyzing and classifying publicly available crystal structures has been developed. It has been used to identify high-resolution protein-ligand complexes that can be assessed by reconstructing the electron density for the ligand using the deposited structure factors. The complexes have been clustered according to the protein sequences, and clusters have been discarded if they do not represent proteins thought to be of direct interest to the pharmaceutical or agrochemical industry. Rules have been used to exclude complexes containing non-drug-like ligands. One complex from each cluster has been selected where a structure of sufficient quality was available. The final Astex diverse set contains 85 diverse, relevant protein-ligand complexes, which have been prepared in a format suitable for docking and are to be made freely available to the entire research community (http://www.ccdc.cam.ac.uk). The performance of the docking program GOLD against the new set is assessed using a variety of protocols. Relatively unbiased protocols give success rates of approximately 80% for redocking into native structures, but it is possible to get success rates of over 90% with some protocols.
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Affiliation(s)
- Michael J Hartshorn
- Astex Therapeutics, Ltd., 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
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16
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Bowman AL, Lerner MG, Carlson HA. Protein flexibility and species specificity in structure-based drug discovery: dihydrofolate reductase as a test system. J Am Chem Soc 2007; 129:3634-40. [PMID: 17335207 DOI: 10.1021/ja068256d] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In structure-based drug discovery, researchers would like to identify all possible scaffolds for a given target. However, techniques that push the boundaries of chemical space could lead to many false positives or inhibitors that lack specificity for the target. Is it possible to broadly identify the appropriate chemical space for the inhibitors and yet maintain target specificity? To address this question, we have turned to dihydrofolate reductase (DHFR), a well-studied metabolic enzyme of pharmacological relevance. We have extended our multiple protein structure (MPS) method for receptor-based pharmacophore models to use multiple X-ray crystallographic structures. Models were created for DHFR from human and Pneumocystis carinii. These models incorporate a fair degree of protein flexibility and are highly selective for known DHFR inhibitors over drug-like non-inhibitors. Despite sharing a highly conserved active site, the pharmacophore models reflect subtle differences between the human and P. carinii forms, which identify species-specific, high-affinity inhibitors. We also use structures of DHFR from Candida albicans as a counter example. The available crystal structures show little flexibility, and the resulting models give poorer performance in identifying species-specific inhibitors. Therapeutic success for this system may depend on achieving species specificity between the related human host and these key fungal targets. The MPS technique is a promising advance for structure-based drug discovery for DHFR and other proteins of biomedical interest.
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Affiliation(s)
- Anna L Bowman
- Department of Medicinal Chemistry and Biophysics Research Division, University of Michigan, Ann Arbor, Michigan 48109-1065, USA
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Kim KH. Outliers in SAR and QSAR: is unusual binding mode a possible source of outliers? J Comput Aided Mol Des 2007; 21:63-86. [PMID: 17334823 DOI: 10.1007/s10822-007-9106-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2006] [Accepted: 01/09/2007] [Indexed: 11/30/2022]
Abstract
A lead optimization is usually carried out by structure-activity relationship (SAR) and/or quantitative structure-activity relationship (QSAR) studies. One of the assumptions in SAR and QSAR studies is that similar analogs bind to the same binding site in a similar binding mode. One often observes that there are outliers, especially in QSAR. However, most QSAR studies are carried out focusing their attention to the development of QSAR and leave the outliers without much attention. We searched a number of ligand-bound X-ray crystal structures from the protein structure database to find evidences that could indicate a possible source of outliers in SAR or QSAR. Our results show that unusual binding mode could be a source of outliers.
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Affiliation(s)
- Ki Hwan Kim
- Hope Drug Discovery Research Laboratory, 260 Southgate Drive, Vernon Hills, IL 60061, USA.
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18
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Senkovich O, Bhatia V, Garg N, Chattopadhyay D. Lipophilic antifolate trimetrexate is a potent inhibitor of Trypanosoma cruzi: prospect for chemotherapy of Chagas' disease. Antimicrob Agents Chemother 2005; 49:3234-8. [PMID: 16048931 PMCID: PMC1196212 DOI: 10.1128/aac.49.8.3234-3238.2005] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Trypanosoma cruzi, a protozoan parasite, is the causative agent for Chagas' disease, which poses serious public health problem in Latin America. The two drugs available for the treatment of this disease are effective only against recent infections and are toxic. Dihydrofolate reductase (DHFR) has a proven track record as a drug target. The lipophilic antifolate trimetrexate (TMQ), which is an FDA-approved drug for the treatment of Pneumocystis carinii infection in AIDS patients, is a potent inhibitor of T. cruzi DHFR activity, with an inhibitory constant of 6.6 nM. The compound is also highly effective in killing T. cruzi parasites. The 50 and 90% lethal dose values against the trypomastigote are 19 and 36 nM, and the corresponding values for the amastigote form are 26 and 72 nM, respectively. However, as TMQ is also a good inhibitor of human DHFR, further improvement of the selectivity of this drug would be preferable. Identification of a novel antifolate selective against T. cruzi would open up new therapeutic avenues for treatment of Chagas' disease.
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Affiliation(s)
- Olga Senkovich
- University of Alabama at Birmingham, CBSE-250, 1025 18th Street South, Birmingham, AL 35294, USA
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19
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Bernacki K, Kalyanaraman C, Jacobson MP. Virtual Ligand Screening against Escherichia coli Dihydrofolate Reductase: Improving Docking Enrichment Using Physics-Based Methods. ACTA ACUST UNITED AC 2005; 10:675-81. [PMID: 16170049 DOI: 10.1177/1087057105281220] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Motivated by their participation in the McMaster Data-Mining and Docking Competition, the authors developed 2 new computational technologies and applied them to docking against Escherichia coli dihydrofolate reductase: a receptor preparation procedure that incorporates rotamer optimization of side chains and a physics-based rescoring procedure for estimating relative binding affinities of the protein-ligand complexes. Both methods use the same energy function, consisting of the all-atom OPLS-AA force field and a generalized Born solvent model, which treats the protein receptor and small-molecule ligands in a consistent manner. Thus, the energy function is similar to that used in more sophisticated approaches, such as free-energy perturbation and the molecular mechanics Poisson-Boltzmann/surface area, but sampling during the rescoring procedure is limited to simple energy minimization of the ligand. The use of a highly efficient minimization algorithm permitted the authors to apply this rescoring procedure to hundreds of thousands of protein-ligand complexes during the competition, using a modest Linux cluster. To test these methods, they used the 12 competitive inhibitors identified in the training set, plus methotrexate, as positive controls in enrichment studies with both the training and test sets, each containing 50,000 compounds. The key conclusion is that combining the receptor preparation and rescoring methods makes it possible to identify most of the positive controls within the top few tenths of a percent of the rank-ordered training and test set libraries.
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Affiliation(s)
- Katarzyna Bernacki
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA
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20
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Brenk R, Irwin JJ, Shoichet BK. Here be dragons: docking and screening in an uncharted region of chemical space. ACTA ACUST UNITED AC 2005; 10:667-74. [PMID: 16170052 PMCID: PMC1532927 DOI: 10.1177/1087057105281047] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
To compare virtual and high-throughput screening in an unbiased way, 50,000 compounds were docked into the 3-dimensional structure of dihydrofolate reductase prospectively, and the results were compared to a subsequent experimental screening of the same library. Undertaking these calculations demanded careful database curation and control calculations with annotated inhibitors. These ultimately led to a ranked list of more likely and less likely inhibitors and to the prediction that relatively few inhibitors would be found in the empirical screen. The latter prediction turned out to be correct, with arguably no validated inhibitors found experimentally. Subsequent retesting of high-scoring docked molecules may have found 2 true inhibitors, although this remains uncertain due to experimental ambiguities. The implications of this study for screening campaigns are considered.
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Affiliation(s)
- Ruth Brenk
- University of California, San Francisco, Department of Pharmaceutical Chemistry, 1700 4th Street, San Francisco, CA 94143-2550, USA
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21
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Affiliation(s)
- Ivan M Kompis
- ARPIDA Ltd, Dammstrasse 36, 4142 Münchenstein, Switzerland
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22
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Kontoyianni M, Sokol GS, McClellan LM. Evaluation of library ranking efficacy in virtual screening. J Comput Chem 2005; 26:11-22. [PMID: 15526325 DOI: 10.1002/jcc.20141] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
We present the results of a comprehensive study in which we explored how the docking procedure affects the performance of a virtual screening approach. We used four docking engines and applied 10 scoring functions to the top-ranked docking solutions of seeded databases against six target proteins. The scores of the experimental poses were placed within the total set to assess whether the scoring function required an accurate pose to provide the appropriate rank for the seeded compounds. This method allows a direct comparison of library ranking efficacy. Our results indicate that the LigandFit/Ligscore1 and LigandFit/GOLD docking/scoring combinations, and to a lesser degree FlexX/FlexX, Glide/Ligscore1, DOCK/PMF (Tripos implementation), LigandFit1/Ligscore2 and LigandFit/PMF (Tripos implementation) were able to retrieve the highest number of actives at a 10% fraction of the database when all targets were looked upon collectively. We also show that the scoring functions rank the observed binding modes higher than the inaccurate poses provided that the experimental poses are available. This finding stresses the discriminatory ability of the scoring algorithms, when better poses are available, and suggests that the number of false positives can be lowered with conformers closer to bioactive ones.
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Affiliation(s)
- Maria Kontoyianni
- Johnson & Johnson Pharmaceutical Research & Development, L.L.C., Computer Assisted Drug Discovery, Welsh and McKean Roads, P.O. Box 776, Spring House, Pennsylvania 19477, USA.
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23
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Shi R, Lin SX. Cofactor Hydrogen Bonding onto the Protein Main Chain Is Conserved in the Short Chain Dehydrogenase/Reductase Family and Contributes to Nicotinamide Orientation. J Biol Chem 2004; 279:16778-85. [PMID: 14966133 DOI: 10.1074/jbc.m313156200] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Human estrogenic 17beta-hydroxysteroid dehydrogenase (17beta-HSD1), a member of the short chain dehydrogenase/reductase (SDR) family, is responsible for the biosynthesis of all active estrogens. The crystal structures of two C19-steroid ternary complexes (17beta-HSD1-androstanedione-NADP and 17beta-HSD1-androstenedione-NADP) reveal the critical role of Leu149 in regulating the substrate specificity and provide novel insight into the different fates of a conserved glutamate residue in the estrogen-specific proteins upon the binding of the keto and hydroxyl groups of steroids. The whole NADP molecule can be unambiguously defined in the NADP binary complex, whereas both ternary complexes show that the nicotinamide moiety of NADP cannot be located in the density maps. In both ternary complexes, the expected position of carboxamide oxygen of NADP is occupied by a water molecule, which makes a bifurcated hydrogen bond with the O3 of C19-steroid and the main chain nitrogen of Val188. These results demonstrate that the hydrogen bonding interaction between the main chain amide group and the carboxamide group of NAD(P)(H) plays an important role in anchoring the nicotinamide ring to the enzyme. This finding is substantiated by structural analyses of all 33 NAD(P)(H) complexes of different SDR proteins, because 29 structures of 33 show this interaction. This common feature reveals a general mechanism among the SDR family, providing a rational basis for inhibitor design against biologically relevant SDR targets.
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Affiliation(s)
- Rong Shi
- Oncology and Molecular Endocrinology Research Center, Laval University Medical Center (CHUQ) and Laval University, Quebec G1V 4G2, Canada
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Zolli-Juran M, Cechetto JD, Hartlen R, Daigle DM, Brown ED. High throughput screening identifies novel inhibitors of Escherichia coli dihydrofolate reductase that are competitive with dihydrofolate. Bioorg Med Chem Lett 2003; 13:2493-6. [PMID: 12852950 DOI: 10.1016/s0960-894x(03)00480-3] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
This communication describes the high-throughput screen of a diverse library of 50,000 small molecules against Escherichia coli dihydrofolate reductase to detect inhibitors. Sixty-two compounds were identified as having significant inhibitory activity against the enzyme. Secondary screening of these revealed twelve molecules that were competitive with dihydrofolate, nine of which have not been previously characterized as inhibitors of dihydrofolate reductase. These novel molecules ranged in potency (K(i)) from 26 nM to 11 microM and may represent fresh starting points for new small molecule therapeutics directed against dihydrofolate reductase.
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Affiliation(s)
- Michela Zolli-Juran
- McMaster HTS Lab, Department of Biochemistry, McMaster University, Hamilton, ON, Canada L8N 3Z5
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Bottoms CA, Smith PE, Tanner JJ. A structurally conserved water molecule in Rossmann dinucleotide-binding domains. Protein Sci 2002; 11:2125-37. [PMID: 12192068 PMCID: PMC2373605 DOI: 10.1110/ps.0213502] [Citation(s) in RCA: 108] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
A computational comparison of 102 high-resolution (</=1.90 A) enzyme-dinucleotide (NAD, NADP, FAD) complexes was performed to investigate the role of solvent in dinucleotide recognition by Rossmann fold domains. The typical binding site contains about 9-12 water molecules, and about 30% of the hydrogen bonds between the protein and the dinucleotide are water mediated. Detailed inspection of the structures reveals a structurally conserved water molecule bridging dinucleotides with the well-known glycine-rich phosphate-binding loop. This water molecule displays a conserved hydrogen-bonding pattern. It forms hydrogen bonds to the dinucleotide pyrophosphate, two of the three conserved glycine residues of the phosphate-binding loop, and a residue at the C-terminus of strand four of the Rossmann fold. The conserved water molecule is also present in high-resolution structures of apo enzymes. However, the water molecule is not present in structures displaying significant deviations from the classic Rossmann fold motif, such as having nonstandard topology, containing a very short phosphate-binding loop, or having alpha-helix "A" oriented perpendicular to the beta-sheet. Thus, the conserved water molecule appears to be an inherent structural feature of the classic Rossmann dinucleotide-binding domain.
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26
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Current awareness on yeast. Yeast 2002; 19:91-8. [PMID: 11754486 DOI: 10.1002/yea.819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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