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Hoffman PS. Antibacterial Discovery: 21st Century Challenges. Antibiotics (Basel) 2020; 9:antibiotics9050213. [PMID: 32353943 PMCID: PMC7277910 DOI: 10.3390/antibiotics9050213] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 04/22/2020] [Accepted: 04/24/2020] [Indexed: 12/17/2022] Open
Abstract
It has been nearly 50 years since the golden age of antibiotic discovery (1945–1975) ended; yet, we still struggle to identify novel drug targets and to deliver new chemical classes of antibiotics to replace those rendered obsolete by drug resistance. Despite herculean efforts utilizing a wide range of antibiotic discovery platform strategies, including genomics, bioinformatics, systems biology and postgenomic approaches, success has been at best incremental. Obviously, finding new classes of antibiotics is really hard, so repeating the old strategies, while expecting different outcomes, seems to boarder on insanity. The key questions dealt with in this review include: (1) If mutation based drug resistance is the major challenge to any new antibiotic, is it possible to find drug targets and new chemical entities that can escape this outcome; (2) Is the number of novel chemical classes of antibacterials limited by the number of broad spectrum drug targets; and (3) If true, then should we focus efforts on subgroups of pathogens like Gram negative or positive bacteria only, anaerobic bacteria or other group where the range of common essential genes is likely greater?. This review also provides some examples of existing drug targets that appear to escape the specter of mutation based drug resistance, and provides examples of some intermediate spectrum strategies as well as modern molecular and genomic approaches likely to improve the odds of delivering 21st century medicines to combat multidrug resistant pathogens.
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Affiliation(s)
- Paul S Hoffman
- Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia, Charlottesville, VA 22908, USA
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Elshaffei IM, Gupta N, Wu CH, Wu DC, Hammad LN, Abo-Elmatty DM, Mesbah NM, Wu GY. Effects of short RNA structural analogues against hepatitis C virus genotypes 2, 3 and 4 in replicon cells. J Dig Dis 2015; 16:449-55. [PMID: 25873200 DOI: 10.1111/1751-2980.12250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
OBJECTIVE To determine whether computer-predicted short RNA structural analogues could inhibit hepatitis C virus (HCV) genotype 2a, 3a and 4a replication in cultured cells. METHODS Short RNA sequences, X12, X12a and X12b, designed to be identical in secondary structure to the X region in the 3'-untranslated region (3'-UTR) of the HCV 1b genome, as well as shorter stem-loop components of X region, were inserted into a plasmid and transfected into separate Huh7.5 human hepatoma cells stably transfected with subgenomic replicons for genotypes 2a, 3a and 4a. All replicons included a firefly luciferase reporter gene. After 48 h of plasmid transfection, the inhibition of HCV replication was determined by HCV RNA isolation and quantification by real-time polymerase chain reaction and luciferase assays. RESULTS All the secondary structural analogues to genotype 1b X region cross-inhibited genotype 2a, 3a and 4a replicons. The maximum inhibition by genotype 1b X region structural analogues was obtained against genotype 2a cells in which X12, X12a and X12b inhibited replication by 30%, 63% and 72%, respectively (P < 0.05 for all), compared to an unrelated hepatitis B viral analogue. CONCLUSIONS Despite substantial sequence dissimilarity, HCV RNA genotype 1b X region analogues cross-inhibited the replication of HCV genotypes 2a, 3a and 4a. Particular conformations and not the sequence of the stem-loops of the X region are involved in HCV replication.
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Affiliation(s)
- Ismail M Elshaffei
- Department of Biochemistry, Faculty of Pharmacy, Misr International University, Cairo, Egypt
| | - Nidhi Gupta
- Department of Medicine, Division of Gastroenterology-Hepatology, UCONN HEALTH, USA
| | - Catherine H Wu
- Department of Medicine, Division of Gastroenterology-Hepatology, UCONN HEALTH, USA
| | - David C Wu
- Department of Medicine, Division of Gastroenterology-Hepatology, UCONN HEALTH, USA
| | - Lamiaa N Hammad
- Department of Biochemistry, Faculty of Pharmacy, Misr International University, Cairo, Egypt
| | - Dina M Abo-Elmatty
- Department of Biochemistry, Faculty of Pharmacy, Suez Canal University, Ismailia, Egypt
| | - Noha M Mesbah
- Department of Biochemistry, Faculty of Pharmacy, Suez Canal University, Ismailia, Egypt
| | - George Y Wu
- Department of Medicine, Division of Gastroenterology-Hepatology, UCONN HEALTH, USA
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Gupta N, Wu CH, Wu GY. Secondary Structural Elements of the HCV X-region Involved in Viral Replication. J Clin Transl Hepatol 2015; 3:1-8. [PMID: 26356238 PMCID: PMC4542080 DOI: 10.14218/jcth.2015.00003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 02/26/2015] [Accepted: 03/01/2015] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND AND AIMS The noncoding regions in the 3'-untranslated region (UTR) of the hepatitis C virus (HCV) genome contain secondary structures that are important for replication. The aim of this study was to identify detailed conformational elements of the X-region involved in HCV replication. METHODS Ribonucleic acid (RNA) structural analogs X94, X12, and X12c were constructed to have identical conformation but 94%, 12%, and 0% sequence identity, respectively, to the X region of HCV genotype 2a. Effects of structural analogs on replication of HCV genotypes 1b and 2a HCV RNA were studied by quantitative reverse transcriptase polymerase chain reaction. RESULTS In replicon BB7 cells, a constitutive replication model, HCV RNA levels decreased to 55%, 52%, 53%, and 54% after transfection with expression plasmids generating RNA structural analogs 5B-46, X-94, X-12, and X-12c, respectively (p<0.001 for all). In an HCV genotype 2a infection model, RNA analogs 5B-46, X-94, and X-12 in hepatic cells inhibited replication to 11%, 9%, and 12%, respectively. Because the X-12 analog was only 12% identical to the corresponding sequence of HCV genotype 2a, the sequence per se, or antisense effects were unlikely to be involved. CONCLUSIONS The data suggest that conformation of secondary structures in 3'-UTR of HCV RNA genome is required for HCV replication. Stable expression of RNA analogs predicted to have identical stem-loop structures might inhibit HCV infection of hepatocytes in liver and may represent a novel approach to design anti-HCV agents.
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Affiliation(s)
| | | | - George Y. Wu
- Correspondence to: George Y. Wu, Department of Medicine, Division of Gastroenterology-Hepatology, University of Connecticut Health Center, 263 Farmington Ave, Farmington, CT 06030-1845, USA. Tel: +1-800-535-6232; +1-860-679-7692, Fax: +1-860-679-3159. E-mail:
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Multiple virtual screening approaches for finding new hepatitis C virus RNA-dependent RNA polymerase inhibitors: structure-based screens and molecular dynamics for the pursue of new poly pharmacological inhibitors. BMC Bioinformatics 2012; 13 Suppl 17:S5. [PMID: 23282180 PMCID: PMC3521232 DOI: 10.1186/1471-2105-13-s17-s5] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The RNA polymerase NS5B of Hepatitis C virus (HCV) is a well-characterised drug target with an active site and four allosteric binding sites. This work presents a workflow for virtual screening and its application to Drug Bank screening targeting the Hepatitis C Virus (HCV) RNA polymerase non-nucleoside binding sites. Potential polypharmacological drugs are sought with predicted active inhibition on viral replication, and with proven positive pharmaco-clinical profiles. The approach adopted was receptor-based. Docking screens, guided with contact pharmacophores and neural-network activity prediction models on all allosteric binding sites and MD simulations, constituted our analysis workflow for identification of potential hits. Steps included: 1) using a two-phase docking screen with Surflex and Glide Xp. 2) Ranking based on scores, and important H interactions. 3) a machine-learning target-trained artificial neural network PIC prediction model used for ranking. This provided a better correlation of IC50 values of the training sets for each site with different docking scores and sub-scores. 4) interaction pharmacophores-through retrospective analysis of protein-inhibitor complex X-ray structures for the interaction pharmacophore (common interaction modes) of inhibitors for the five non-nucleoside binding sites were constructed. These were used for filtering the hits according to the critical binding feature of formerly reported inhibitors. This filtration process resulted in identification of potential new inhibitors as well as formerly reported ones for the thumb II and Palm I sites (HCV-81) NS5B binding sites. Eventually molecular dynamics simulations were carried out, confirming the binding hypothesis and resulting in 4 hits.
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Smolic R, Smolic M, Andorfer JH, Wu CH, Smith RM, Wu GY. Inhibition of hepatitis C virus replication by single-stranded RNA structural mimics. World J Gastroenterol 2010; 16:2100-8. [PMID: 20440850 PMCID: PMC2864835 DOI: 10.3748/wjg.v16.i17.2100] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM: To examine the effect of hepatitis C virus (HCV) structural mimics of regulatory regions of the genome on HCV replication.
METHODS: HCV RNA structural mimics were constructed and tested in a HCV genotype 1b aBB7 replicon, and a Japanese fulminant hepatitis-1 (JFH-1) HCV genotype 2a infection model. All sequences were computer-predicted to adopt stem-loop structures identical to the corresponding elements in full-length viral RNA. Huh7.5 cells bearing the BB7 replicon or infected with JFH-1 virus were transfected with expression vectors generating HCV mimics and controls. Cellular HCV RNA and protein levels were quantified by real-time polymerase chain reaction and Western blotting, respectively. To evaluate possible antisense effects, complementary RNAs spanning a mimic were prepared.
RESULTS: In the BB7 genotype 1b replicon system, mimics of the polymerase (NS-5B), X and BA regions inhibited replication by more than 90%, 50%, and 60%, respectively. In the JFH-1 genotype 2 infection system, mimics that were only 74% and 46% identical in sequence relative to the corresponding region in JFH-1 inhibited HCV replication by 91.5% and 91.2%, respectively, as effectively as a mimic with complete identity to HCV genotype 2a. The inhibitory effects were confirmed by NS3 protein levels. Antisense RNA molecules spanning the 74% identical mimic had no significant effects.
CONCLUSION: HCV RNA structural mimics can inhibit HCV RNA replication in replicon and infectious HCV systems and do so independent of close sequence identity with the target.
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Identification of novel inhibitors of HCV RNA-dependent RNA polymerase by pharmacophore-based virtual screening and in vitro evaluation. Bioorg Med Chem 2009; 17:2975-82. [PMID: 19332375 DOI: 10.1016/j.bmc.2009.03.024] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2009] [Revised: 03/10/2009] [Accepted: 03/11/2009] [Indexed: 12/17/2022]
Abstract
Hepatitis C virus (HCV) is the major etiological agent of non-A, non-B hepatitis where no effective treatment is available. The HCV NS5B with RNA-dependent RNA polymerase (RdRp) activity is a key target for the treatment of HCV infection. Here we report novel NS5B polymerase inhibitors identified by virtual screening and in vitro evaluation of their inhibitory activities. On the basis of a newly identified binding pocket of NS5B, distinct from the nucleotide binding site but highly conserved among various HCV isolates, we performed virtual screening of compounds that fit this binding pocket from the available chemical database of 3.5 million compounds. The inhibitory activities of the in silico selected 119 compounds were estimated with in vitro RdRp assay. Three compounds with IC50 values of about 20 microM were identified, and their kinetic analyses suggest that these compounds are noncompetitive inhibitors with respect to the ribonucleotide substrate. Furthermore, the single-point mutations of the conserved residues in the binding pocket of NS5B resulted in the significant decrease of the RdRp activity, indicating that the binding pocket presented here might be important for the therapeutic intervention of HCV. These novel inhibitors would be useful for the development of effective anti-HCV agents.
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Trepanier JB, Tanner JE, Alfieri C. Reduction in intracellular HCV RNA and virus protein expression in human hepatoma cells following treatment with 2′-O-methyl-modified anti-core deoxyribozyme. Virology 2008; 377:339-44. [DOI: 10.1016/j.virol.2008.04.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2008] [Revised: 03/25/2008] [Accepted: 04/17/2008] [Indexed: 12/11/2022]
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Vallet S, Gouriou S, Nkontchou G, Hotta H, Vilerio M, Legrand-Quillien MC, Beaugrand M, Trinchet JC, Nousbaum JB, Dény P, Gaudy C, Goudeau A, Picard B, Payan C. Is hepatitis C virus NS3 protease quasispecies heterogeneity predictive of progression from cirrhosis to hepatocellular carcinoma? J Viral Hepat 2007; 14:96-106. [PMID: 17244249 DOI: 10.1111/j.1365-2893.2006.00773.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
We investigated whether an HCV NS3 protease quasispecies heterogeneity was associated with progression from viral cirrhosis to hepatocellular carcinoma (HCC). The NS3 protease quasispecies structure of 10 HCV-1b cirrhotic patients (controls) was compared with that of 10 paired HCV-1b cirrhotic patients who displayed progression to HCC (cases). NS3 protease genetic complexity and diversity did not differ significantly between cases and controls. Amino acid substitutions were detected at 20 (11%) and 25 (14%) sites in at least two variants of the NS3 protease in cases and controls, respectively. Significant differences in the percentage of substituted clones were observed for 10 NS3 sites. Mutations Y56F, I71V, T72I, Q86P, P89S, S101G/D, R117H, S122G/T/N, V132I and V170I were more frequently observed in the NS3 protease sequences of controls than in those of cases. Residue V107 was substituted in NS3 cases but not in controls. However, these differences did not allow the definition of a specific NS3 profile related to HCC occurrence. The NS3 secondary structure B1-1 previously identified as potentially predictive of HCC was identified with a higher frequency in cases quasispecies (84.2%) than in controls (55.9%; P < 0.05). Our results suggest that there may be a relationship to fibrosis progression when diversity parameters are considered together with secondary structure profiles. Further investigations are required to determine the cellular interactions of HCV NS3 protease in the context of carcinogenesis.
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Affiliation(s)
- S Vallet
- Microbiologie, CHU Morvan, Brest, France.
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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.
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Affiliation(s)
- John J Barker
- Evotec UK, 111 Milton Park, Abingdon, Oxfordshire, OX14 4RZ, UK.
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Vallet S, Gouriou S, Nousbaum JB, Legrand-Quillien MC, Goudeau A, Picard B. Genetic heterogeneity of the NS3 protease gene in hepatitis C virus genotype 1 from untreated infected patients. J Med Virol 2005; 75:528-37. [PMID: 15714495 DOI: 10.1002/jmv.20302] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
NS3 protease is essential for hepatitis C Virus (HCV) replication, and is one of the most promising targets for specific anti-HCV therapy. Its natural polymorphism has not been studied at the quasispecies level. In the present work, the genetic heterogeneity of the NS3 protease gene was analyzed in 17 HCV genotype 1 (5 subtypes 1a and 12 subtypes 1b) samples collected from infected patients before anti-viral therapy. A total of 294 clones were sequenced. Although the protease NS3 is considered to be one of the less variable genes in the HCV genome, variability of both nucleotide and amino acid sequences was found. In variants belonging to 1a and 1b subtypes, 224 and 267 of 543 positions showed one or more nucleotide substitutions, respectively. Forty and 74 of the 181 NS3 amino acid positions showed at least one mutation in HCV-1a and HCV-1b isolates, respectively. Most substitutions were conservative. This substantial polymorphism of the NS3 protease produced by HCV-1a and HCV-1b suggests that, despite the numerous functional and structural constraints, the enzyme is sufficiently flexible to tolerate substitutions.
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Affiliation(s)
- Sophie Vallet
- Département de Microbiologie, CHU Morvan, 2 avenue Foch, 19609 Brest cedex, France.
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Abstract
The life cycle of the malaria parasite contains three distinct invasive forms, or zoites. For at least two of these--the sporozoite and the blood-stage merozoite--invasion into their respective host cell requires the activity of parasite proteases. This review summarizes the evidence for this, discusses selected well-described proteolytic modifications linked to invasion, and describes recent progress towards identifying the proteases involved.
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Affiliation(s)
- Michael J Blackman
- Division of Parasitology, National Institute for Medical Research, Mill Hill, London NW7 1AA, UK.
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