1
|
Approaches to the Structure-Based Design of Antivirulence Drugs: Therapeutics for the Post-Antibiotic Era. Molecules 2019; 24:molecules24030378. [PMID: 30678155 PMCID: PMC6384752 DOI: 10.3390/molecules24030378] [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: 12/22/2018] [Revised: 01/14/2019] [Accepted: 01/18/2019] [Indexed: 01/02/2023] Open
Abstract
The alarming rise of multidrug-resistant bacterial strains, coupled with decades of stagnation in the field of antibiotic development, necessitates exploration of new therapeutic approaches to treat bacterial infections. Targeting bacterial virulence is an attractive alternative to traditional antibiotics in that this approach disarms pathogens that cause human diseases, without placing immediate selective pressure on the target bacterium or harming commensal species. The growing number of validated virulence protein targets for which structural information has been obtained, along with advances in computational power and screening algorithms, make the rational design of antivirulence drugs a promising avenue to explore. Here, we review the principles of structure-based drug design and the exciting opportunities this technique presents for antivirulence drug discovery.
Collapse
|
2
|
Gazi MA, Kibria MG, Mahfuz M, Islam MR, Ghosh P, Afsar MNA, Khan MA, Ahmed T. Functional, structural and epitopic prediction of hypothetical proteins of Mycobacterium tuberculosis H37Rv: An in silico approach for prioritizing the targets. Gene 2016; 591:442-55. [PMID: 27374154 DOI: 10.1016/j.gene.2016.06.057] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Revised: 04/27/2016] [Accepted: 06/28/2016] [Indexed: 01/11/2023]
Abstract
The global control of tuberculosis (TB) remains a great challenge from the standpoint of diagnosis, detection of drug resistance, and treatment. Major serodiagnostic limitations include low sensitivity and high cost in detecting TB. On the other hand, treatment measures are often hindered by low efficacies of commonly used drugs and resistance developed by the bacteria. Hence, there is a need to look into newer diagnostic and therapeutic targets. The proteome information available suggests that among the 3906 proteins in Mycobacterium tuberculosis H37Rv, about quarter remain classified as hypothetical uncharacterized set. This study involves a combination of a number of bioinformatics tools to analyze those hypothetical proteins (HPs). An entire set of 999 proteins was primarily screened for protein sequences having conserved domains with high confidence using a combination of the latest versions of protein family databases. Subsequently, 98 of such potential target proteins were extensively analyzed by means of physicochemical characteristics, protein-protein interaction, sub-cellular localization, structural similarity and functional classification. Next, we predicted antigenic proteins from the entire set and identified B and T cell epitopes of these proteins in M. tuberculosis H37Rv. We predicted the function of these HPs belong to various classes of proteins such as enzymes, transporters, receptors, structural proteins, transcription regulators and other proteins. However, the structural similarity prediction of the annotated proteins substantiated the functional classification of those proteins. Consequently, based on higher antigenicity score and sub-cellular localization, we choose two (NP_216420.1, NP_216903.1) of the antigenic proteins to exemplify B and T cell epitope prediction approach. Finally we found 15 epitopes those located partially or fully in the linear epitope region. We found 21 conformational epitopes by using Ellipro server as well. In silico methodology used in this study and the data thus generated for HPs of M. tuberculosis H37Rv may facilitate swift experimental identification of potential serodiagnostic and therapeutic targets for treatment and control.
Collapse
Affiliation(s)
- Md Amran Gazi
- Nutrition and Clinical Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Bangladesh.
| | - Mohammad Golam Kibria
- Parasitology Laboratory, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Bangladesh.
| | - Mustafa Mahfuz
- Nutrition and Clinical Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Bangladesh.
| | - Md Rezaul Islam
- International Max Planck Research School, Grisebachstraße 5, 37077 Göttingen, Germany.
| | - Prakash Ghosh
- Parasitology Laboratory, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Bangladesh.
| | - Md Nure Alam Afsar
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Bangladesh.
| | - Md Arif Khan
- Bio-Bio-1 Research Foundation, Sangskriti Bikash Kendra Bhaban, 1/E/1, Poribag, Dhaka 1000, Bangladesh.
| | - Tahmeed Ahmed
- Nutrition and Clinical Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Bangladesh.
| |
Collapse
|
3
|
Design, synthesis and mode of action of novel 2-(4-aminophenyl)benzothiazole derivatives bearing semicarbazone and thiosemicarbazone moiety as potent antimicrobial agents. Med Chem Res 2015. [DOI: 10.1007/s00044-015-1479-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
|
4
|
Malty RH, Jessulat M, Jin K, Musso G, Vlasblom J, Phanse S, Zhang Z, Babu M. Mitochondrial targets for pharmacological intervention in human disease. J Proteome Res 2014; 14:5-21. [PMID: 25367773 PMCID: PMC4286170 DOI: 10.1021/pr500813f] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
![]()
Over the past several years, mitochondrial
dysfunction has been
linked to an increasing number of human illnesses, making mitochondrial
proteins (MPs) an ever more appealing target for therapeutic intervention.
With 20% of the mitochondrial proteome (312 of an estimated 1500 MPs)
having known interactions with small molecules, MPs appear to be highly
targetable. Yet, despite these targeted proteins functioning in a
range of biological processes (including induction of apoptosis, calcium
homeostasis, and metabolism), very few of the compounds targeting
MPs find clinical use. Recent work has greatly expanded the number
of proteins known to localize to the mitochondria and has generated
a considerable increase in MP 3D structures available in public databases,
allowing experimental screening and in silico prediction of mitochondrial
drug targets on an unprecedented scale. Here, we summarize the current
literature on clinically active drugs that target MPs, with a focus
on how existing drug targets are distributed across biochemical pathways
and organelle substructures. Also, we examine current strategies for
mitochondrial drug discovery, focusing on genetic, proteomic, and
chemogenomic assays, and relevant model systems. As cell models and
screening techniques improve, MPs appear poised to emerge as relevant
targets for a wide range of complex human diseases, an eventuality
that can be expedited through systematic analysis of MP function.
Collapse
Affiliation(s)
- Ramy H Malty
- Department of Biochemistry, Research and Innovation Centre, University of Regina , Regina, Saskatchewan S4S 0A2, Canada
| | | | | | | | | | | | | | | |
Collapse
|
5
|
Nanoliter-scale protein crystallization and screening with a microfluidic droplet robot. Sci Rep 2014; 4:5046. [PMID: 24854085 PMCID: PMC5154416 DOI: 10.1038/srep05046] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Accepted: 05/02/2014] [Indexed: 01/09/2023] Open
Abstract
Large-scale screening of hundreds or even thousands of crystallization conditions while with low sample consumption is in urgent need, in current structural biology research. Here we describe a fully-automated droplet robot for nanoliter-scale crystallization screening that combines the advantages of both automated robotics technique for protein crystallization screening and the droplet-based microfluidic technique. A semi-contact dispensing method was developed to achieve flexible, programmable and reliable liquid-handling operations for nanoliter-scale protein crystallization experiments. We applied the droplet robot in large-scale screening of crystallization conditions of five soluble proteins and one membrane protein with 35–96 different crystallization conditions, study of volume effects on protein crystallization, and determination of phase diagrams of two proteins. The volume for each droplet reactor is only ca. 4–8 nL. The protein consumption significantly reduces 50–500 fold compared with current crystallization stations.
Collapse
|
6
|
Holler TP, Evdokimov AG, Narasimhan L. Structural biology approaches to antibacterial drug discovery. Expert Opin Drug Discov 2013; 2:1085-101. [PMID: 23484874 DOI: 10.1517/17460441.2.8.1085] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Antibacterial drug discovery has undertaken a major experiment in the 12 years since the first bacterial genomes were sequenced. Genome mining has identified hundreds of potential targets that have been distilled to a relatively small number of broad-spectrum targets ('low-hanging fruit') using the genetics tools of modern microbiology. Prosecuting these targets with high-throughput screens has led to a disappointingly small number of lead series that have mostly evaporated under closer scrutiny. In the meantime, multi-drug resistant pathogens are becoming a serious challenge in the clinic and the community and the number of pharmaceutical firms pursuing antibacterial discovery has declined. Filling the antibacterial development pipeline with novel chemical series is a significant challenge that will require the collaboration of scientists from many disciplines. Fortunately, advancements in the tools of structural biology and of in silico modeling are opening up new avenues of research that may help deal with the problems associated with discovering novel antibiotics.
Collapse
Affiliation(s)
- Tod P Holler
- Pfizer Global Research and Development, 2800 Plymouth Road, Ann Arbor, MI 48105, USA +1 734 622 5954 ; +1 734 622 2963 ; Tod.Holler@pfizer. com
| | | | | |
Collapse
|
7
|
Wei S, Wu W, Ji Z. Synthesis and antibacterial activities of 1-alkyl-3-methacryloyl (acryloyl) of benzimidazolone (thione) derivatives. Int J Mol Sci 2012; 13:4819-4830. [PMID: 22606011 PMCID: PMC3344247 DOI: 10.3390/ijms13044819] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2012] [Revised: 03/24/2012] [Accepted: 04/06/2012] [Indexed: 11/25/2022] Open
Abstract
A series of (28) 1-alkyl-3-methacryloyl (acryloyl)-benzimidazolone (thione) deriv-atives were synthesized. The structures of the new derivatives were confirmed by 1H-NMR, 13C-NMR and ESI-MS spectral analysis. The antibacterial activities of these compounds against several strains of bacteria, such as Bacillus cereus, Bacillus subtilis, Escherichia coli, Staphylococcus aureus and Pseudomonas aeruginosa, were evaluated by methods of paper disc-diffusion and broth mciro-dilution. Methacryloyl derivatives displayed higher antibacterial activities against tested bacterial strains than those of acryloyl derivatives in in vitro tests. A structure-activity relationship (SAR) study revealed that the presences of the methacryloyl moieties is essential to the antibacterial activities of the compounds.
Collapse
Affiliation(s)
| | | | - Zhiqin Ji
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +86-029-87092191; Fax: +86-029-87093987
| |
Collapse
|
8
|
Ceccarelli M, Vargiu AV, Ruggerone P. A kinetic Monte Carlo approach to investigate antibiotic translocation through bacterial porins. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2012; 24:104012. [PMID: 22353387 DOI: 10.1088/0953-8984/24/10/104012] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Many relevant biological processes take place on time scales not reachable by standard all-atom computer simulations. The translocation of antibiotics through non-specific bacterial porins is an example. Microscopic effects compete to determine penetration routes and, consequently, free energy barriers to be overcome. Since bacteria can develop resistance to treatment also by reducing their antibiotic permeability, to understand the microscopic aspects of antibiotic translocation is an important step to rationalize drug design. Here, to investigate the translocation we propose a complete numerical model that combines the diffusion-controlled rate theory and a kinetic Monte Carlo scheme based on both experimental data and microscopically well-founded all-atom simulations. Within our model, an antibiotic translocating through an hour-glass-shaped channel can be described as a molecule moving on a potential of mean force featuring several affinity sites and a high central barrier. The implications of our results for the characterization of antibiotic translocation at in vivo concentrations are discussed. The presence of an affinity site close to the mouth of the channel seems to favor the translocation of antibiotics, the affinity site acting as a particle reservoir. Possible connections between results and the appearance of mutations in clinical strains are also outlined.
Collapse
Affiliation(s)
- Matteo Ceccarelli
- Dipartimento di Fisica, Università degli Studi di Cagliari, Campus Monserrato, I-09042 Monserrato, Italy.
| | | | | |
Collapse
|
9
|
The C-terminal domain of the novel essential protein Gcp is critical for interaction with another essential protein YeaZ of Staphylococcus aureus. PLoS One 2011; 6:e20163. [PMID: 21625506 PMCID: PMC3098269 DOI: 10.1371/journal.pone.0020163] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2011] [Accepted: 04/15/2011] [Indexed: 11/19/2022] Open
Abstract
Previous studies have demonstrated that the novel protein Gcp is essential for the viability of various bacterial species including Staphylococcus aureus; however, the reason why it is required for bacterial growth remains unclear. In order to explore the potential mechanisms of this essentiality, we performed RT-PCR analysis and revealed that the gcp gene (sa1854) was co-transcribed with sa1855, yeaZ (sa1856) and sa1857 genes, indicating these genes are located in the same operon. Furthermore, we demonstrated that Gcp interacts with YeaZ using a yeast two-hybrid (Y2H) system and in vitro pull down assays. To characterize the Gcp-YeaZ interaction, we performed alanine scanning mutagenesis on the residues of C-terminal segment of Gcp. We found that the mutations of the C-terminal Y317-F322 region abolished the interaction of Gcp and YeaZ, and the mutations of the D324-N329 and S332-Y336 regions alleviated Gcp binding to YeaZ. More importantly, we demonstrated that these key regions of Gcp are also necessary for the bacterial survival since these mutated Gcp could not complement the depletion of endogenous Gcp. Taken together, our data suggest that the interaction of Gcp and YeaZ may contribute to the essentiality of Gcp for S. aureus survival. Our findings provide new insights into the potential mechanisms and biological functions of this novel essential protein.
Collapse
|
10
|
Simmons KJ, Chopra I, Fishwick CWG. Structure-based discovery of antibacterial drugs. Nat Rev Microbiol 2011; 8:501-10. [PMID: 20551974 DOI: 10.1038/nrmicro2349] [Citation(s) in RCA: 108] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The modern era of antibacterial chemotherapy began in the 1930s, and the next four decades saw the discovery of almost all the major classes of antibacterial agents that are currently in use. However, bacterial resistance to many of these drugs is becoming an increasing problem. As such, the discovery of drugs with novel modes of action will be vital to meet the threats created by the emergence of resistance. Success in discovering inhibitors using high-throughput screening of chemical libraries is rare. In this Review we explore the exciting opportunities for antibacterial-drug discovery arising from structure-based drug design.
Collapse
Affiliation(s)
- Katie J Simmons
- Antimicrobial Research Centre, University of Leeds, Leeds, UK
| | | | | |
Collapse
|
11
|
Min J, Zhang X, Wang L, Zou X, Zhang Q, He J. Mutational analysis of the interaction between a potential inhibitor luteolin and enoyl-ACP reductase (FabI) from Salmonella enterica. ACTA ACUST UNITED AC 2011. [DOI: 10.1016/j.molcatb.2010.10.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
12
|
Moy TI, Conery AL, Larkins-Ford J, Wu G, Mazitschek R, Casadei G, Lewis K, Carpenter AE, Ausubel FM. High-throughput screen for novel antimicrobials using a whole animal infection model. ACS Chem Biol 2009; 4:527-33. [PMID: 19572548 DOI: 10.1021/cb900084v] [Citation(s) in RCA: 145] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The nematode Caenorhabditis elegans is a unique whole animal model system for identifying small molecules with in vivo anti-infective properties. C. elegans can be infected with a broad range of human pathogens, including Enterococcus faecalis, an important human nosocomial pathogen. Here, we describe an automated, high-throughput screen of 37,200 compounds and natural product extracts for those that enhance survival of C. elegans infected with E. faecalis. Using a robot to dispense live, infected animals into 384-well plates and automated microscopy and image analysis, we identified 28 compounds and extracts not previously reported to have antimicrobial properties, including six structural classes that cure infected C. elegans animals but do not affect the growth of the pathogen in vitro, thus acting by a mechanism of action distinct from antibiotics currently in clinical use.
Collapse
Affiliation(s)
- Terence I. Moy
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115
- Department of Molecular Biology
- Center for Computational and Integrative Biology
| | - Annie L. Conery
- Department of Molecular Biology
- Center for Computational and Integrative Biology
| | - Jonah Larkins-Ford
- Department of Molecular Biology
- Center for Computational and Integrative Biology
| | - Gang Wu
- Department of Molecular Biology
- Center for Computational and Integrative Biology
| | - Ralph Mazitschek
- Center for Systems Biology, Massachusetts General Hospital, Boston, Massachusetts 02114
| | - Gabriele Casadei
- Department of Biology, Northeastern University, Boston, Massachusetts 02115
| | - Kim Lewis
- Department of Biology, Northeastern University, Boston, Massachusetts 02115
| | - Anne E. Carpenter
- Imaging Platform, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142
| | - Frederick M. Ausubel
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115
- Department of Molecular Biology
- Center for Computational and Integrative Biology
| |
Collapse
|
13
|
Ioerger TR, Sacchettini JC. Structural genomics approach to drug discovery for Mycobacterium tuberculosis. Curr Opin Microbiol 2009; 12:318-25. [PMID: 19481971 DOI: 10.1016/j.mib.2009.04.006] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2009] [Revised: 04/27/2009] [Accepted: 04/27/2009] [Indexed: 11/28/2022]
Abstract
Structural genomics has become a powerful tool for studying microorganisms at the molecular level. Advances in technology have enabled the assembly of high-throughput pipelines that can be used to automate X-ray crystal structure determination for many proteins in the genome of a target organism. In this paper, we describe the methods used in the Tuberculosis Structural Genomics Consortium (TBSGC), ranging from protein production and crystallization to diffraction data collection and processing. The TBSGC is unique in that it uses biological importance as a primary criterion for target selection. The over-riding goal is to solve structures of proteins that may be potential drug targets, in order to support drug discovery efforts. We describe the crystal structures of several significant proteins in the M. tuberculosis genome that have been solved by the TBSGC over the past few years. We conclude by describing the high-throughput screening facilities and virtual screening facilities we have implemented for identifying small-molecule inhibitors of proteins whose structures have been solved.
Collapse
Affiliation(s)
- Thomas R Ioerger
- Department of Computer Science and Engineering, Texas A&M University, USA
| | | |
Collapse
|
14
|
Wu D, Zhang L, Kong Y, Du J, Chen S, Chen J, Ding J, Jiang H, Shen X. Enzymatic characterization and crystal structure analysis of the D-alanine-D-alanine ligase from Helicobacter pylori. Proteins 2009; 72:1148-60. [PMID: 18320587 DOI: 10.1002/prot.22009] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
D-Alanine-D-alanine ligase is the second enzyme in the D-Ala branch of bacterial cell wall peptidoglycan assembly, and recognized as an attractive antimicrobial target. In this work, the D-Ala-D-Ala ligase of Helicobacter pylori strain SS1 (HpDdl) was kinetically and structurally characterized. The determined apparent K(m) of ATP (0.87 microM), the K(m1) (1.89 mM) and K(m2) of D-Ala (627 mM), and the k(cat) (115 min(-1)) at pH 8.0 indicated its relatively weak binding affinity and poor catalytic activity against the substrate D-Ala in vitro. However, by complementary assay of expressing HpDdl in Escherichia coli Delta ddl mutant, HpDdl was confirmed to be capable of D-Ala-D-Ala ligating in vivo. Through sequence alignment with other members of the D-Ala-D-X ligase superfamily, HpDdl keeps two conservatively substituted residues (Ile16 and Leu241) and two nonconserved residues (Leu308 and Tyr311) broadly located in the active region of the enzyme. Kinetic analyses against the corresponding HpDdl mutants (I16V, L241Y, L241F, L308T, and Y311S) suggested that these residues, especially Leu308 and Tyr311, might partly contribute to the unique catalytic properties of the enzyme. This was fairly proved by the crystal structure of HpDdl, which revealed that there is a 3(10)-helix (including residues from Gly306 to Leu312) near the D-Ala binding region in the C-terminal domain, where HpDdl has two sequence deletions compared with other homologs. Such 3(10)-helix may participate in D-Ala binding and conformational change of the enzyme. Our present work hopefully provides useful information for understanding the D-Ala-D-Ala ligase of Helicobacter pylori.
Collapse
Affiliation(s)
- Dalei Wu
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | | | | | | | | | | | | | | | | |
Collapse
|
15
|
Natural products in drug discovery: present status and perspectives. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2009; 655:13-27. [PMID: 20047031 DOI: 10.1007/978-1-4419-1132-2_2] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Natural products and their derivatives have been and continue to be rich sources for drug discovery. However, natural products are not drugs. They are produce in nature and through biological assays they are identified as leads, which become candidates for drug development. More than 60% of the drugs that are in the market derive from natural sources. During the last two decades, research aimed at exploiting natural products as a resource has seriously declined. This is in part due to the development of new technologies such as combinatorial chemistry, metagenomics and high-throughput screening. However, the new drug discovery approaches did not fulfilled the initial expectations. This has lead to a renewed interest in natural products, determined by the urgent need for new drugs, in particular to fight against infections caused by multi-resistant pathogens.
Collapse
|
16
|
Abstract
The continued increase in antibiotic resistance among bacterial pathogens, coupled with a decrease in infectious disease research among pharmaceutical companies, has escalated the need for novel and effective antibacterial chemotherapies. While current agents have emerged almost exclusively from whole-cell screening of natural products and small molecules that cause microbial death, recent advances in target identification and assay development have resulted in a flood of target-driven drug discovery methods. Whether genome-based methodologies will yield new classes of agents that conventional methods have been unable to is yet to be seen. At the end of the day, perhaps a synergy between old and new approaches will harvest the next generation of antibacterial treatments.
Collapse
|
17
|
Piedra D, Lois S, de la Cruz X. Preservation of protein clefts in comparative models. BMC STRUCTURAL BIOLOGY 2008; 8:2. [PMID: 18199319 PMCID: PMC2249585 DOI: 10.1186/1472-6807-8-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2007] [Accepted: 01/16/2008] [Indexed: 11/29/2022]
Abstract
BACKGROUND Comparative, or homology, modelling of protein structures is the most widely used prediction method when the target protein has homologues of known structure. Given that the quality of a model may vary greatly, several studies have been devoted to identifying the factors that influence modelling results. These studies usually consider the protein as a whole, and only a few provide a separate discussion of the behaviour of biologically relevant features of the protein. Given the value of the latter for many applications, here we extended previous work by analysing the preservation of native protein clefts in homology models. We chose to examine clefts because of their role in protein function/structure, as they are usually the locus of protein-protein interactions, host the enzymes' active site, or, in the case of protein domains, can also be the locus of domain-domain interactions that lead to the structure of the whole protein. RESULTS We studied how the largest cleft of a protein varies in comparative models. To this end, we analysed a set of 53507 homology models that cover the whole sequence identity range, with a special emphasis on medium and low similarities. More precisely we examined how cleft quality - measured using six complementary parameters related to both global shape and local atomic environment, depends on the sequence identity between target and template proteins. In addition to this general analysis, we also explored the impact of a number of factors on cleft quality, and found that the relationship between quality and sequence identity varies depending on cleft rank amongst the set of protein clefts (when ordered according to size), and number of aligned residues. CONCLUSION We have examined cleft quality in homology models at a range of seq.id. levels. Our results provide a detailed view of how quality is affected by distinct parameters and thus may help the user of comparative modelling to determine the final quality and applicability of his/her cleft models. In addition, the large variability in model quality that we observed within each sequence bin, with good models present even at low sequence identities (between 20% and 30%), indicates that properly developed identification methods could be used to recover good cleft models in this sequence range.
Collapse
Affiliation(s)
- David Piedra
- Institut de Recerca Biomèdica, C/Josep Samitier, 1-5, 08028 Barcelona, Spain
| | - Sergi Lois
- Institut de Recerca Biomèdica, C/Josep Samitier, 1-5, 08028 Barcelona, Spain
- Instituto de Biología Molecular de Barcelona, CID, Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, Spain
| | - Xavier de la Cruz
- Institut de Recerca Biomèdica, C/Josep Samitier, 1-5, 08028 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| |
Collapse
|
18
|
Abstract
Bacterial populations produce a small number of dormant persister cells that exhibit multidrug tolerance. All resistance mechanisms do essentially the same thing: prevent the antibiotic from hitting a target. By contrast, tolerance apparently works by shutting down the targets. Bactericidal antibiotics kill bacteria by corrupting their targets, rather than merely inhibiting them. Shutting down the targets then protects from killing. The number of persisters in a growing population of bacteria rises at mid-log and reaches a maximum of approximately 1% at stationary state. Similarly, slow-growing biofilms produce substantial numbers of persisters. The ability of a biofilm to limit the access of the immune system components, and the ability of persisters to sustain an antibiotic attack could then account for the recalcitrance of such infections in vivo and for their relapsing nature. Isolation of Escherichia coli persisters by lysing a population or by sorting GFP-expressing cells with diminished translation allowed to obtain a gene expression profile. The profile indicated downregulated biosynthetic pathways, consistent with their dormant nature, and indicated overexpression of toxin/antitoxin (TA) modules. Stochastic overexpression of toxins that inhibit essential functions such as translation may contribute to persister formation. Ectopic expression of RelE, MazF, and HipA toxins produced multidrug tolerant cells. Apart from TA modules, glpD and plsB were identified as potential persister genes by overexpression cloning of a genomic library and selection for antibiotic tolerance. Yeast Candida albicans forms recalcitrant biofilm infections that are tolerant to antibiotics, similarly to bacterial biofilms. C. albicans biofilms produce multidrug tolerant persisters that are not mutants, but rather phenotypic variants of the wild type. Unlike bacterial persisters, however, C. albicans persisters were only observed in a biofilm, but not in a planktonic stationary population. Identification of persister genes opens the way to a rational design of anti-biofilm therapy. Combination of a conventional antibiotic with a compound inhibiting persister formation or maintenance may produce an effective therapeutic. Other approaches to the problem include sterile-surface materials, prodrug antibiotics, and cyclical application of conventional antimicrobials.
Collapse
|
19
|
Park HS, Yoon YM, Jung SJ, Kim CM, Kim JM, Kwak JH. Antistaphylococcal activities of CG400549, a new bacterial enoyl-acyl carrier protein reductase (FabI) inhibitor. J Antimicrob Chemother 2007; 60:568-74. [PMID: 17606482 DOI: 10.1093/jac/dkm236] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES This study was performed to analyse in vitro and in vivo activities of CG400549, a new FabI inhibitor, against clinical isolates of staphylococci. The mode of action of CG400549 and resistance mechanism of Staphylococcus aureus against CG400549 were also investigated by genetic approaches. METHODS In vitro activity of CG400549 was evaluated by the 2-fold agar sdilution method as described by the CLSI, and compared with those of oxacillin, erythromycin, ciprofloxacin, sparfloxacin, moxifloxacin, gemifloxacin, vancomycin, linezolid and quinupristin-dalfopristin. In vivo activity of CG400549 was determined against systemic infections in mice. Time-kill curves of CG400549 were analysed at concentrations of 1 x , 2 x and 4 x MIC against S. aureus strains. RESULTS CG400549 had the lowest MICs among the test compounds against 238 clinical isolates of S. aureus (MIC90, 0.25 mg/L) and 51 clinical isolates of coagulase-negative staphylococci (MIC90, 1 mg/L). The activity of CG400549 was irrespective of whether the strains were methicillin-susceptible or -resistant. Furthermore, CG400549 was effective by oral or subcutaneous administration against systemic infections in mice. In a time-kill study, CG400549 at concentrations of 1 x MIC, 2 x MIC and 4 x MIC had a bacteriostatic activity during 24 h. A FabI-overexpressing S. aureus strain gave rise to an increase in the MIC of CG400549 compared with the parental strain, while the susceptibilities of the FabI-overexpressing S. aureus strain to the other antibacterial agents such as oxacillin, erythromycin and ciprofloxacin were not affected. This result showed that the mode of action of CG400549 was via inhibition of FabI, which is involved in biosynthesis of fatty acids in bacteria. Study of the resistance mechanism of S. aureus showed that CG400549-resistant mutants of S. aureus had an alteration in FabI at Phe-204 to Leu. CONCLUSIONS CG400549 had potent in vitro and in vivo activity against staphylococci, including methicillin-, ciprofloxacin- and multidrug-resistant staphylococci strains. This compound could be a good candidate for clinical development as a novel anti-MRSA drug.
Collapse
Affiliation(s)
- Hee Soo Park
- School of Life and Food Sciences, Handong Global University, Pohang 791-708, South Korea
| | | | | | | | | | | |
Collapse
|
20
|
Lerner CG, Hajduk PJ, Wagner R, Wagenaar FL, Woodall C, Gu YG, Searle XB, Florjancic AS, Zhang T, Clark RF, Cooper CS, Mack JC, Yu L, Cai M, Betz SF, Chovan LE, McCall JO, Black-Schaefer CL, Kakavas SJ, Schurdak ME, Comess KM, Walter KA, Edalji R, Dorwin SA, Smith RA, Hebert EJ, Harlan JE, Metzger RE, Merta PJ, Baranowski JL, Coen ML, Thornewell SJ, Shivakumar AG, Saiki AY, Soni N, Bui M, Balli DJ, Sanders WJ, Nilius AM, Holzman TF, Fesik SW, Beutel BA. From Bacterial Genomes to Novel Antibacterial Agents: Discovery, Characterization, and Antibacterial Activity of Compounds that Bind to HI0065 (YjeE) from Haemophilus influenzae. Chem Biol Drug Des 2007; 69:395-404. [PMID: 17581233 DOI: 10.1111/j.1747-0285.2007.00521.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
As part of a fully integrated and comprehensive strategy to discover novel antibacterial agents, NMR- and mass spectrometry-based affinity selection screens were performed to identify compounds that bind to protein targets uniquely found in bacteria and encoded by genes essential for microbial viability. A biphenyl acid lead series emerged from an NMR-based screen with the Haemophilus influenzae protein HI0065, a member of a family of probable ATP-binding proteins found exclusively in eubacteria. The structure-activity relationships developed around the NMR-derived biphenyl acid lead were consistent with on-target antibacterial activity as the Staphylococcus aureus antibacterial activity of the series correlated extremely well with binding affinity to HI0065, while the correlation of binding affinity with B-cell cytotoxicity was relatively poor. Although further studies are needed to conclusively establish the mode of action of the biphenyl series, these compounds represent novel leads that can serve as the basis for the development of novel antibacterial agents that appear to work via an unprecedented mechanism of action. Overall, these results support the genomics-driven hypothesis that targeting bacterial essential gene products that are not present in eukaryotic cells can identify novel antibacterial agents.
Collapse
Affiliation(s)
- Claude G Lerner
- Abbott Global Pharmaceutical Research and Development, Abbott Park, IL 60064-6098, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
21
|
Barker JJ. Antibacterial drug discovery and structure-based design. Drug Discov Today 2006; 11:391-404. [PMID: 16635801 DOI: 10.1016/j.drudis.2006.03.001] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2005] [Revised: 12/06/2005] [Accepted: 03/14/2006] [Indexed: 10/24/2022]
Abstract
Bacterial resistance continues to develop and pose a significant threat, both in hospitals and, more recently, in the community. A focus on other therapeutic areas by the larger pharmaceutical companies has left a shortfall in the pipeline of novel antibacterials. Recently, many new structures have been studied by structure-genomics initiatives, delivering a wealth of targets to consider. Using the tools of structure-based design, antibacterial discovery must exploit these targets to accelerate the process of drug discovery.
Collapse
Affiliation(s)
- John J Barker
- Evotec UK, 111 Milton Park, Abingdon, Oxfordshire, OX14 4RZ, UK.
| |
Collapse
|
22
|
Schmid MB. Crystallizing new approaches for antimicrobial drug discovery. Biochem Pharmacol 2006; 71:1048-56. [PMID: 16458857 DOI: 10.1016/j.bcp.2005.12.024] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2005] [Revised: 12/07/2005] [Accepted: 12/09/2005] [Indexed: 11/29/2022]
Abstract
Over the past decade, the sequences of microbial genomes have accumulated, changing the strategies for the discovery of novel anti-infective agents. Targets have become plentiful, yet new antimicrobial agents have been slow to emerge from this effort. In part, this reflects the long discovery and development times needed to bring new drugs to market. In addition, bottlenecks have been revealed in the antimicrobial drug discovery process at the steps of identifying good leads, and optimizing those leads into drug candidates. The fruit of structural genomics may provide opportunities to overcome these bottlenecks and fill the antimicrobial pipeline, by using the tools of structure guided drug discovery (SGDD).
Collapse
Affiliation(s)
- Molly B Schmid
- Keck Graduate Institute, 535 Watson Drive, Claremont, CA 91711, USA.
| |
Collapse
|
23
|
Abstract
Through understanding the intricacies of host-pathogen interactions, it is now possible to inhibit the growth of microbes, especially viruses, by targeting host-cell proteins and functions. This new antimicrobial strategy has proved effective in the laboratory and in the clinic, and it has great potential for the future.
Collapse
Affiliation(s)
- Paul Kellam
- Virus Genomics and Bioinformatics Group, Division of Infection and Immunity, University College London, London W1T 4JF, UK.
| |
Collapse
|
24
|
Pucci MJ. Use of genomics to select antibacterial targets. Biochem Pharmacol 2006; 71:1066-72. [PMID: 16412986 DOI: 10.1016/j.bcp.2005.12.004] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2005] [Revised: 11/29/2005] [Accepted: 12/06/2005] [Indexed: 01/08/2023]
Abstract
The problem of antibiotic resistance has eroded the usefulness of our arsenal of effective antibiotics. There is a need for new strategies to discover and develop new, effective drugs. The advent of the microbial genomics era has provided a wealth of information on a variety of microorganisms. This has allowed the identification and/or validation of a number of gene products that could serve as targets for the discovery of novel antibacterial agents. New genetic techniques and approaches have arisen in an attempt to exploit this newly available genomic data. Both random and targeted gene disruption efforts have proven effective in this process. Many of these methods would have been difficult to accomplish without DNA sequence and bioinformatics analyses. Several targets have been selected to further characterize and screen for inhibitors and one has yielded two clinical candidates.
Collapse
Affiliation(s)
- Michael J Pucci
- Achillion Pharmaceuticals, Inc., 300 George Street, New Haven, CT 06511, USA.
| |
Collapse
|
25
|
Mills SD. When will the genomics investment pay off for antibacterial discovery? Biochem Pharmacol 2006; 71:1096-102. [PMID: 16387281 DOI: 10.1016/j.bcp.2005.11.025] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2005] [Revised: 11/17/2005] [Accepted: 11/28/2005] [Indexed: 12/11/2022]
Abstract
Effective solutions to antibacterial resistance are among the key unmet medical needs driving the antibacterial industry. A major thrust in a number of companies is the development of agents with new modes of action in order to bypass the increasing emergence of antibacterial resistance. However, few antibacterials marketed in the last 30 years have novel modes of action. Most recently, genomics and target-based screening technologies have been emphasized as a means to facilitate this and expedite the antibacterial discovery process. And although no new antibacterials have yet been marketed as result of these technologies, genomics has delivered well-validated novel bacterial targets as well as a host of genetic approaches to support the antibacterial discovery process. Likewise, high throughput screening technologies have delivered the capacity to perform robust screenings of large compound collections to identify target inhibitors for lead generation. One of the principal challenges still facing antibacterial discovery is to become proficient at optimizing target inhibitors into broad-spectrum antibacterials with appropriate in vivo properties. Genomics-based technologies clearly have the potential for additional application throughout the discovery process especially in the areas of structural biology and safety assessment.
Collapse
Affiliation(s)
- Scott D Mills
- Infection Discovery, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, MA 02451 USA.
| |
Collapse
|
26
|
Dieckman LJ, Hanly WC, Collart ER. Strategies for high-throughput gene cloning and expression. GENETIC ENGINEERING 2006; 27:179-90. [PMID: 16382877 DOI: 10.1007/0-387-25856-6_10] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
High-throughput approaches for gene cloning and expression require the development of new, nonstandard tools for use by molecular biologists and biochemists. We have developed and implemented a series of methods that enable the production of expression constructs in 96-well plate format. A screening process is described that facilitates the identification of bacterial clones expressing soluble protein. Application of the solubility screen then provides a plate map that identifies the location of wells containing clones producing soluble proteins. A series of semi-automated methods can then be applied for validation of solubility and production of freezer stocks for the protein production group. This process provides an 80% success rate for the identification of clones producing soluble protein and results in a significant decrease in the level of effort required for the labor-intensive components of validation and preparation of freezer stocks. This process is customized for large-scale structural genomics programs that rely on the production of large amounts of soluble proteins for crystallization trials.
Collapse
Affiliation(s)
- L J Dieckman
- Biosciences Division, Argonne National Laboratory, Argonne, Illinois 60439, USA
| | | | | |
Collapse
|
27
|
Pucci MJ. Overview of antibacterial target selection. CURRENT PROTOCOLS IN PHARMACOLOGY 2006; Chapter 13:Unit13A.2. [PMID: 21953397 DOI: 10.1002/0471141755.ph13a02s31] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Affiliation(s)
- Michael J Pucci
- Achillion Pharmaceuticals, Inc., New Haven, Connecticut, USA
| |
Collapse
|
28
|
Abstract
Recent work shows that the inhibition of the SOS stress response in Escherichia coli reduces the development of resistance to the antibiotics ciprofloxacin and rifampicin. Recent work shows that the inhibition of the SOS stress response in Escherichia coli reduces the development of resistance to the antibiotics ciprofloxacin and rifampicin. This finding may help in the battle against the rise of resistance to antimicrobial drugs.
Collapse
Affiliation(s)
- Matthew B Avison
- Department of Cellular and Molecular Medicine, Bristol Centre for Antimicrobial Research and Evaluation, University of Bristol, School of Medical Sciences, University Walk, Bristol BS8 1TD, UK.
| |
Collapse
|
29
|
Bayley MJ, Gardiner EJ, Willett P, Artymiuk PJ. A fourier fingerprint-based method for protein surface representation. J Chem Inf Model 2005; 45:696-707. [PMID: 15921459 DOI: 10.1021/ci049647j] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A crucial enabling technology for structural genomics is the development of algorithms that can predict the putative function of novel protein structures: the proposed functions can subsequently be experimentally tested by functional studies. Testable assignments of function can be made if it is possible to attribute a putative, or indeed probable, function on the basis of the shapes of the binding sites on the surface of a protein structure. However the comparison of the surfaces of 3D protein structures is a computationally demanding task. Here we present four surface representations that can be used locally to describe the global shape of specifically bounded local region models. The most successful of these representations is obtained by a Fourier analysis of the distribution of surface curvature on concentric spheres around a surface point and summarizes a 24 A diameter spherically clipped region of protein surface by a fingerprint of 18 Fourier amplitude values. Searching experiments using these fingerprints on a set of 366 proteins demonstrate that this provides an effective and an efficient technique for the matching of protein surfaces.
Collapse
Affiliation(s)
- Martin J Bayley
- Krebs Institute for Biomolecular Research, Department of Information Studies, University of Sheffield, Western Bank, Sheffield S10 2TN, United Kingdom
| | | | | | | |
Collapse
|
30
|
|
31
|
Worthey EA, Myler PJ. Protozoan genomes: gene identification and annotation. Int J Parasitol 2005; 35:495-512. [PMID: 15826642 DOI: 10.1016/j.ijpara.2005.02.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2004] [Revised: 01/25/2005] [Accepted: 02/06/2005] [Indexed: 12/01/2022]
Abstract
The draft sequence of several complete protozoan genomes is now available and genome projects are ongoing for a number of other species. Different strategies are being implemented to identify and annotate protein coding and RNA genes in these genomes, as well as study their genomic architecture. Since the genomes vary greatly in size, GC-content, nucleotide composition, and degree of repetitiveness, genome structure is often a factor in choosing the methodology utilised for annotation. In addition, the approach taken is dictated, to a greater or lesser extent, by the particular reasons for carrying out genome-wide analyses and the level of funding available for projects. Nevertheless, these projects have provided a plethora of material that will aid in understanding the biology and evolution of these parasites, as well as identifying new targets that can be used to design urgently required drug treatments for the diseases they cause.
Collapse
Affiliation(s)
- E A Worthey
- Seattle Biomedical Research Institute, 307 Westlake Ave N., Seattle, WA 98109-2591, USA
| | | |
Collapse
|
32
|
Butler MS. Natural products to drugs: natural product derived compounds in clinical trials. Nat Prod Rep 2005; 22:162-95. [PMID: 15806196 DOI: 10.1039/b402985m] [Citation(s) in RCA: 337] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Natural product and natural product-derived compounds that are being evaluated in clinical trials or in registration (current 31 December 2004) have been reviewed. Natural product derived drugs launched in the United States of America, Europe and Japan since 1998 and new natural product templates discovered since 1990 are discussed.
Collapse
Affiliation(s)
- Mark S Butler
- MerLion Pharmaceuticals, 1 Science Park Road, The Capricorn #05-01, Singapore Science Park II, Singapore 117528.
| |
Collapse
|
33
|
Current Awareness on Comparative and Functional Genomics. Comp Funct Genomics 2005. [PMCID: PMC2448604 DOI: 10.1002/cfg.419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
|
34
|
Saunders J. Toxic mechanisms. Nat Rev Microbiol 2004. [DOI: 10.1038/nrmicro991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|