Drug Repositioning
Redirecting an Anticancer to an Antibacterial Hit Against Methicillin-Resistant Staphylococcus aureus.
Redirecting an Anticancer to an Antibacterial Hit Against Methicillin-Resistant Staphylococcus aureus.
Front Microbiol. 2019;10:350
Authors: Jang HJ, Chung IY, Lim C, Chung S, Kim BO, Kim ES, Kim SH, Cho YH
Abstract
YM155 is a clinically evaluated anticancer with a fused naphthoquinone-imidazolium scaffold. In this study, we demonstrated that based on weak or cryptic antibacterial activity of YM155 against methicillin-resistant Staphylococcus aureus (MRSA) (MIC of 50 μg/ml), some congeneric compounds with short alkyl chains (e.g., c5 with a hexyl chain) at the N3 position of the scaffold, displayed more potent antibacterial activity against MRSA (MIC of 3.13 μg/ml), which is in a clinically achievable range. Their antibacterial activity was evident against Gram-negative bacteria, only in the presence of the outer membrane-permeabilizing agent, polymyxin B. The antibacterial efficacy of c5 was confirmed using the Drosophila systemic infection model. We also characterized five spontaneous c5-resistant MRSA mutants that carry mutations in the ubiE gene, for quinone metabolism and respiratory electron transfer, and subsequently exhibited reduced respiration activity. The antibacterial activity of c5 was compromised either by an antioxidant, N-acetylcysteine, or in an anaerobic condition. These suggest that the antibacterial mechanism of c5 involves the generation of reactive oxygen species (ROS), presumably during respiratory electron transport. This study provides an insight into "drug redirecting," through a chemical modification, based on an ROS-generating pharmacophore.
PMID: 30858845 [PubMed]
Utilisation of the Prestwick Chemical Library to identify drugs that inhibit the growth of mycobacteria.
Utilisation of the Prestwick Chemical Library to identify drugs that inhibit the growth of mycobacteria.
PLoS One. 2019;14(3):e0213713
Authors: Kanvatirth P, Jeeves RE, Bacon J, Besra GS, Alderwick LJ
Abstract
Tuberculosis (TB) is an infectious bacterial disease that kills approximately 1.3 million people every year. Despite global efforts to reduce both the incidence and mortality associated with TB, the emergence of drug resistant strains has slowed any progress made towards combating the spread of this deadly disease. The current TB drug regimen is inadequate, takes months to complete and poses significant challenges when administering to patients suffering from drug resistant TB. New treatments that are faster, simpler and more affordable are urgently required. Arguably, a good strategy to discover new drugs is to start with an old drug. Here, we have screened a library of 1200 FDA approved drugs from the Prestwick Chemical library using a GFP microplate assay. Drugs were screened against GFP expressing strains of Mycobacterium smegmatis and Mycobacterium bovis BCG as surrogates for Mycobacterium tuberculosis, the causative agent of TB in humans. We identified several classes of drugs that displayed antimycobacterial activity against both M. smegmatis and BCG, however each organism also displayed some selectivity towards certain drug classes. Variant analysis of whole genomes sequenced for resistant mutants raised to florfenicol, vanoxerine and pentamidine highlight new pathways that could be exploited in drug repurposing programmes.
PMID: 30861059 [PubMed - in process]
Repurposing strategies for Chagas disease therapy: the effect of imatinib and derivatives against Trypanosoma cruzi.
Repurposing strategies for Chagas disease therapy: the effect of imatinib and derivatives against Trypanosoma cruzi.
Parasitology. 2019 Mar 12;:1-7
Authors: Simões-Silva MR, De Araújo JS, Peres RB, Da Silva PB, Batista MM, De Azevedo LD, Bastos MM, Bahia MT, Boechat N, Soeiro MNC
Abstract
Chagas disease (CD) is a neglected parasitic condition endemic in the Americas caused by Trypanosoma cruzi. Patients present an acute phase that may or not be symptomatic, followed by lifelong chronic stage, mostly indeterminate, or with cardiac and/or digestive progressive lesions. Benznidazole (BZ) and nifurtimox are the only drugs approved for treatment but not effective in the late chronic phase and many strains of the parasite are naturally resistant. New alternative therapy is required to address this serious public health issue. Repositioning and combination represent faster, and cheaper trial strategies encouraged for neglected diseases. The effect of imatinib (IMB), a tyrosine kinase inhibitor designed for use in neoplasias, was assessed in vitro on T. cruzi and mammalian host cells. In comparison with BZ, IMB was moderately active against different strains and forms of the parasite. The combination IMB + BZ in fixed-ratio proportions was additive. Novel 14 derivatives of IMB were screened and a 3,2-difluoro-2-phenylacetamide (3e) was as potent as BZ on T. cruzi but had low selectivity index. The results demonstrate the importance of phenotypic assays, encourage the improvement of IMB derivatives to reach selectivity and testify to the use of repurposing and combination in drug screening for CD.
PMID: 30859917 [PubMed - as supplied by publisher]
Binding site comparisons for target-centered drug discovery.
Binding site comparisons for target-centered drug discovery.
Expert Opin Drug Discov. 2019 Mar 11;:1-10
Authors: Konc J
Abstract
INTRODUCTION: The success of binding site comparisons in drug discovery is based on the recognized fact that many different proteins have similar binding sites. Indeed, binding site comparisons have found many uses in drug development and have the potential to dramatically cut the cost and shorten the time necessary for the development of new drugs. Areas covered: The authors review recent methods for comparing protein binding sites and their use in drug repurposing and polypharmacology. They examine emerging fields including the use of binding site comparisons in precision medicine, the prediction of structured water molecules, the search for targets of natural compounds, and their application in the development of protein-based drugs by loop modeling and for comparison of RNA binding sites. Expert opinion: Binding site comparisons have produced many interesting results in drug development, but relatively little work has been done on protein-protein interaction sites, which are particularly relevant in view of the success of biological drugs. Growth of protein loop modeling for modulating biological drugs is anticipated. The fusion of currently distinct methods for the comparison of RNA and protein binding sites into a single comprehensive approach could allow the search for new selective ribosomal antibiotics and initiate pharmaceutical research into other nucleoproteins.
PMID: 30856011 [PubMed - as supplied by publisher]
Design of a Novel and Selective IRAK4 Inhibitor Using Topological Water Network Analysis and Molecular Modeling Approaches.
Design of a Novel and Selective IRAK4 Inhibitor Using Topological Water Network Analysis and Molecular Modeling Approaches.
Molecules. 2018 Nov 29;23(12):
Authors: Lee MH, Balupuri A, Jung YR, Choi S, Lee A, Cho YS, Kang NS
Abstract
Protein kinases are deeply involved in immune-related diseases and various cancers. They are a potential target for structure-based drug discovery, since the general structure and characteristics of kinase domains are relatively well-known. However, the ATP binding sites in protein kinases, which serve as target sites, are highly conserved, and thus it is difficult to develop selective kinase inhibitors. To resolve this problem, we performed molecular dynamics simulations on 26 kinases in the aqueous solution, and analyzed topological water networks (TWNs) in their ATP binding sites. Repositioning of a known kinase inhibitor in the ATP binding sites of kinases that exhibited a TWN similar to interleukin-1 receptor-associated kinase 4 (IRAK4) allowed us to identify a hit molecule. Another hit molecule was obtained from a commercial chemical library using pharmacophore-based virtual screening and molecular docking approaches. Pharmacophoric features of the hit molecules were hybridized to design a novel compound that inhibited IRAK4 at low nanomolar levels in the in vitro assay.
PMID: 30501110 [PubMed - indexed for MEDLINE]
Treatment Avenues in Myalgic Encephalomyelitis/Chronic Fatigue Syndrome: A Split-gender Pharmacogenomic Study of Gene-expression Modules.
Treatment Avenues in Myalgic Encephalomyelitis/Chronic Fatigue Syndrome: A Split-gender Pharmacogenomic Study of Gene-expression Modules.
Clin Ther. 2019 Mar 06;:
Authors: Jeffrey MG, Nathanson L, Aenlle K, Barnes ZM, Baig M, Broderick G, Klimas NG, Fletcher MA, Craddock TJA
Abstract
PURPOSE: Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a debilitating multisymptom illness impacting up to 1 million people in the United States. As the pathogenesis and etiology of this complex condition are unclear, prospective treatments are limited. Identifying US Food and Drug Administration-approved drugs that may be repositioned as treatments for ME/CFS may offer a rapid and cost-effective solution.
METHODS: Here we used gene-expression data from 33 patients with Fukuda-defined ME/CFS (23 females, 10 males) and 21 healthy demographically comparable controls (15 females, 6 males) to identify differential expression of predefined gene-module sets based on nonparametric statistics. Differentially expressed gene modules were then annotated via over-representation analysis using the Consensus Pathway database. Differentially expressed modules were then regressed onto measures of fatigue and cross-referenced with drug atlas and pharmacogenomics databases to identify putative treatment agents.
FINDINGS: The top 1% of modules identified in males indicated small effect sizes in modules associated with immune regulation and mitochondrial dysfunction. In females, modules identified included those related to immune factors and cardiac/blood factors, returning effect sizes ranging from very small to intermediate (0.147 < Cohen δ < 0.532). Regression analysis indicated that B-cell receptors, T-cell receptors, tumor necrosis factor α, transforming growth factor β, and metabolic and cardiac modules were strongly correlated with multiple composite measures of fatigue. Cross-referencing identified genes with pharmacogenomics data indicated immunosuppressants as potential treatments of ME/CFS symptoms.
IMPLICATIONS: The findings from our analysis suggest that ME/CFS symptoms are perpetuated by immune dysregulation that may be approached via immune modulation-based treatment strategies. (Clin Ther. 2019;41:XXX-XXX) © 2019 Elsevier Inc.
PMID: 30851951 [PubMed - as supplied by publisher]
"drug repositioning" OR "drug repurposing"; +6 new citations
6 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results:
"drug repositioning" OR "drug repurposing"
These pubmed results were generated on 2019/03/09
PubMed comprises more than millions of citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.
"drug repositioning" OR "drug repurposing"; +6 new citations
6 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results:
"drug repositioning" OR "drug repurposing"
These pubmed results were generated on 2019/03/09
PubMed comprises more than millions of citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.
Repositioning of fluoroquinolones from antibiotic to anti-cancer agents: An underestimated truth.
Repositioning of fluoroquinolones from antibiotic to anti-cancer agents: An underestimated truth.
Biomed Pharmacother. 2019 Mar;111:934-946
Authors: Yadav V, Talwar P
Abstract
Increasing development costs and higher failure rate in clinical trials has reduced the repertoire of newer drugs in the market for clinical use. The most appropriate approach to end the search for newer drugs is "Repositioning", as it requires less time and money to explore new indication of existing drug or failed drug. In the past, several drugs have been repositioned for different indication but the full potential remains unharnessed. With rise in cancer prevalence and treatment costs, it is imperative to search for newer drugs and the use of repositioning approach may help us. Fluoroquinolones has been used as antibiotics for over four decades now, but recent research highlighted their use as pharmacological compounds with multifaceted implication. Repositioning of fluoroquinolones into anti-cancer molecule seems to be a highly plausible option owing to their profound immunomodulatory, pro-apoptotic, anti-proliferative and anti-metastatic potential. The present review provides a comprehensive account of the recent and past explorations pertaining to the anti-cancer activity of fluoroquinolones and also discusses the various approaches that are being considered to remodel them for the treatment of cancer.
PMID: 30841473 [PubMed - in process]
Repurposing of dexpramipexole to treatment of neonatal hypoxic/ischemic encephalopathy.
Repurposing of dexpramipexole to treatment of neonatal hypoxic/ischemic encephalopathy.
Neurosci Lett. 2018 11 20;687:234-240
Authors: Muzzi M, Buonvicino D, Urru M, Tofani L, Chiarugi A
Abstract
Dexpramipexole (DEX) is a drug with a good safety profile in humans, known for its ability to increase mitochondrial ATP production and prompt neuroprotection in adult rodents subjected to cerebral ischemia. In the present study we evaluated the effect of DEX in rat pups subjected to common carotid artery occlusion plus hypoxia (CCAoH, the classic Rice-Vannucci model). Because of the wide range of infarct size distribution in the CCAoH model, a priori subanalysis based on the effect of DEX on mild/moderate or severe brain injuries was conducted. The subanalysis showed that the drug (3 mg/kg bid i.p, after the hypoxic insult) decreased the infarction size in pups with mild/moderate injuries. Next, we developed a distal middle cerebral artery occlusion plus hypoxia (dMCAoH) model, characterized by an intra-experimental infarct size variability lower than that of the CCAoH model. Post-ischemic treatment with DEX (3 mg/kg bid i.p, after the hypoxic insult) reduced brain infarcts in pups exposed to dMCAoH. For the first time, we show that DEX reduces brain injury in different models of neonatal HIE. In light of the favorable safety profile of DEX in humans, the drug might have a realistic translational potential to treatment of perinatal cerebrovascular disorders.
PMID: 30287306 [PubMed - indexed for MEDLINE]
"drug repositioning" OR "drug repurposing"; +6 new citations
6 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results:
"drug repositioning" OR "drug repurposing"
These pubmed results were generated on 2019/03/07
PubMed comprises more than millions of citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.
The FICI paradigm: correcting flaws in antimicrobial in vitro synergy screens at their inception.
The FICI paradigm: correcting flaws in antimicrobial in vitro synergy screens at their inception.
Biochem Pharmacol. 2019 Mar 02;:
Authors: Gómara M, Ramón-García S
Abstract
Antibiotics have become the corner stone of modern medicine. However, our society is currently facing one of the greatest challenges of its time: the emergence of antimicrobial resistance. It is estimated that if no new therapies are implemented by 2050, 10 million people will die worldwide every year as a result of infections caused by bacteria resistant to current antibiotics; new antimicrobials are thus urgently needed. However, drug development is a tedious and very costly endeavor of hundreds of millions that can take up to 15-20 years from the bench discovery to the bedside. Under this scenario, drug repurposing, which consists in identifying new uses for old, clinically approved drugs, has gathered momentum within the pharmaceutical industry. Because most of these drugs have safety and toxicity information packages available, clinical evaluation could be done in a much shorter period than standard timelines. Synergistic combinations of these clinically approved drugs could also be a promising approach to identify novel antimicrobial therapies that might provide rational choices of available drugs to shorten treatment, increase efficacy, reduce toxicity, prevent resistance and treat infections caused by drug-resistant strains. However, although simple in its conception, translating results from in vitro synergy screens into in vivo efficacy or the clinical practice has proven to be a paramount challenge. In this Commentary, we will discuss common flaws at the inception of synergy research programs, with a special focus on the use of the Fractional Inhibitory Concentration Index (FICI), and evaluate potential interventions that can be made at different developmental pre-clinical stages in order to improve the odds of translation from in vitro studies.
PMID: 30836058 [PubMed - as supplied by publisher]
Drug repurposing for antimicrobial discovery.
Drug repurposing for antimicrobial discovery.
Nat Microbiol. 2019 Mar 04;:
Authors: Farha MA, Brown ED
Abstract
Antimicrobial resistance continues to be a public threat on a global scale. The ongoing need to develop new antimicrobial drugs that are effective against multi-drug-resistant pathogens has spurred the research community to invest in various drug discovery strategies, one of which is drug repurposing-the process of finding new uses for existing drugs. While still nascent in the antimicrobial field, the approach is gaining traction in both the public and private sector. While the approach has particular promise in fast-tracking compounds into clinical studies, it nevertheless has substantial obstacles to success. This Review covers the art of repurposing existing drugs for antimicrobial purposes. We discuss enabling screening platforms for antimicrobial discovery and present encouraging findings of novel antimicrobial therapeutic strategies. Also covered are general advantages of repurposing over de novo drug development and challenges of the strategy, including scientific, intellectual property and regulatory issues.
PMID: 30833727 [PubMed - as supplied by publisher]
Repositioning secnidazole as a novel virulence factors attenuating agent in Pseudomonas aeruginosa.
Repositioning secnidazole as a novel virulence factors attenuating agent in Pseudomonas aeruginosa.
Microb Pathog. 2019 Feb;127:31-38
Authors: Saleh MM, Abbas HA, Askoura MM
Abstract
Long-term treatment with antibiotics gives rise to the evolution of multi-drug resistant bacteria which are hard to be treated. Virulence factors inhibitors depend on disarming of microbial pathogens through reducing expression of virulence factors, abolishing the pathogen capability to harm the host. In the present study, the influence of secnidazole on Pseudomonas aeruginosa virulence factors expression was characterized. Production of Pseudomonas aeruginosa virulence factors such as pyocyanin, pyoverdin, elastase, rhamnolipids, proteases and hemolysins was examined following treatment of bacteria with sub-inhibitory concentration of secnidazole. Interestingly, secnidazole showed a powerful inhibitory effect on Pseudomonas aeruginosa virulence factors. Our results were further confirmed using qRT-PCR showing that there was a significant decrease in the expression of quorum sensing genes; lasI, lasR, rhlI, rhlR, pqsA and pqsR that regulate expression of virulence factors in Pseudomonas aeruginosa. Moreover, in vivo experiment using mice as infection model showed that secnidazole-treated bacteria were less capable to kill mice as compared to untreated bacteria. Importantly, there was a significant reduction in mortality in mice injected with secnidazole-treated bacteria relative to mice inoculated with untreated bacteria. In summary, our data showed that secnidazole could play a role in attenuating Pseudomonas aeruginosa through reducing virulence factors production. Moreover, our data clearly suggest that secnidazole could be involved in the treatment of Pseudomonas aeruginosa infections in order to control infection and lower the development of bacterial resistance to antibiotics.
PMID: 30500409 [PubMed - indexed for MEDLINE]
Potential Anticancer Activity of Auranofin.
Potential Anticancer Activity of Auranofin.
Chem Pharm Bull (Tokyo). 2019;67(3):186-191
Authors: Onodera T, Momose I, Kawada M
Abstract
Gold compounds have a long history of use in medicine. Auranofin was developed more than 30 years ago as an oral therapy for rheumatoid arthritis. Now, however, auranofin is rarely used in clinical practice despite its efficacy for treating rheumatoid arthritis because more novel antirheumatic medications are available. Although its use in clinical practice has decreased, studies on auranofin have continued and it shows promise for the treatment of several different diseases, including cancer and bacterial and parasitic infections. Several potential novel applications of auranofin for treating human disease have been proposed. Auranofin inhibits the activity of thioredoxin reductase (TrxR), an enzyme of the thioredoxin (Trx) system that is important for maintaining the intracellular redox state. Particularly in cancers, TrxR inhibition leads to an increase in cellular oxidative stress and induces apoptosis. TrxR overexpression is associated with aggressive tumor progression and poor survival in patients with breast, ovarian, and lung cancers. The Trx system may represent an attractive target for the development of new cancer treatments. Therefore, the TrxR inhibitor auranofin may be a potent anticancer agent. This review summarizes the current understanding of auranofin for cancer therapy.
PMID: 30827998 [PubMed - in process]
Repurposing glyburide as antileishmanial agent to fight against leishmaniasis.
Repurposing glyburide as antileishmanial agent to fight against leishmaniasis.
Protein Pept Lett. 2019 Feb 28;:
Authors: Rub A, Shaker K, Kashif M, Arish M, Dukhyil AAB, Alshehri BM, Alaidarous MA, Banawas S, Amir K
Abstract
BACKGROUND: Leishmaniasis is caused by a protozoan parasite, Leishmania. It is common in more than 98 countries throughout the world. Due to insufficient availability of antileishmanial chemotherapeutics, it is an urgent need to search for new molecules which have better efficacy, low toxicity, and low cost.
OBJECTIVES: There is a high rate of diabetes cases throughout the world that is why we planned to test the antileishmanial activity of glyburide, an effective sugar lowing drug used for the treatment of diabetes. In this study, glyburide showed a significant decrease in the parasite growth and survival in vitro in a dose-dependent manner.
METHODS: Anti-leishmanial activity of glyburide was checked by culturing Leishmania donovani promastigotes in the presence of glyburide in a dose and time dependent manner. Docking study against Leishmania donovani-Trypanothione synthetase (LdTrySyn) protein was performed using Autodock Vina tool.
RESULTS: Growth reversibility assay shows that growth of treated parasite was not reversed when transferred to fresh culture media after 7 days. Moreover, docking studies show efficient interactions of glyburide with key residues in the catalytic site of Leishmania donovani-Trypanothione synthetase (LdTrySyn), a very important leishmanial enzyme involved in parasites survival by detoxification of nitric oxide (NO) species, generated by the mammalian host as a defense mechanism. Thus this study proves that the drug-repurposing is a state of art strategy for identification of new and potent antileishmanial molecules.
CONCLUSION: The results suggest that glyburide binds to LdTrySyn and inhibits its activity that further leads to altered parasite morphology and inhibition of parasite growth. Glyburide may also be used in combination with other anti-leishmanial drugs to potentiate the response of the chemotherapy. Overall this study provides information about combination therapy as well as a single drug treatment for the infected patients suffering from diabetes. This study also provides raw information for further in vivo disease model studies to confirm the hypothesis.
PMID: 30827222 [PubMed - as supplied by publisher]
Activation of TAp73 and inhibition of TrxR by Verteporfin for improved cancer therapy in TP53 mutant pancreatic tumors.
Activation of TAp73 and inhibition of TrxR by Verteporfin for improved cancer therapy in TP53 mutant pancreatic tumors.
Future Sci OA. 2019 Feb;5(2):FSO366
Authors: Acedo P, Fernandes A, Zawacka-Pankau J
Abstract
Aim: TAp73 is a tumor suppressor, which compensates for p53 loss and induces apoptosis in tumors in response to genotoxic stress or small-molecule treatments. Pancreatic ductal adenocarcinoma has a late onset of the disease, responds poorly to the existing therapies and has a very low survival rates.
Result: Here, using drug-repurposing approach, we found that protoporphyrin IX (PpIX) and benzoporphyrin derivative (BPD) monoacid ring A activate TAp73 and induce apoptosis in pancreatic cancer cells. PpIX and BPD induce reactive oxygen species and inhibit thioredoxin reductase 1.
Conclusion: Thus, PpIX and BPD target cancer cells' vulnerabilities namely activate TAp73 tumor suppressor and inhibit oncogenic Trx1. Our findings may contribute to faster repurposing of PpIX and BPD to treat pancreatic tumors.
PMID: 30820346 [PubMed]
Pentoxifylline for Renal Protection in Diabetic Kidney Disease. A Model of Old Drugs for New Horizons.
Pentoxifylline for Renal Protection in Diabetic Kidney Disease. A Model of Old Drugs for New Horizons.
J Clin Med. 2019 Feb 27;8(3):
Authors: Donate-Correa J, Tagua VG, Ferri C, Martín-Núñez E, Hernández-Carballo C, Ureña-Torres P, Ruiz-Ortega M, Ortiz A, Mora-Fernández C, Navarro-González JF
Abstract
Diabetic kidney disease is one of the most relevant complications in diabetes mellitus patients, which constitutes the main cause of end-stage renal disease in the western world. Delaying the progression of this pathology requires new strategies that, in addition to the control of traditional risk factors (glycemia and blood pressure), specifically target the primary pathogenic mechanisms. Nowadays, inflammation is recognized as a critical novel pathogenic factor in the development and progression of renal injury in diabetes mellitus. Pentoxifylline is a nonspecific phosphodiesterase inhibitor with rheologic properties clinically used for more than 30 years in the treatment of peripheral vascular disease. In addition, this compound also exerts anti-inflammatory actions. In the context of diabetic kidney disease, pentoxifylline has shown significant antiproteinuric effects and a delay in the loss of estimated glomerular filtration rate, although at the present time there is no definitive evidence regarding renal outcomes. Moreover, recent studies have reported that this drug can be associated with a positive impact on new factors related to kidney health, such as Klotho. The use of pentoxifylline as renoprotective therapy for patients with diabetic kidney disease represents a new example of drug repositioning.
PMID: 30818852 [PubMed]
Extensive Reliability Evaluation of Docking-Based Target-Fishing Strategies.
Extensive Reliability Evaluation of Docking-Based Target-Fishing Strategies.
Int J Mol Sci. 2019 Feb 27;20(5):
Authors: Lapillo M, Tuccinardi T, Martinelli A, Macchia M, Giordano A, Poli G
Abstract
The development of target-fishing approaches, aimed at identifying the possible protein targets of a small molecule, represents a hot topic in medicinal chemistry. A successful target-fishing approach would allow for the elucidation of the mechanism of action of all therapeutically interesting compounds for which the actual target is still unknown. Moreover, target-fishing would be essential for preventing adverse effects of drug candidates, by predicting their potential off-targets, and it would speed up drug repurposing campaigns. However, due to the huge number of possible protein targets that a small-molecule might interact with, experimental target-fishing approaches are out of reach. In silico target-fishing represents a valuable alternative, and examples of receptor-based approaches, exploiting the large number of crystallographic protein structures determined to date, have been reported in the literature. To the best of our knowledge, no proper evaluation of such approaches is, however, reported yet. In the present work, we extensively assessed the reliability of docking-based target-fishing strategies. For this purpose, a set of X-ray structures belonging to different targets was selected, and a dataset of compounds, including 10 experimentally active ligands for each target, was created. A target-fishing benchmark database was then obtained, and used to assess the performance of 13 different docking procedures, in identifying the correct target of the dataset ligands. Moreover, a consensus docking-based target-fishing strategy was developed and evaluated. The analysis highlighted that specific features of the target proteins could affect the reliability of the protocol, which however, proved to represent a valuable tool in the proper applicability domain. Our study represents the first extensive performance assessment of docking-based target-fishing approaches, paving the way for the development of novel efficient receptor-based target fishing strategies.
PMID: 30818741 [PubMed - in process]
"drug repositioning" OR "drug repurposing"; +7 new citations
7 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results:
"drug repositioning" OR "drug repurposing"
These pubmed results were generated on 2019/03/01
PubMed comprises more than millions of citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.