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Ghadermarzi S, Li X, Li M, Kurgan L. Sequence-Derived Markers of Drug Targets and Potentially Druggable Human Proteins. Front Genet 2019; 10:1075. [PMID: 31803227 PMCID: PMC6872670 DOI: 10.3389/fgene.2019.01075] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 10/09/2019] [Indexed: 12/16/2022] Open
Abstract
Recent research shows that majority of the druggable human proteome is yet to be annotated and explored. Accurate identification of these unexplored druggable proteins would facilitate development, screening, repurposing, and repositioning of drugs, as well as prediction of new drug–protein interactions. We contrast the current drug targets against the datasets of non-druggable and possibly druggable proteins to formulate markers that could be used to identify druggable proteins. We focus on the markers that can be extracted from protein sequences or names/identifiers to ensure that they can be applied across the entire human proteome. These markers quantify key features covered in the past works (topological features of PPIs, cellular functions, and subcellular locations) and several novel factors (intrinsic disorder, residue-level conservation, alternative splicing isoforms, domains, and sequence-derived solvent accessibility). We find that the possibly druggable proteins have significantly higher abundance of alternative splicing isoforms, relatively large number of domains, higher degree of centrality in the protein-protein interaction networks, and lower numbers of conserved and surface residues, when compared with the non-druggable proteins. We show that the current drug targets and possibly druggable proteins share involvement in the catalytic and signaling functions. However, unlike the drug targets, the possibly druggable proteins participate in the metabolic and biosynthesis processes, are enriched in the intrinsic disorder, interact with proteins and nucleic acids, and are localized across the cell. To sum up, we formulate several markers that can help with finding novel druggable human proteins and provide interesting insights into the cellular functions and subcellular locations of the current drug targets and potentially druggable proteins.
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Affiliation(s)
- Sina Ghadermarzi
- Department of Computer Science, Virginia Commonwealth University, Richmond, VA, United States
| | - Xingyi Li
- School of Computer Science and Engineering, Central South University, Changsha, China
| | - Min Li
- School of Computer Science and Engineering, Central South University, Changsha, China
| | - Lukasz Kurgan
- Department of Computer Science, Virginia Commonwealth University, Richmond, VA, United States
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Bhardwaj P, Biswas GP, Bhunia B. Docking-based inverse virtual screening strategy for identification of novel protein targets for triclosan. CHEMOSPHERE 2019; 235:976-984. [PMID: 31561314 DOI: 10.1016/j.chemosphere.2019.07.027] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 07/02/2019] [Accepted: 07/03/2019] [Indexed: 06/10/2023]
Abstract
Triclosan (TCS) is chemically designated as 5-chloro-2-(2,4-dichlorophenoxy) phenol and is considered as endocrine-disrupting chemical (EDC). The various diseases found due to exposure of TCS, have been linked with modulation of the human enoyl-acyl carrier protein-reductase (hER). However, the new protein targets for TCS other than hER, which are responsible for various diseases, are still unknown. In the present study, a bioinformatics approach was used to identify new possible targets for TCS. A text mining study was initially performed to understand the association of TCS in various biochemical processes. Discovery studio software 4.1 was used to carry out inverse virtual screening for 226 numbers of pathway proteins by docking study using CHARMm based docking tool, and twenty proteins were screened. CDOCKER energy values lower than -12.65 kcal/mol was considered for the screening of selected proteins. Three new proteins; Receptor-interacting protein 1 (RIP1), Apoptosis signal-regulating kinase 1 (ASK1) and B-cell lymphoma 2 (Bcl-2) from Apoptosis Signaling Pathway revealed best CDOCKER energy with triclosan which was -26.88, -23.34 and -22.96 kcal/mol respectively. The interaction of TCS with RIP1 and ASK1 were mostly hydrophobic; however, hydrogen bond type interaction was found in TCS/Bcl2 complex. Therefore, docking-based inverse virtual screening study suggests that TCS has other targets rather than hER, which can modulate various biochemical processes. The docking protocol was validated through evaluation of root-mean-square deviation (RMSD), key interaction score system (KISS) and the relationship between the docking energy and toxicity data available in ToxCast database. Low RMSD value (0.55 ˚A) and high KISS score (0.66) along with higher correlation (R2 = 0.9798) between docking affinity and toxicity indicated that docking protocol can be used to optimize the binding energetics.
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Affiliation(s)
- Prashant Bhardwaj
- Department of Computer Science and Engineering, Indian Institute of Technology (Indian School of Mines) Dhanbad, 826004, India; Department of Computer Science and Engineering, National Institute of Technology, Agartala, 799046, India.
| | - G P Biswas
- Department of Computer Science and Engineering, Indian Institute of Technology (Indian School of Mines) Dhanbad, 826004, India.
| | - Biswanath Bhunia
- Department of Bio Engineering, National Institute of Technology, Agartala, 799046, India.
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Mishra R, Rana S. A rational search for discovering potential neutraligands of human complement fragment 5a (hC5a). Bioorg Med Chem 2019; 27:115052. [DOI: 10.1016/j.bmc.2019.115052] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 08/15/2019] [Accepted: 08/17/2019] [Indexed: 12/13/2022]
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Mabonga L, Kappo AP. Protein-protein interaction modulators: advances, successes and remaining challenges. Biophys Rev 2019; 11:559-581. [PMID: 31301019 PMCID: PMC6682198 DOI: 10.1007/s12551-019-00570-x] [Citation(s) in RCA: 114] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 06/24/2019] [Indexed: 12/12/2022] Open
Abstract
Modulating disease-relevant protein-protein interactions (PPIs) using small-molecule inhibitors is a quite indispensable diagnostic and therapeutic strategy in averting pathophysiological cues and disease progression. Over the years, targeting intracellular PPIs as drug design targets has been a challenging task owing to their highly dynamic and expansive interfacial areas (flat, featureless and relatively large). However, advances in PPI-focused drug discovery technology have been reported and a few drugs are already on the market, with some potential drug-like candidates already in clinical trials. In this article, we review the advances, successes and remaining challenges in the application of small molecules as valuable PPI modulators in disease diagnosis and therapeutics.
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Affiliation(s)
- Lloyd Mabonga
- Biotechnology and Structural Biology (BSB) Group, Department of Biochemistry and Microbiology, University of Zululand, KwaDlangezwa, 3886, South Africa
| | - Abidemi Paul Kappo
- Biotechnology and Structural Biology (BSB) Group, Department of Biochemistry and Microbiology, University of Zululand, KwaDlangezwa, 3886, South Africa.
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Dutta Gupta S, Bommaka MK, Banerjee A. Inhibiting protein-protein interactions of Hsp90 as a novel approach for targeting cancer. Eur J Med Chem 2019; 178:48-63. [PMID: 31176095 DOI: 10.1016/j.ejmech.2019.05.073] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 05/17/2019] [Accepted: 05/27/2019] [Indexed: 12/26/2022]
Abstract
The ninety kilo Dalton molecular weight heat shock protein (Hsp90) is an attractive target for the discovery of novel anticancer agents. Several strategies have been employed for the development of inhibitors against this polypeptide. The most successful strategy is targeting the N-terminal ATP binding region of the chaperone. However, till date not a single molecule reached Phase-IV of clinical trials from this class of Hsp90 inhibitors. The other approach is to target the Cterminal region of the protein. The success with this approach has been limited due to lack of well-defined ligand binding pocket in this terminal. The other promising strategy is to prevent the interaction of client proteins/co-chaperones with Hsp90 protein, i.e., protein-protein interaction inhibitors of Hsp90. The review focuses on advantage of this approach along with the recent advances in the discovery of inhibitors by following this strategy. Additionally, the biology of the client protein/co-chaperone binding site of Hsp90 is also discussed.
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Affiliation(s)
- Sayan Dutta Gupta
- Department of Pharmaceutical Chemistry, Gokaraju Rangaraju College of Pharmacy, Osmania University, Hyderabad, India.
| | - Manish Kumar Bommaka
- Department of Pharmaceutical Chemistry, Gokaraju Rangaraju College of Pharmacy, Osmania University, Hyderabad, India; School of Chemistry, University of Hyderabad, Hyderabad, India
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Mushtaque M, Avecilla F, Hafeez ZB, Rizvi MMA. Synthesis, Characterization, Molecular Docking, and Anticancer Evaluation of 4‐Thiazolidinone Analogues. J Heterocycl Chem 2019. [DOI: 10.1002/jhet.3549] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Md Mushtaque
- Department of ChemistrySchool of Physical and Molecular Sciences, Al‐Falah University Faridabad Haryana 121004 India
| | - Fernando Avecilla
- GrupoXenomar, Centro de Investigacións Científicas Avanzadas (CICA), Departamento de Química, Facultade de CienciasUniversidade da Coruña, Campus de A Coruña Coruña 15071 A Spain
| | - Zubair Bin Hafeez
- Department of BiosciencesJamia Millia Islamia New Delhi 110025 India
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Di Pizio A, Behrens M, Krautwurst D. Beyond the Flavour: The Potential Druggability of Chemosensory G Protein-Coupled Receptors. Int J Mol Sci 2019; 20:E1402. [PMID: 30897734 PMCID: PMC6471708 DOI: 10.3390/ijms20061402] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 03/08/2019] [Accepted: 03/12/2019] [Indexed: 12/21/2022] Open
Abstract
G protein-coupled receptors (GPCRs) belong to the largest class of drug targets. Approximately half of the members of the human GPCR superfamily are chemosensory receptors, including odorant receptors (ORs), trace amine-associated receptors (TAARs), bitter taste receptors (TAS2Rs), sweet and umami taste receptors (TAS1Rs). Interestingly, these chemosensory GPCRs (csGPCRs) are expressed in several tissues of the body where they are supposed to play a role in biological functions other than chemosensation. Despite their abundance and physiological/pathological relevance, the druggability of csGPCRs has been suggested but not fully characterized. Here, we aim to explore the potential of targeting csGPCRs to treat diseases by reviewing the current knowledge of csGPCRs expressed throughout the body and by analysing the chemical space and the drug-likeness of flavour molecules.
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Affiliation(s)
- Antonella Di Pizio
- Leibniz-Institute for Food Systems Biology at the Technical University of Munich, Freising, 85354, Germany.
| | - Maik Behrens
- Leibniz-Institute for Food Systems Biology at the Technical University of Munich, Freising, 85354, Germany.
| | - Dietmar Krautwurst
- Leibniz-Institute for Food Systems Biology at the Technical University of Munich, Freising, 85354, Germany.
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V. Živković J, G. Kalauzović S, R. Milosavljević M, G. Kalauzović K. IN SILICOEVALUATION OF SELECTED BENZIMIDAZOLE DERIVATIVES IN THE DISCOVERY OF NEW POTENT ANTIMICROBIAL AGENTS. ACTA MEDICA MEDIANAE 2019. [DOI: 10.5633/amm.2019.0115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Daniyan MO, Ojo OT. In silico identification and evaluation of potential interaction of Azadirachta indica phytochemicals with Plasmodium falciparum heat shock protein 90. J Mol Graph Model 2019; 87:144-164. [DOI: 10.1016/j.jmgm.2018.11.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 10/31/2018] [Accepted: 11/30/2018] [Indexed: 01/13/2023]
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60
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Molecular simulation of peptides coming of age: Accurate prediction of folding, dynamics and structures. Arch Biochem Biophys 2019; 664:76-88. [DOI: 10.1016/j.abb.2019.01.033] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 01/23/2019] [Accepted: 01/28/2019] [Indexed: 12/24/2022]
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Ibarra IA, Islas-Jácome A, González-Zamora E. Synthesis of polyheterocycles via multicomponent reactions. Org Biomol Chem 2019; 16:1402-1418. [PMID: 29238790 DOI: 10.1039/c7ob02305g] [Citation(s) in RCA: 145] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Polyheterocycles are one of the most desired synthetic targets due to their numerous and valuable applications in various fields. Multicomponent reactions (MCRs) are highly convergent one-pot processes, in which three or more reagents are combined sequentially to construct complex products, with almost all the atoms coming from the starting reagents. In this context, the syntheses of 'heterocycles' via MCR-based processes have been reviewed a number of times. However, there is not a single review (recent or otherwise) covering the synthesis of 'polyheterocycles' via a direct MCR or via a one-pot process involving MCRs coupled to further cyclizations (via ionic, metal-catalyzed, pericyclic, or free-radical-mediated cyclizations). This issue is consequently the main topic of the present review, which considers work from the last decade. The work is categorized according to the key processes involved in the syntheses of polyheterocycles, aiming to give readers an easy understanding of this MCR-based chemistry and to provide insights for further investigations. The reaction mechanisms providing novel elements to these MCR-based methods for the synthesis of polyheterocycles are also discussed.
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Affiliation(s)
- Ilich A Ibarra
- Laboratorio de Fisicoquímica y Reactividad de Superficies (LaFReS), Instituto de Investigaciones en Materiales, Universidad Nacional Autónoma de México, Circuito Exterior s/n, CU, Del. Coyoacán, 04510, Ciudad de México, Mexico
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Guan L, Yang H, Cai Y, Sun L, Di P, Li W, Liu G, Tang Y. ADMET-score - a comprehensive scoring function for evaluation of chemical drug-likeness. MEDCHEMCOMM 2019; 10:148-157. [PMID: 30774861 PMCID: PMC6350845 DOI: 10.1039/c8md00472b] [Citation(s) in RCA: 227] [Impact Index Per Article: 45.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 11/29/2018] [Indexed: 01/04/2023]
Abstract
Chemical absorption, distribution, metabolism, excretion, and toxicity (ADMET), play key roles in drug discovery and development. A high-quality drug candidate should not only have sufficient efficacy against the therapeutic target, but also show appropriate ADMET properties at a therapeutic dose. A lot of in silico models are hence developed for prediction of chemical ADMET properties. However, it is still not easy to evaluate the drug-likeness of compounds in terms of so many ADMET properties. In this study, we proposed a scoring function named the ADMET-score to evaluate drug-likeness of a compound. The scoring function was defined on the basis of 18 ADMET properties predicted via our web server admetSAR. The weight of each property in the ADMET-score was determined by three parameters: the accuracy rate of the model, the importance of the endpoint in the process of pharmacokinetics, and the usefulness index. The FDA-approved drugs from DrugBank, the small molecules from ChEMBL and the old drugs withdrawn from the market due to safety concerns were used to evaluate the performance of the ADMET-score. The indices of the arithmetic mean and p-value showed that the ADMET-score among the three data sets differed significantly. Furthermore, we learned that there was no obvious linear correlation between the ADMET-score and QED (quantitative estimate of drug-likeness). These results suggested that the ADMET-score would be a comprehensive index to evaluate chemical drug-likeness, and might be helpful for users to select appropriate drug candidates for further development.
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Affiliation(s)
- Longfei Guan
- Shanghai Key Laboratory of New Drug Design , School of Pharmacy , East China University of Science and Technology , 130 Meilong Road , Shanghai 200237 , China .
| | - Hongbin Yang
- Shanghai Key Laboratory of New Drug Design , School of Pharmacy , East China University of Science and Technology , 130 Meilong Road , Shanghai 200237 , China .
| | - Yingchun Cai
- Shanghai Key Laboratory of New Drug Design , School of Pharmacy , East China University of Science and Technology , 130 Meilong Road , Shanghai 200237 , China .
| | - Lixia Sun
- Shanghai Key Laboratory of New Drug Design , School of Pharmacy , East China University of Science and Technology , 130 Meilong Road , Shanghai 200237 , China .
| | - Peiwen Di
- Shanghai Key Laboratory of New Drug Design , School of Pharmacy , East China University of Science and Technology , 130 Meilong Road , Shanghai 200237 , China .
| | - Weihua Li
- Shanghai Key Laboratory of New Drug Design , School of Pharmacy , East China University of Science and Technology , 130 Meilong Road , Shanghai 200237 , China .
| | - Guixia Liu
- Shanghai Key Laboratory of New Drug Design , School of Pharmacy , East China University of Science and Technology , 130 Meilong Road , Shanghai 200237 , China .
| | - Yun Tang
- Shanghai Key Laboratory of New Drug Design , School of Pharmacy , East China University of Science and Technology , 130 Meilong Road , Shanghai 200237 , China .
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Correa MF, Dos Santos Fernandes JP. QSAR Modeling of Histamine H3R Antagonists/inverse Agonists as Future Drugs for Neurodegenerative Diseases. Curr Neuropharmacol 2018; 16:749-757. [PMID: 28820054 PMCID: PMC6080103 DOI: 10.2174/1570159x15666170818100644] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 07/04/2017] [Accepted: 08/16/2017] [Indexed: 11/22/2022] Open
Abstract
Background Histamine H3 receptor (H3R) is associated with several neuropsychological diseases, and thus it is an important target involved in several CNS disorders, such as narcolepsy, attention deficit hyperactivity disorder and schizophrenia. Since QSAR modeling is a feasible approach to explain the role of the molecular substituents in the biological activity, it can help in improving the design of better H3R ligands for these conditions. Methods This article reviews papers previously published in literature to show the current status of the contribution from QSAR modeling to reach H3R antagonists/inverse agonists. Results Classical and 3D-QSAR models were retrieved, showing that the steric and hydrophobic properties of the H3R ligands are most important to reach good affinity. Conclusion Although QSAR methods are valuable to design better H3R antagonists/inverse agonists, pharmacokinetics should also be considered in future models to ensure good CNS penetration.
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Affiliation(s)
- Michelle Fidelis Correa
- Departamento de Ciencias Farmaceuticas, Universidade Federal de Sao Paulo, Rua Sao Nicolau 210, Centro 09913- 030, Diadema-SP, Brazil
| | - Joao Paulo Dos Santos Fernandes
- Departamento de Ciencias Farmaceuticas, Universidade Federal de Sao Paulo, Rua Sao Nicolau 210, Centro 09913- 030, Diadema-SP, Brazil
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Machado D, Azzali E, Couto I, Costantino G, Pieroni M, Viveiros M. Adjuvant therapies against tuberculosis: discovery of a 2-aminothiazole targeting Mycobacterium tuberculosis energetics. Future Microbiol 2018; 13:1383-1402. [PMID: 30259757 DOI: 10.2217/fmb-2018-0110] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
AIM To evaluate the activity of the 2-aminothiazole UPAR-174 following an unexplored approach: targeting Mycobacterium tuberculosis with lipophilic compounds that present antituberculosis and efflux inhibitory activity. METHODS Antituberculosis activity was assessed against replicating, nonreplicating and intracellular bacilli. Its capacity to inhibit active efflux was determined. ATP quantification and membrane potential analysis were performed. Intracellular activity was studied on human-monocyte-derived macrophages. RESULTS UPAR-174 is an efflux inhibitor active against replicating, nonreplicating and intracellular M. tuberculosis. It dissipates the membrane potential and causes ATP depletion. CONCLUSION Targeting M. tuberculosis with lipophilic efflux inhibitors, exploring their dual activity - dissipation of the proton motive force and efflux inhibition - represents an attractive strategy to fight against drug-resistant tuberculosis.
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Affiliation(s)
- Diana Machado
- Global Health & Tropical Medicine, GHTM, Instituto de Higiene e Medicina Tropical, IHMT, Universidade Nova de Lisboa, UNL, Lisboa, Portugal
| | - Elisa Azzali
- P4T group, Department of Food & Drug, University of Parma, Parco Area delle Scienze 27/A, Parma, Italy.,Aptuit (Verona) Srl, an Evotec Company, Via Alessandro Fleming, 4, 37135 Verona, Italy
| | - Isabel Couto
- Global Health & Tropical Medicine, GHTM, Instituto de Higiene e Medicina Tropical, IHMT, Universidade Nova de Lisboa, UNL, Lisboa, Portugal
| | - Gabriele Costantino
- P4T group, Department of Food & Drug, University of Parma, Parco Area delle Scienze 27/A, Parma, Italy
| | - Marco Pieroni
- P4T group, Department of Food & Drug, University of Parma, Parco Area delle Scienze 27/A, Parma, Italy
| | - Miguel Viveiros
- Global Health & Tropical Medicine, GHTM, Instituto de Higiene e Medicina Tropical, IHMT, Universidade Nova de Lisboa, UNL, Lisboa, Portugal
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Tu LH, Tseng NH, Tsai YR, Lin TW, Lo YW, Charng JL, Hsu HT, Chen YS, Chen RJ, Wu YT, Chan YT, Chen CS, Fang JM, Chen YR. Rationally designed divalent caffeic amides inhibit amyloid-β fibrillization, induce fibril dissociation, and ameliorate cytotoxicity. Eur J Med Chem 2018; 158:393-404. [PMID: 30227353 DOI: 10.1016/j.ejmech.2018.08.084] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Revised: 08/28/2018] [Accepted: 08/28/2018] [Indexed: 12/16/2022]
Abstract
One of the pathologic hallmarks in Alzheimer's disease (AD) is extracellular senile plaques composed of amyloid-β (Aβ) fibrils. Blocking Aβ self-assembly or disassembling Aβ aggregates by small molecules would be potential therapeutic strategies to treat AD. In this study, we synthesized a series of rationally designed divalent compounds and examined their effects on Aβ fibrillization. A divalent amide (2) derived from two molecules of caffeic acid with a propylenediamine linker of ∼5.0 Å in length, which is close to the distance of adjacent β sheets in Aβ fibrils, showed good potency to inhibit Aβ(1-42) fibrillization. Furthermore, compound 2 effectively dissociated the Aβ(1-42) preformed fibrils. The cytotoxicity induced by Aβ(1-42) aggregates in human neuroblastoma was reduced in the presence of 2, and feeding 2 to Aβ transgenic C. elegans rescued the paralysis phenotype. In addition, the binding and stoichiometry of 2 to Aβ(1-40) were demonstrated by using electrospray ionization-traveling wave ion mobility-mass spectrometry, while molecular dynamic simulation was conducted to gain structural insights into the Aβ(1-40)-2 complex.
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Affiliation(s)
- Ling-Hsien Tu
- Genomics Research Center, Academia Sinica, Taipei, 115, Taiwan
| | | | - Ya-Ru Tsai
- Department of Chemistry, National Taiwan University, Taipei, 106, Taiwan
| | - Tien-Wei Lin
- Genomics Research Center, Academia Sinica, Taipei, 115, Taiwan
| | - Yi-Wei Lo
- Genomics Research Center, Academia Sinica, Taipei, 115, Taiwan
| | - Jien-Lin Charng
- Genomics Research Center, Academia Sinica, Taipei, 115, Taiwan
| | - Hua-Ting Hsu
- Genomics Research Center, Academia Sinica, Taipei, 115, Taiwan
| | - Yu-Sheng Chen
- Department of Chemistry, National Taiwan University, Taipei, 106, Taiwan
| | - Rong-Jie Chen
- Genomics Research Center, Academia Sinica, Taipei, 115, Taiwan
| | - Ying-Ta Wu
- Genomics Research Center, Academia Sinica, Taipei, 115, Taiwan
| | - Yi-Tsu Chan
- Department of Chemistry, National Taiwan University, Taipei, 106, Taiwan
| | - Chang-Shi Chen
- Department of Biochemistry and Molecular Biology, National Cheng Kung University, Tainan, Taiwan
| | - Jim-Min Fang
- Genomics Research Center, Academia Sinica, Taipei, 115, Taiwan; Department of Chemistry, National Taiwan University, Taipei, 106, Taiwan.
| | - Yun-Ru Chen
- Genomics Research Center, Academia Sinica, Taipei, 115, Taiwan.
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Stewart MP, Langer R, Jensen KF. Intracellular Delivery by Membrane Disruption: Mechanisms, Strategies, and Concepts. Chem Rev 2018; 118:7409-7531. [PMID: 30052023 PMCID: PMC6763210 DOI: 10.1021/acs.chemrev.7b00678] [Citation(s) in RCA: 406] [Impact Index Per Article: 67.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Intracellular delivery is a key step in biological research and has enabled decades of biomedical discoveries. It is also becoming increasingly important in industrial and medical applications ranging from biomanufacture to cell-based therapies. Here, we review techniques for membrane disruption-based intracellular delivery from 1911 until the present. These methods achieve rapid, direct, and universal delivery of almost any cargo molecule or material that can be dispersed in solution. We start by covering the motivations for intracellular delivery and the challenges associated with the different cargo types-small molecules, proteins/peptides, nucleic acids, synthetic nanomaterials, and large cargo. The review then presents a broad comparison of delivery strategies followed by an analysis of membrane disruption mechanisms and the biology of the cell response. We cover mechanical, electrical, thermal, optical, and chemical strategies of membrane disruption with a particular emphasis on their applications and challenges to implementation. Throughout, we highlight specific mechanisms of membrane disruption and suggest areas in need of further experimentation. We hope the concepts discussed in our review inspire scientists and engineers with further ideas to improve intracellular delivery.
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Affiliation(s)
- Martin P. Stewart
- Department of Chemical Engineering, Massachusetts Institute
of Technology, Cambridge, USA
- The Koch Institute for Integrative Cancer Research,
Massachusetts Institute of Technology, Cambridge, USA
| | - Robert Langer
- Department of Chemical Engineering, Massachusetts Institute
of Technology, Cambridge, USA
- The Koch Institute for Integrative Cancer Research,
Massachusetts Institute of Technology, Cambridge, USA
| | - Klavs F. Jensen
- Department of Chemical Engineering, Massachusetts Institute
of Technology, Cambridge, USA
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68
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Machado D, Girardini M, Viveiros M, Pieroni M. Challenging the Drug-Likeness Dogma for New Drug Discovery in Tuberculosis. Front Microbiol 2018; 9:1367. [PMID: 30018597 PMCID: PMC6037898 DOI: 10.3389/fmicb.2018.01367] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 06/06/2018] [Indexed: 01/28/2023] Open
Abstract
The emergence of multi- and extensively drug resistant tuberculosis worldwide poses a great threat to human health and highlight the need to discover and develop new, effective and inexpensive antituberculosis agents. High-throughput screening assays against well-validated drug targets and structure based drug design have been employed to discover new lead compounds. However, the great majority fail to demonstrate any antimycobacterial activity when tested against Mycobacterium tuberculosis in whole-cell screening assays. This is mainly due to some of the intrinsic properties of the bacilli, such as the extremely low permeability of its cell wall, slow growth, drug resistance, drug tolerance, and persistence. In this sense, understanding the pathways involved in M. tuberculosis drug tolerance, persistence, and pathogenesis, may reveal new approaches for drug development. Moreover, the need for compounds presenting a novel mode of action is of utmost importance due to the emergence of resistance not only to the currently used antituberculosis agents, but also to those in the pipeline. Cheminformatics studies have shown that drugs endowed with antituberculosis activity have the peculiarity of being more lipophilic than many other antibacterials, likely because this leads to improved cell penetration through the extremely waxy mycobacterial cell wall. Moreover, the interaction of the lipophilic moiety with the membrane alters its stability and functional integrity due to the disruption of the proton motive force, resulting in cell death. When a ligand-based medicinal chemistry campaign is ongoing, it is always difficult to predict whether a chemical modification or a functional group would be suitable for improving the activity. Nevertheless, in the “instruction manual” of medicinal chemists, certain functional groups or certain physicochemical characteristics (i.e., high lipophilicity) are considered red flags to look out for in order to safeguard drug-likeness and avoid attritions in the drug discovery process. In this review, we describe how antituberculosis compounds challenge established rules such as the Lipinski's “rule of five” and how medicinal chemistry for antituberculosis compounds must be thought beyond such dogmatic schemes.
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Affiliation(s)
- Diana Machado
- Global Health and Tropical Medicine, GHTM, Instituto de Higiene e Medicina Tropical, IHMT, Universidade Nova de Lisboa, UNL, Lisbon, Portugal
| | - Miriam Girardini
- P4T Group, Department of Food and Drug, University of Parma, Parma, Italy
| | - Miguel Viveiros
- Global Health and Tropical Medicine, GHTM, Instituto de Higiene e Medicina Tropical, IHMT, Universidade Nova de Lisboa, UNL, Lisbon, Portugal
| | - Marco Pieroni
- P4T Group, Department of Food and Drug, University of Parma, Parma, Italy
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Khalid S, Hanif R, Jabeen I, Mansoor Q, Ismail M. Pharmacophore modeling for identification of anti-IGF-1R drugs and in-vitro validation of fulvestrant as a potential inhibitor. PLoS One 2018; 13:e0196312. [PMID: 29787591 PMCID: PMC5963753 DOI: 10.1371/journal.pone.0196312] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 04/10/2018] [Indexed: 01/10/2023] Open
Abstract
Insulin-like growth factor 1 receptor (IGF-1R) is an important therapeutic target for breast cancer treatment. The alteration in the IGF-1R associated signaling network due to various genetic and environmental factors leads the system towards metastasis. The pharmacophore modeling and logical approaches have been applied to analyze the behaviour of complex regulatory network involved in breast cancer. A total of 23 inhibitors were selected to generate ligand based pharmacophore using the tool, Molecular Operating Environment (MOE). The best model consisted of three pharmacophore features: aromatic hydrophobic (HyD/Aro), hydrophobic (HyD) and hydrogen bond acceptor (HBA). This model was validated against World drug bank (WDB) database screening to identify 189 hits with the required pharmacophore features and was further screened by using Lipinski positive compounds. Finally, the most effective drug, fulvestrant, was selected. Fulvestrant is a selective estrogen receptor down regulator (SERD). This inhibitor was further studied by using both in-silico and in-vitro approaches that showed the targeted effect of fulvestrant in ER+ MCF-7 cells. Results suggested that fulvestrant has selective cytotoxic effect and a dose dependent response on IRS-1, IGF-1R, PDZK1 and ER-α in MCF-7 cells. PDZK1 can be an important inhibitory target using fulvestrant because it directly regulates IGF-1R.
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Affiliation(s)
- Samra Khalid
- Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
- Northern Institute for Cancer Research, Newcastle upon Tyne Hospitals NHS Foundation Trust, The Medical School, University of Newcastle upon Tyne, Newcastle upon Tyne, United Kingdom
| | - Rumeza Hanif
- Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
- * E-mail:
| | - Ishrat Jabeen
- Research Center for Modeling & Simulation (RCMS), National University of Sciences and Technology, Islamabad, Pakistan
| | - Qaisar Mansoor
- Institute of Biomedical and Genetic Engineering (IBGE), KRL Hospital, Islamabad, Pakistan
| | - Muhammad Ismail
- Institute of Biomedical and Genetic Engineering (IBGE), KRL Hospital, Islamabad, Pakistan
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Che JX, Wang ZL, Dong XW, Hu YH, Xie X, Hu YZ. Bicyclo[2.2.1]heptane containing N, N'-diarylsquaramide CXCR2 selective antagonists as anti-cancer metastasis agents. RSC Adv 2018; 8:11061-11069. [PMID: 35541503 PMCID: PMC9078949 DOI: 10.1039/c8ra01806e] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 03/09/2018] [Indexed: 11/21/2022] Open
Abstract
CXCR1 and CXCR2 are CXC chemokine receptors (CXCRs), corresponding to cytokines of the CXC chemokine family. CXCR2 was found to be 77% homologous to CXCR1. Antagonism of the chemokine receptor CXCR2 has been proposed as a new strategy for the treatment of metastatic cancer. In order to find a CXCR2 selective antagonist, a bicyclo[2.2.1]heptane containing N,N'-diarylsquaramide (compound 2e) was identified by introducing a bridge ring system into the N,N'-diarylsquaramide skeleton, and it exhibited good CXCR2 antagonistic activity (CXCR2IC50 = 48 nM) and good selectivity (CXCR1IC50/CXCR2IC50 = 60.4). Furthermore, an in vitro biological assay of compound 2e also demonstrated its good anti-cancer metastatic effect against the pancreatic cancer cell line CFPAC1. In addition, compound 2e showed an extremely high stability in simulated intestinal fluid (SIF) and simulated gastric fluid (SGF), as well as in rat and human plasma, but not in rat and human liver microsomes. In vivo pharmacokinetic studies in rats indicated that 2e has an excellent PK profile (10 mg kg-1 po, C max = 2863 ng mL-1, t 1/2 = 2.58 h). Moreover, molecular docking was further implemented to propose the preponderant configuration of compound 2e, providing important and useful guidelines for further development.
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Affiliation(s)
- Jin-Xin Che
- ZJU-ENS Joint Laboratory of Medicinal Chemistry, College of Pharmaceutical Sciences, Zhejiang University Hangzhou PR China
| | - Zhi-Long Wang
- State Key Laborarory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences Shanghai PR China
| | - Xiao-Wu Dong
- ZJU-ENS Joint Laboratory of Medicinal Chemistry, College of Pharmaceutical Sciences, Zhejiang University Hangzhou PR China
| | - You-Hong Hu
- State Key Laborarory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences Shanghai PR China
| | - Xin Xie
- State Key Laborarory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences Shanghai PR China
- CAS Key Laboratory of Receptor Research, The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences Shanghai PR China
| | - Yong-Zhou Hu
- ZJU-ENS Joint Laboratory of Medicinal Chemistry, College of Pharmaceutical Sciences, Zhejiang University Hangzhou PR China
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Mignani S, Rodrigues J, Tomas H, Jalal R, Singh PP, Majoral JP, Vishwakarma RA. Present drug-likeness filters in medicinal chemistry during the hit and lead optimization process: how far can they be simplified? Drug Discov Today 2018. [DOI: https://doi.org/10.1016/j.drudis.2018.01.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Mignani S, Rodrigues J, Tomas H, Jalal R, Singh PP, Majoral JP, Vishwakarma RA. Present drug-likeness filters in medicinal chemistry during the hit and lead optimization process: how far can they be simplified? Drug Discov Today 2018; 23:605-615. [PMID: 29330127 DOI: 10.1016/j.drudis.2018.01.010] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 11/16/2017] [Accepted: 01/04/2018] [Indexed: 02/08/2023]
Abstract
During the past decade, decreasing the attrition rate of drug development candidates reaching the market has become one of the major challenges in pharmaceutical research and drug development (R&D). To facilitate the decision-making process, and to increase the probability of rapidly finding and developing high-quality compounds, a variety of multiparametric guidelines, also known as rules and ligand efficiency (LE) metrics, have been developed. However, what are the 'best' descriptors and how far can we simplify these drug-likeness prediction tools in terms of the numerous, complex properties that they relate to?
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Affiliation(s)
- Serge Mignani
- Université Paris Descartes, PRES Sorbonne Paris Cité, CNRS UMR 860, Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologique, 45, Rue des Saints Peres, 75006 Paris, France; CQM - Centro de Química da Madeira, MMRG, Universidade da Madeira, Campus da Penteada, 9020-105 Funchal, Portugal; Medicinal Chemistry Division, Indian Institute of Integrative Medicine (Council of Scientific and Industrial Research), Canal Road, Jammu 180001, India.
| | - João Rodrigues
- CQM - Centro de Química da Madeira, MMRG, Universidade da Madeira, Campus da Penteada, 9020-105 Funchal, Portugal; School of Materials Science and Engineering/Center for Nano Energy Materials, Northwestern Polytechnical University, Xi'an, Shaanxi Province 710072, China.
| | - Helena Tomas
- CQM - Centro de Química da Madeira, MMRG, Universidade da Madeira, Campus da Penteada, 9020-105 Funchal, Portugal
| | - Rachid Jalal
- Cadi Ayyad University, Sciences and Technics Faculty, BP 549 Marrakech, Morocco
| | - Parvinder Pal Singh
- Medicinal Chemistry Division, Indian Institute of Integrative Medicine (Council of Scientific and Industrial Research), Canal Road, Jammu 180001, India.
| | - Jean-Pierre Majoral
- Laboratoire de Chimie de Coordination du CNRS, 205 route de Narbonne, BP 44099, 31077 Toulouse Cedex 4, France; Université de Toulouse, UPS, INPT, 31077 Toulouse Cedex 4, France.
| | - Ram A Vishwakarma
- Medicinal Chemistry Division, Indian Institute of Integrative Medicine (Council of Scientific and Industrial Research), Canal Road, Jammu 180001, India.
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González-Medina M, Medina-Franco JL. Platform for Unified Molecular Analysis: PUMA. J Chem Inf Model 2017; 57:1735-1740. [PMID: 28737911 DOI: 10.1021/acs.jcim.7b00253] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
We introduce a free platform for chemoinformatic-based diversity analysis and visualization of chemical space of user supplied data sets. Platform for Unified Molecular Analysis (PUMA) integrates metrics used to characterize compound databases including visualization of chemical space, scaffold content, and analysis of chemical diversity. The user's input is a file with SMILES, database names, and compound IDs. PUMA computes molecular properties of pharmaceutical relevance, Murcko scaffolds, and diversity analysis. The user can interactively navigate through the graphs and export image files and the raw data of the diversity calculations. The platform links two public online resources: Consensus Diversity Plots for the assessment of global diversity and Activity Landscape Plotter to analyze structure-activity relationships. Herein, we describe the functionalities of PUMA and exemplify its use through the analysis of compound databases of general interest. PUMA is freely accessible at the authors web-site https://www.difacquim.com/d-tools/ .
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Affiliation(s)
- Mariana González-Medina
- School of Chemistry, Department of Pharmacy, Universidad Nacional Autónoma de México , Avenida Universidad 3000, Mexico City 04510, Mexico
| | - José L Medina-Franco
- School of Chemistry, Department of Pharmacy, Universidad Nacional Autónoma de México , Avenida Universidad 3000, Mexico City 04510, Mexico
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Gómez-Verjan J, Rodríguez-Hernández K, Reyes-Chilpa R. Bioactive Coumarins and Xanthones From Calophyllum Genus and Analysis of Their Druglikeness and Toxicological Properties. STUDIES IN NATURAL PRODUCTS CHEMISTRY 2017; 53. [PMCID: PMC7152109 DOI: 10.1016/b978-0-444-63930-1.00008-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Calophyllum spp. (Calophyllaceae) is a genus of tropical trees valued in the chemopharmacological industry as an important source of biogenetically related coumarins and xanthones, which can lead to the development of new drugs due to their relevant pharmacological activities and diversity of molecular structural. These compounds have relevant pharmacological activities, such as: cytotoxicity against human tumor cell lines (especially leukemia), parasites (Plasmodium, Leshmania, and Trypanosoma), retroviruses (e.g., HIV), and Mycobacterium tuberculosis. Chemoinformatic and toxicoinformatic tools were used here to perform a computational analysis of 70 coumarins and 70 xanthones isolated from this genus in order to explore their potential as new drugs. Most coumarins from this genus possess similar patterns of druglikeness with differences in its physicochemical properties. Xanthones, on the other hand, show quite similar physicochemical properties and druglikeness. It is interesting to note that the vast majority of these compounds (57 coumarins and 59 xanthones) are in compliance with Lipinski´s Rule of Five. Remarkably, two xanthones (2-hydroxyxanthone and caledonixanthone-B) have leadlikeness potential that accordingly with chemoinformatic analysis may target MAO A and B, respectively, and therefore may exhibit antidepressant potential. These compounds also target tyrosine-phosphorilation-regulated kinase 1A (DYRK1A) which is over-expressed in a variety of hematological and brain cancers, therefore they could act as anticancer compounds. Several toxicological predictions were also depicted. Coumarins could be an irritant and may affect the reproductive system, while xanthones may have mutagenic results. To our knowledge, this is the first chemoinformatic report on the main active compounds of this genus and its potential for drug development.
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Affiliation(s)
- J.C. Gómez-Verjan
- Department of Basic Research, National Institute of Geriatrics, Mexico City, Mexico
| | | | - R. Reyes-Chilpa
- Instituto de Química, Universidad Nacional Autónoma de México, México City, México,Corresponding author:
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Global vision of druggability issues: applications and perspectives. Drug Discov Today 2016; 22:404-415. [PMID: 27939283 DOI: 10.1016/j.drudis.2016.11.021] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Revised: 10/10/2016] [Accepted: 11/25/2016] [Indexed: 02/04/2023]
Abstract
During the preliminary stage of a drug discovery project, the lack of druggability information and poor target selection are the main causes of frequent failures. Elaborating on accurate computational druggability prediction methods is a requirement for prioritizing target selection, designing new drugs and avoiding side effects. In this review, we describe a survey of recently reported druggability prediction methods mainly based on networks, statistical pocket druggability predictions and virtual screening. An application for a frequent mutation of p53 tumor suppressor is presented, illustrating the complementarity of druggability prediction approaches, the remaining challenges and potential new drug development perspectives.
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76
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Ogungbe IV, Setzer WN. The Potential of Secondary Metabolites from Plants as Drugs or Leads against Protozoan Neglected Diseases-Part III: In-Silico Molecular Docking Investigations. Molecules 2016; 21:E1389. [PMID: 27775577 PMCID: PMC6274513 DOI: 10.3390/molecules21101389] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 10/06/2016] [Accepted: 10/12/2016] [Indexed: 12/11/2022] Open
Abstract
Malaria, leishmaniasis, Chagas disease, and human African trypanosomiasis continue to cause considerable suffering and death in developing countries. Current treatment options for these parasitic protozoal diseases generally have severe side effects, may be ineffective or unavailable, and resistance is emerging. There is a constant need to discover new chemotherapeutic agents for these parasitic infections, and natural products continue to serve as a potential source. This review presents molecular docking studies of potential phytochemicals that target key protein targets in Leishmania spp., Trypanosoma spp., and Plasmodium spp.
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Affiliation(s)
- Ifedayo Victor Ogungbe
- Department of Chemistry and Biochemistry, Jackson State University, Jackson, MS 39217, USA.
| | - William N Setzer
- Department of Chemistry, University of Alabama in Huntsville, Huntsville, AL 35899, USA.
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Hu B, Yang YCT, Huang Y, Zhu Y, Lu ZJ. POSTAR: a platform for exploring post-transcriptional regulation coordinated by RNA-binding proteins. Nucleic Acids Res 2016; 45:D104-D114. [PMID: 28053162 PMCID: PMC5210617 DOI: 10.1093/nar/gkw888] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 09/23/2016] [Accepted: 09/27/2016] [Indexed: 01/01/2023] Open
Abstract
We present POSTAR (http://POSTAR.ncrnalab.org), a resource of POST-trAnscriptional Regulation coordinated by RNA-binding proteins (RBPs). Precise characterization of post-transcriptional regulatory maps has accelerated dramatically in the past few years. Based on new studies and resources, POSTAR supplies the largest collection of experimentally probed (∼23 million) and computationally predicted (approximately 117 million) RBP binding sites in the human and mouse transcriptomes. POSTAR annotates every transcript and its RBP binding sites using extensive information regarding various molecular regulatory events (e.g., splicing, editing, and modification), RNA secondary structures, disease-associated variants, and gene expression and function. Moreover, POSTAR provides a friendly, multi-mode, integrated search interface, which helps users to connect multiple RBP binding sites with post-transcriptional regulatory events, phenotypes, and diseases. Based on our platform, we were able to obtain novel insights into post-transcriptional regulation, such as the putative association between CPSF6 binding, RNA structural domains, and Li-Fraumeni syndrome SNPs. In summary, POSTAR represents an early effort to systematically annotate post-transcriptional regulatory maps and explore the putative roles of RBPs in human diseases.
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Affiliation(s)
- Boqin Hu
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, Center for Plant Biology and Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yu-Cheng T Yang
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, Center for Plant Biology and Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China.,Department of Statistics, University of California Los Angeles, Los Angeles, CA 90095-1554, USA
| | - Yiming Huang
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, Center for Plant Biology and Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yumin Zhu
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, Center for Plant Biology and Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Zhi John Lu
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, Center for Plant Biology and Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
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Mariano LNB, Vendramini-Costa DB, Ruiz ALTG, de Carvalho JE, Corrêa R, Cechinel Filho V, Delle Monache F, Niero R. In vitro antiproliferative activity of uncommon xanthones from branches of Garcinia achachairu. PHARMACEUTICAL BIOLOGY 2016; 54:1697-1704. [PMID: 26704644 DOI: 10.3109/13880209.2015.1123279] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Revised: 08/20/2015] [Accepted: 11/11/2015] [Indexed: 06/05/2023]
Abstract
Context Garcinia achachairu Rusby (Clusiaceae) popularly known as 'achachairu' is used in folk medicine to treat rheumatism, inflammation, pain and gastric disorder. Objective The present study investigated the chemical profile and antiproliferative effects of the methanolic extract, fractions and two xanthones, against some carcinoma cell lines in vitro. Materials and methods The compounds were isolated and identified by chromatographic and spectroscopic methods. The extract, fractions and compounds were tested human tumour cell lines of U-251 (glioma), MCF-7 (breast), NCI/ADR-RES (ovary expressing multi-drug resistance phenotype), 786-0 (kidney), NCI-H460 (lung, non-small cells), PC-3 (prostate) and HT-29 (colon), non-tumour cell line HaCat (human keratinocytes) in doses of 0.25-250 μg mL (-) (1) for 48 h. The antiproliferative activity was determined by spectrophotometric quantification (at 540 nm) of the cellular protein content using sulphorhodamine B assay. The prediction of parameters involved in the molecular bioavailability was executed directly by ChemDoodle (version 5.0.1) software (iChemLabs, LLC, Somerset, NJ). Results 3-Demethyl-2-geranyl-4-prenylbellidypholine (1) and 1,5,8-trihydroxy-4',5'-dimethyl-2H-pyrane (2,3:3,2)-4-(3-methylbut-2-enyl) xanthone (2), gartanin (3) and stigmasterol (4) were identified on the basis of spectroscopic techniques. Compounds 1 and 2 exhibited cytocidal activity, especially against breast, prostate and kidney cell lines, with TGI values of 15.8, 4.9, 9.1 and 39.4, 44.7, 40.9 μg/mL, respectively. Discussion and conclusion The presence of two sets of hydrophobic and hydrophilic groups in separate domains in each molecule might play a role in the mediation of tumour-specific action. Our data show that G. achachairu have potent antiproliferative action and should be considered an important source of potent anticancer compounds.
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Affiliation(s)
- Luisa Nathália Bolda Mariano
- a Programa de Pós-Graduação em Ciências Farmacêuticas, Núcleo de Investigações Químico-Farmacêuticas (NIQFAR) , Universidade do Vale do Itajaí - UNIVALI , Itajaí , Santa Catarina , Brazil
| | - Débora Barbosa Vendramini-Costa
- b Centro Pluridisciplinar de Pesquisas Químicas, Biológicas e Agrícolas (CPQBA) - Universidade Estadual de Campinas (UNICAMP) , Campinas , São Paulo , Brazil
| | - Ana Lúcia Tasca Gois Ruiz
- b Centro Pluridisciplinar de Pesquisas Químicas, Biológicas e Agrícolas (CPQBA) - Universidade Estadual de Campinas (UNICAMP) , Campinas , São Paulo , Brazil
| | - João Ernesto de Carvalho
- b Centro Pluridisciplinar de Pesquisas Químicas, Biológicas e Agrícolas (CPQBA) - Universidade Estadual de Campinas (UNICAMP) , Campinas , São Paulo , Brazil
- c Faculdade de Ciências Farmacêuticas - Universidade Estadual de Campinas (UNICAMP), Campinas , Campinas , São Paulo , Brazil
| | - Rogério Corrêa
- a Programa de Pós-Graduação em Ciências Farmacêuticas, Núcleo de Investigações Químico-Farmacêuticas (NIQFAR) , Universidade do Vale do Itajaí - UNIVALI , Itajaí , Santa Catarina , Brazil
| | - Valdir Cechinel Filho
- a Programa de Pós-Graduação em Ciências Farmacêuticas, Núcleo de Investigações Químico-Farmacêuticas (NIQFAR) , Universidade do Vale do Itajaí - UNIVALI , Itajaí , Santa Catarina , Brazil
| | - Franco Delle Monache
- a Programa de Pós-Graduação em Ciências Farmacêuticas, Núcleo de Investigações Químico-Farmacêuticas (NIQFAR) , Universidade do Vale do Itajaí - UNIVALI , Itajaí , Santa Catarina , Brazil
| | - Rivaldo Niero
- a Programa de Pós-Graduação em Ciências Farmacêuticas, Núcleo de Investigações Químico-Farmacêuticas (NIQFAR) , Universidade do Vale do Itajaí - UNIVALI , Itajaí , Santa Catarina , Brazil
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Mangiatordi GF, Alberga D, Trisciuzzi D, Lattanzi G, Nicolotti O. Human Aquaporin-4 and Molecular Modeling: Historical Perspective and View to the Future. Int J Mol Sci 2016; 17:ijms17071119. [PMID: 27420052 PMCID: PMC4964494 DOI: 10.3390/ijms17071119] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Revised: 06/30/2016] [Accepted: 07/02/2016] [Indexed: 12/26/2022] Open
Abstract
Among the different aquaporins (AQPs), human aquaporin-4 (hAQP4) has attracted the greatest interest in recent years as a new promising therapeutic target. Such a membrane protein is, in fact, involved in a multiple sclerosis-like immunopathology called Neuromyelitis Optica (NMO) and in several disorders resulting from imbalanced water homeostasis such as deafness and cerebral edema. The gap of knowledge in its functioning and dynamics at the atomistic level of detail has hindered the development of rational strategies for designing hAQP4 modulators. The application, lately, of molecular modeling has proved able to fill this gap providing a breeding ground to rationally address compounds targeting hAQP4. In this review, we give an overview of the important advances obtained in this field through the application of Molecular Dynamics (MD) and other complementary modeling techniques. The case studies presented herein are discussed with the aim of providing important clues for computational chemists and biophysicists interested in this field and looking for new challenges.
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Affiliation(s)
- Giuseppe Felice Mangiatordi
- Dipartimento di Farmacia-Scienze del Farmaco, Via Orabona, 4, University of Bari "Aldo Moro", 70126 Bari, Italy.
| | - Domenico Alberga
- Institut de Recherche de Chimie Paris CNRS Chimie ParisTech, PSL Research University, 11 rue P. et M. Curie, F-75005 Paris, France.
| | - Daniela Trisciuzzi
- Dipartimento di Farmacia-Scienze del Farmaco, Via Orabona, 4, University of Bari "Aldo Moro", 70126 Bari, Italy.
| | - Gianluca Lattanzi
- INFN-Sez. di Bari and Dipartimento di Medicina Clinica e Sperimentale, University of Foggia, Viale Pinto, 71122 Foggia, Italy.
| | - Orazio Nicolotti
- Dipartimento di Farmacia-Scienze del Farmaco, Via Orabona, 4, University of Bari "Aldo Moro", 70126 Bari, Italy.
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Boland MR, Tatonetti NP. Investigation of 7-dehydrocholesterol reductase pathway to elucidate off-target prenatal effects of pharmaceuticals: a systematic review. THE PHARMACOGENOMICS JOURNAL 2016; 16:411-29. [PMID: 27401223 PMCID: PMC5028238 DOI: 10.1038/tpj.2016.48] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Revised: 04/15/2016] [Accepted: 05/02/2016] [Indexed: 12/18/2022]
Abstract
Mendelian diseases contain important biological information regarding developmental effects of gene mutations that can guide drug discovery and toxicity efforts. In this review, we focus on Smith–Lemli–Opitz syndrome (SLOS), a rare Mendelian disease characterized by compound heterozygous mutations in 7-dehydrocholesterol reductase (DHCR7) resulting in severe fetal deformities. We present a compilation of SLOS-inducing DHCR7 mutations and the geographic distribution of those mutations in healthy and diseased populations. We observed that several mutations thought to be disease causing occur in healthy populations, indicating an incomplete understanding of the condition and highlighting new research opportunities. We describe the functional environment around DHCR7, including pharmacological DHCR7 inhibitors and cholesterol and vitamin D synthesis. Using PubMed, we investigated the fetal outcomes following prenatal exposure to DHCR7 modulators. First-trimester exposure to DHCR7 inhibitors resulted in outcomes similar to those of known teratogens (50 vs 48% born-healthy). DHCR7 activity should be considered during drug development and prenatal toxicity assessment.
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Affiliation(s)
- M R Boland
- Department of Biomedical Informatics, Columbia University, New York, NY, USA.,Observational Health Data Sciences and Informatics, Columbia University, New York, NY, USA
| | - N P Tatonetti
- Department of Biomedical Informatics, Columbia University, New York, NY, USA.,Observational Health Data Sciences and Informatics, Columbia University, New York, NY, USA.,Department of Systems Biology, Columbia University, New York, NY, USA.,Department of Medicine, Columbia University, New York, NY, USA
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81
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Mignani S, Huber S, Tomás H, Rodrigues J, Majoral JP. Compound high-quality criteria: a new vision to guide the development of drugs, current situation. Drug Discov Today 2016; 21:573-84. [PMID: 26802700 DOI: 10.1016/j.drudis.2016.01.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Revised: 01/12/2016] [Accepted: 01/13/2016] [Indexed: 02/08/2023]
Abstract
For several decades, the pharmaceutical industry has suffered due to major issues such as reductions of the number of FDA approved drugs and biologics. Several analyses have been highlighted that the 'druglikeness' is one of the strategies to improve succeed rates of screening such as, for instance, high-throughput screening (HTS), and then hits (as starting point), leads and clinical candidates. It is clear that the improvement of compound quality accelerates the drug discovery projects. The monitoring of several indices to avoid 'molecular obesity' (ADMET problems) of final drugs from good-quality 'low-fat' starting points represents today a powerful strategy of optimization process. The development of the new guides to find drugs highlighting attempts at improving the attrition rate from hits to final medicines by focusing on how to improve the druggability of hits, leads and drugs during the drug discovery process represents a key approach to design next better generation of medicines.
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Affiliation(s)
- Serge Mignani
- Université Paris Descartes, PRES Sorbonne Paris Cité, CNRS UMR 860, Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologique, 45, rue des Saints Pères, 75006 Paris, France.
| | - Scot Huber
- SCYNEXIS, Inc., P.O. Box 12878, Research Triangle Park, NC 27709, USA
| | - Helena Tomás
- CQM - Centro de Química da Madeira, MMRG, Universidade da Madeira, Campus Universitário da Penteada, 9000-390 Funchal, Portugal
| | - João Rodrigues
- CQM - Centro de Química da Madeira, MMRG, Universidade da Madeira, Campus Universitário da Penteada, 9000-390 Funchal, Portugal.
| | - Jean-Pierre Majoral
- Laboratoire de Chimie de Coordination du CNRS, 205 route de Narbonne, BP 44099, 31077 Toulouse Cedex 4, France; Université de Toulouse, UPS, INPT, 31077 Toulouse Cedex 4, France.
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82
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Dalecki AG, Malalasekera AP, Schaaf K, Kutsch O, Bossmann SH, Wolschendorf F. Combinatorial phenotypic screen uncovers unrecognized family of extended thiourea inhibitors with copper-dependent anti-staphylococcal activity. Metallomics 2016; 8:412-21. [PMID: 26935206 PMCID: PMC4838501 DOI: 10.1039/c6mt00003g] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The continuous rise of multi-drug resistant pathogenic bacteria has become a significant challenge for the health care system. In particular, novel drugs to treat infections of methicillin-resistant Staphylococcus aureus strains (MRSA) are needed, but traditional drug discovery campaigns have largely failed to deliver clinically suitable antibiotics. More than simply new drugs, new drug discovery approaches are needed to combat bacterial resistance. The recently described phenomenon of copper-dependent inhibitors has galvanized research exploring the use of metal-coordinating molecules to harness copper's natural antibacterial properties for therapeutic purposes. Here, we describe the results of the first concerted screening effort to identify copper-dependent inhibitors of Staphylococcus aureus. A standard library of 10 000 compounds was assayed for anti-staphylococcal activity, with hits defined as those compounds with a strict copper-dependent inhibitory activity. A total of 53 copper-dependent hit molecules were uncovered, similar to the copper independent hit rate of a traditionally executed campaign conducted in parallel on the same library. Most prominent was a hit family with an extended thiourea core structure, termed the NNSN motif. This motif resulted in copper-dependent and copper-specific S. aureus inhibition, while simultaneously being well tolerated by eukaryotic cells. Importantly, we could demonstrate that copper binding by the NNSN motif is highly unusual and likely responsible for the promising biological qualities of these compounds. A subsequent chemoinformatic meta-analysis of the ChEMBL chemical database confirmed the NNSNs as an unrecognized staphylococcal inhibitor, despite the family's presence in many chemical screening libraries. Thus, our copper-biased screen has proven able to discover inhibitors within previously screened libraries, offering a mechanism to reinvigorate exhausted molecular collections.
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Affiliation(s)
- Alex G Dalecki
- Department of Medicine, University of Alabama at Birmingham, 845 19th Street S, Birmingham, AL 35294, USA.
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83
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Newman DJ, Cragg GM. Natural Products as Sources of New Drugs from 1981 to 2014. JOURNAL OF NATURAL PRODUCTS 2016; 79:629-61. [PMID: 26852623 DOI: 10.1021/acs.jnatprod.5b01055] [Citation(s) in RCA: 3708] [Impact Index Per Article: 463.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
This contribution is a completely updated and expanded version of the four prior analogous reviews that were published in this journal in 1997, 2003, 2007, and 2012. In the case of all approved therapeutic agents, the time frame has been extended to cover the 34 years from January 1, 1981, to December 31, 2014, for all diseases worldwide, and from 1950 (earliest so far identified) to December 2014 for all approved antitumor drugs worldwide. As mentioned in the 2012 review, we have continued to utilize our secondary subdivision of a "natural product mimic", or "NM", to join the original primary divisions and the designation "natural product botanical", or "NB", to cover those botanical "defined mixtures" now recognized as drug entities by the U.S. FDA (and similar organizations). From the data presented in this review, the utilization of natural products and/or their novel structures, in order to discover and develop the final drug entity, is still alive and well. For example, in the area of cancer, over the time frame from around the 1940s to the end of 2014, of the 175 small molecules approved, 131, or 75%, are other than "S" (synthetic), with 85, or 49%, actually being either natural products or directly derived therefrom. In other areas, the influence of natural product structures is quite marked, with, as expected from prior information, the anti-infective area being dependent on natural products and their structures. We wish to draw the attention of readers to the rapidly evolving recognition that a significant number of natural product drugs/leads are actually produced by microbes and/or microbial interactions with the "host from whence it was isolated", and therefore it is considered that this area of natural product research should be expanded significantly.
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Affiliation(s)
- David J Newman
- NIH Special Volunteer, Wayne, Pennsylvania 19087, United States
| | - Gordon M Cragg
- NIH Special Volunteer, Bethesda, Maryland 20814, United States
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84
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Szymańska-Michalak A, Wawrzyniak D, Framski G, Kujda M, Zgoła P, Stawinski J, Barciszewski J, Boryski J, Kraszewski A. New 3'-O-aromatic acyl-5-fluoro-2'-deoxyuridine derivatives as potential anticancer agents. Eur J Med Chem 2016; 115:41-52. [PMID: 26994842 DOI: 10.1016/j.ejmech.2016.03.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Revised: 03/02/2016] [Accepted: 03/03/2016] [Indexed: 12/29/2022]
Abstract
New aromatic and aliphatic 3'-O-acyl-5-fluoro-2'-deoxyuridine derivatives were synthesized and evaluated as candidates for prodrugs against various cancer cell lines. As the most promising candidate for antimalignant therapeutics was found a dual-acting acyl derivative 7h, which apparently released not only the known anticancer nucleoside, 5-fluoro-2'-deoxyuridine (FdU), but also an additional active metabolite, acetylsalicylic acid, reinforcing thus therapeutic effect of FdU. Promising therapeutic indices showed also some aromatic dicarboxylic acids derivatives decorated with FdU esters (11 and 12).
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Affiliation(s)
| | - Dariusz Wawrzyniak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznań, Poland
| | - Grzegorz Framski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznań, Poland
| | - Marta Kujda
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239, Cracow, Poland
| | - Paulina Zgoła
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznań, Poland
| | - Jacek Stawinski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznań, Poland
| | - Jan Barciszewski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznań, Poland
| | - Jerzy Boryski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznań, Poland
| | - Adam Kraszewski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznań, Poland.
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85
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Mignani S, Huber S, Tomás H, Rodrigues J, Majoral JP. Why and how have drug discovery strategies in pharma changed? What are the new mindsets? Drug Discov Today 2016; 21:239-49. [PMID: 26376356 DOI: 10.1016/j.drudis.2015.09.007] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Revised: 06/30/2015] [Accepted: 09/08/2015] [Indexed: 02/08/2023]
Abstract
In the pharmaceutical industry the long-term challenge of drug innovation is the key phrase throughout R&D that refers to increasing the output of original drug candidate molecules. To increase R&D productivity, implementation of new and strategic R&D orientations to develop new approaches or systems to identify hits and leads efficiently has taken place and enabled all scientists working in the drug discovery domain to develop innovative medicines for the 21st century.
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Affiliation(s)
- Serge Mignani
- Université Paris Descartes, PRES Sorbonne Paris Cité, CNRS UMR 860, Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologique, 45, rue des Saints Peres, 75006, Paris, France.
| | - Scot Huber
- SCYNEXIS Inc., P.O. Box 12878, Research Triangle Park, NC 27709, USA
| | - Helena Tomás
- CQM - Centro de Química da Madeira, MMRG, Universidade da Madeira, Campus Universitário da Penteada, 9000-390 Funchal, Portugal
| | - João Rodrigues
- CQM - Centro de Química da Madeira, MMRG, Universidade da Madeira, Campus Universitário da Penteada, 9000-390 Funchal, Portugal.
| | - Jean-Pierre Majoral
- Laboratoire de Chimie de Coordination du CNRS, 205 route de Narbonne, BP 44099, 31077 Toulouse Cedex 4, France; Université de Toulouse, UPS, INPT, 31077 Toulouse Cedex 4, France.
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86
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Egieyeh SA, Syce J, Malan SF, Christoffels A. Prioritization of anti-malarial hits from nature: chemo-informatic profiling of natural products with in vitro antiplasmodial activities and currently registered anti-malarial drugs. Malar J 2016; 15:50. [PMID: 26823078 PMCID: PMC4731946 DOI: 10.1186/s12936-016-1087-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2015] [Accepted: 01/09/2016] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND A large number of natural products have shown in vitro antiplasmodial activities. Early identification and prioritization of these natural products with potential for novel mechanism of action, desirable pharmacokinetics and likelihood for development into drugs is advantageous. Chemo-informatic profiling of these natural products were conducted and compared to currently registered anti-malarial drugs (CRAD). METHODS Natural products with in vitro antiplasmodial activities (NAA) were compiled from various sources. These natural products were sub-divided into four groups based on inhibitory concentration (IC50). Key molecular descriptors and physicochemical properties were computed for these compounds and analysis of variance used to assess statistical significance amongst the sets of compounds. Molecular similarity analysis, estimation of drug-likeness, in silico pharmacokinetic profiling, and exploration of structure-activity landscape were also carried out on these sets of compounds. RESULTS A total of 1040 natural products were selected and a total of 13 molecular descriptors were analysed. Significant differences were observed among the sub-groups of NAA and CRAD for at least 11 of the molecular descriptors, including number of hydrogen bond donors and acceptors, molecular weight, polar and hydrophobic surface areas, chiral centres, oxygen and nitrogen atoms, and shape index. The remaining molecular descriptors, including clogP, number of rotatable bonds and number of aromatic rings, did not show any significant difference when comparing the two compound sets. Molecular similarity and chemical space analysis identified natural products that were structurally diverse from CRAD. Prediction of the pharmacokinetic properties and drug-likeness of these natural products identified over 50% with desirable drug-like properties. Nearly 70% of all natural products were identified as potentially promiscuous compounds. Structure-activity landscape analysis highlighted compound pairs that form 'activity cliffs'. In all, prioritization strategies for the NAA were proposed. CONCLUSIONS Chemo-informatic profiling of NAA and CRAD have produced a wealth of information that may guide decisions and facilitate anti-malarial drug development from natural products. Articulation of the information provided within an interactive data-mining environment led to a prioritized list of NAA.
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Affiliation(s)
- Samuel Ayodele Egieyeh
- South African Medial Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville, Cape Town, South Africa. .,School of Pharmacy, University of the Western Cape, Bellville, Cape Town, South Africa.
| | - James Syce
- School of Pharmacy, University of the Western Cape, Bellville, Cape Town, South Africa.
| | - Sarel F Malan
- School of Pharmacy, University of the Western Cape, Bellville, Cape Town, South Africa.
| | - Alan Christoffels
- South African Medial Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Bellville, Cape Town, South Africa.
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87
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Sharma OP, Kumar MS. Essential proteins and possible therapeutic targets of Wolbachia endosymbiont and development of FiloBase--a comprehensive drug target database for Lymphatic filariasis. Sci Rep 2016; 6:19842. [PMID: 26806463 PMCID: PMC4726333 DOI: 10.1038/srep19842] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 10/27/2015] [Indexed: 11/26/2022] Open
Abstract
Lymphatic filariasis (Lf) is one of the oldest and most debilitating tropical diseases. Millions of people are suffering from this prevalent disease. It is estimated to infect over 120 million people in at least 80 nations of the world through the tropical and subtropical regions. More than one billion people are in danger of getting affected with this life-threatening disease. Several studies were suggested its emerging limitations and resistance towards the available drugs and therapeutic targets for Lf. Therefore, better medicine and drug targets are in demand. We took an initiative to identify the essential proteins of Wolbachia endosymbiont of Brugia malayi, which are indispensable for their survival and non-homologous to human host proteins. In this current study, we have used proteome subtractive approach to screen the possible therapeutic targets for wBm. In addition, numerous literatures were mined in the hunt for potential drug targets, drugs, epitopes, crystal structures, and expressed sequence tag (EST) sequences for filarial causing nematodes. Data obtained from our study were presented in a user friendly database named FiloBase. We hope that information stored in this database may be used for further research and drug development process against filariasis. URL: http://filobase.bicpu.edu.in.
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Affiliation(s)
- Om Prakash Sharma
- Centre for Bioinformatics, School of Life Science, Pondicherry University, Pondicherry-605014, India
| | - Muthuvel Suresh Kumar
- Centre for Bioinformatics, School of Life Science, Pondicherry University, Pondicherry-605014, India
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88
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Batool N, Waqar M, Batool S. Comparative genomics study for identification of putative drug targets in Salmonella typhi Ty2. Gene 2016; 576:544-59. [PMID: 26555890 DOI: 10.1016/j.gene.2015.11.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2015] [Revised: 11/02/2015] [Accepted: 11/03/2015] [Indexed: 11/16/2022]
Abstract
Typhoid presents a major health concern in developing countries with an estimated annual infection rate of 21 million. The disease is caused by Salmonella typhi, a pathogenic bacterium acquiring multiple drug resistance. We aim to identify proteins that could prove to be putative drug targets in the genome of S. typhi str. Ty2. We employed comparative and subtractive genomics to identify targets that are absent in humans and are essential to S. typhi Ty2. We concluded that 46 proteins essential to pathogen are absent in the host genome. Filtration on the basis of drug target prioritization singled out 20 potentially therapeutic targets. Their absence in the host and specificity to S. typhi Ty2 makes them ideal targets for treating typhoid in Homo sapiens. 3D structures of two of the final target enzymes, MurA and MurB have been predicted via homology modeling which are then used for a docking study.
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Affiliation(s)
- Nisha Batool
- Department of Biosciences, COMSATS Institute of Information Technology, Park Road, Chak Shahzad, Islamabad 45520, Pakistan.
| | - Maleeha Waqar
- Department of Biosciences, COMSATS Institute of Information Technology, Park Road, Chak Shahzad, Islamabad 45520, Pakistan.
| | - Sidra Batool
- Department of Biosciences, COMSATS Institute of Information Technology, Park Road, Chak Shahzad, Islamabad 45520, Pakistan.
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89
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Abstract
INTRODUCTION The hybridization of biologically active molecules is a powerful tool for drug discovery used to target a variety of diseases. It offers the prospect of better drugs for the treatment of a number of illnesses including cancer, malaria, tuberculosis and AIDS. Hybrid drugs can provide combination therapies in a single multi-functional agent and, by doing so, be more specific and powerful than conventional classic treatments. This research field is in great expansion and attracts many researchers worldwide. AREA COVERED This review covers the main research published between early 2013 to mid-2015 and takes into account several previous reviews on the subject. Its intention is to showcase the most recent advances reported towards the development of molecular hybrids in drug discovery. Particular attention is given to anticancer hybrids throughout the review. EXPERT OPINION Current advances show that molecular hybrids of biologically active molecules can lead to powerful therapeutics. Natural products play a key role in this field. It is also believed that toxin hybrids present a great opportunity for future progress and should be further explored. Furthermore, the synthesis of hybrid organometallics should be systematically studied as it can lead to potent drugs. The crucial requirement for growth still remains the efficacy of synthesis. Hence, the development of efficient synthetic methods allowing rapid access to diverse series of hybrids must be further investigated by researchers.
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Affiliation(s)
- Gervais Bérubé
- a Département de Chimie, Biochimie et Physique , Université du Québec à Trois-Rivières , Québec , Canada
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90
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Mushtaque M, Ahamad S, Jahan M, Hussain K, Khan MS. Azole-based compounds as antiamoebic agents: a perspective using theoretical calculations. RSC Adv 2016. [DOI: 10.1039/c5ra20552b] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Diseases caused by protozoal organisms are responsible for significant mortality and morbidity worldwide. Amoebiasis caused byEntamoeba histolyticais an example of such diseases.
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Affiliation(s)
- Md. Mushtaque
- School of Physical and Molecular Sciences (Chemistry)
- Al-Falah University
- Faridabad
- India
| | - Shahzaib Ahamad
- Department of Biotechnology
- College of Engineering & Technology
- IFTM
- Moradabad
- India
| | - Meriyam Jahan
- School of Physical and Molecular Sciences (Chemistry)
- Al-Falah University
- Faridabad
- India
| | - Kakul Hussain
- Medical Lab Science Department
- College of Applied Medical Sciences
- Salmanbin Abdulaziz University
- Wadi Adadawasir
- Saudi Arabia
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91
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Mitsopoulos C, Schierz AC, Workman P, Al-Lazikani B. Distinctive Behaviors of Druggable Proteins in Cellular Networks. PLoS Comput Biol 2015; 11:e1004597. [PMID: 26699810 PMCID: PMC4689399 DOI: 10.1371/journal.pcbi.1004597] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 10/13/2015] [Indexed: 01/12/2023] Open
Abstract
The interaction environment of a protein in a cellular network is important in defining the role that the protein plays in the system as a whole, and thus its potential suitability as a drug target. Despite the importance of the network environment, it is neglected during target selection for drug discovery. Here, we present the first systematic, comprehensive computational analysis of topological, community and graphical network parameters of the human interactome and identify discriminatory network patterns that strongly distinguish drug targets from the interactome as a whole. Importantly, we identify striking differences in the network behavior of targets of cancer drugs versus targets from other therapeutic areas and explore how they may relate to successful drug combinations to overcome acquired resistance to cancer drugs. We develop, computationally validate and provide the first public domain predictive algorithm for identifying druggable neighborhoods based on network parameters. We also make available full predictions for 13,345 proteins to aid target selection for drug discovery. All target predictions are available through canSAR.icr.ac.uk. Underlying data and tools are available at https://cansar.icr.ac.uk/cansar/publications/druggable_network_neighbourhoods/. The need for well-validated targets for drug discovery is more pressing than ever, especially in cancer in view of resistance to current therapeutics coupled with late stage drug failures. Target prioritization and selection methodologies have typically not taken the protein interaction environment into account. Here we analyze a large representation of the human interactome comprising almost 90,000 interactions between 13,345 proteins. We assess these interactions using an extensive set of topological, graphical and community parameters, and we identify behaviors that distinguish the protein interaction environments of drug targets from the general interactome. Moreover, we identify clear distinctions between the network environment of cancer-drug targets and targets from other therapeutics areas. We use these distinguishing properties to build a predictive methodology to prioritize potential drug targets based on network parameters alone and we validate our predictive models using current FDA-approved drug targets. Our models provide an objective, interactome-based target prioritization methodology to complement existing structure-based and ligand-based prioritization methods. We provide our interactome-based predictions alongside other druggability predictors within the public canSAR resource (cansar.icr.ac.uk).
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Affiliation(s)
- Costas Mitsopoulos
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, United Kingdom
| | - Amanda C. Schierz
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, United Kingdom
| | - Paul Workman
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, United Kingdom
| | - Bissan Al-Lazikani
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, United Kingdom
- * E-mail:
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92
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Mondal SI, Ferdous S, Jewel NA, Akter A, Mahmud Z, Islam MM, Afrin T, Karim N. Identification of potential drug targets by subtractive genome analysis of Escherichia coli O157:H7: an in silico approach. Adv Appl Bioinform Chem 2015; 8:49-63. [PMID: 26677339 PMCID: PMC4677596 DOI: 10.2147/aabc.s88522] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Bacterial enteric infections resulting in diarrhea, dysentery, or enteric fever constitute a huge public health problem, with more than a billion episodes of disease annually in developing and developed countries. In this study, the deadly agent of hemorrhagic diarrhea and hemolytic uremic syndrome, Escherichia coli O157:H7 was investigated with extensive computational approaches aimed at identifying novel and broad-spectrum antibiotic targets. A systematic in silico workflow consisting of comparative genomics, metabolic pathways analysis, and additional drug prioritizing parameters was used to identify novel drug targets that were essential for the pathogen’s survival but absent in its human host. Comparative genomic analysis of Kyoto Encyclopedia of Genes and Genomes annotated metabolic pathways identified 350 putative target proteins in E. coli O157:H7 which showed no similarity to human proteins. Further bio-informatic approaches including prediction of subcellular localization, calculation of molecular weight, and web-based investigation of 3D structural characteristics greatly aided in filtering the potential drug targets from 350 to 120. Ultimately, 44 non-homologous essential proteins of E. coli O157:H7 were prioritized and proved to have the eligibility to become novel broad-spectrum antibiotic targets and DNA polymerase III alpha (dnaE) was the top-ranked among these targets. Moreover, druggability of each of the identified drug targets was evaluated by the DrugBank database. In addition, 3D structure of the dnaE was modeled and explored further for in silico docking with ligands having potential druggability. Finally, we confirmed that the compounds N-coeleneterazine and N-(1,4-dihydro-5H-tetrazol-5-ylidene)-9-oxo-9H-xanthene-2-sulfon-amide were the most suitable ligands of dnaE and hence proposed as the potential inhibitors of this target protein. The results of this study could facilitate the discovery and release of new and effective drugs against E. coli O157:H7 and other deadly human bacterial pathogens.
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Affiliation(s)
- Shakhinur Islam Mondal
- Genetic Engineering and Biotechnology Department, Shahjalal University of Science and Technology, Sylhet, Bangladesh ; Division of Microbiology, Department of Infectious Diseases, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Sabiha Ferdous
- Genetic Engineering and Biotechnology Department, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - Nurnabi Azad Jewel
- Genetic Engineering and Biotechnology Department, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - Arzuba Akter
- Biochemistry and Molecular Biology Department, Shahjalal University of Science and Technology, Sylhet, Bangladesh ; Division of Microbiology, Department of Infectious Diseases, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Zabed Mahmud
- Genetic Engineering and Biotechnology Department, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - Md Muzahidul Islam
- Genetic Engineering and Biotechnology Department, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - Tanzila Afrin
- Department of Pharmacy, East West University, Aftabnagar, Bangladesh
| | - Nurul Karim
- Biochemistry and Molecular Biology Department, Jahangirnagar University, Savar, Bangladesh ; Division of Parasitology, Department of Infectious Diseases, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
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93
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Lavanya P, Ramaiah S, Anbarasu A. Computational analysis reveal inhibitory action of nimbin against dengue viral envelope protein. Virusdisease 2015; 26:243-54. [PMID: 26645034 DOI: 10.1007/s13337-015-0280-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2014] [Accepted: 09/16/2015] [Indexed: 11/29/2022] Open
Abstract
Dengue has emerged to be global health problem worldwide. Hence there is an immediate need to adopt new strategies in the development of effective anti-dengue drugs. Extracts from the leaves of Azadirachta indica has been traditionally used in folk medicine for viral infections. In the present study we report the anti-viral potency of nimbin, the active compound from the neem leaf extract against the envelope protein of dengue virus. Progression of viral entry into the host cell is facilitated by the envelope protein of dengue virus, suggesting; it as an effective anti-viral target. Nimbin is found to be effective against the envelope protein of all four types of dengue virus (dengue 1-4), which is evident from our in silico analysis. Our findings suggest the clinical importance of nimbin, which can serve as effective lead compound for further analysis.
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Affiliation(s)
- P Lavanya
- Medical and Biological Computing Laboratory, School of Biosciences and Technology, VIT University, Vellore, Tamil Nadu 632014 India
| | - Sudha Ramaiah
- Medical and Biological Computing Laboratory, School of Biosciences and Technology, VIT University, Vellore, Tamil Nadu 632014 India
| | - Anand Anbarasu
- Medical and Biological Computing Laboratory, School of Biosciences and Technology, VIT University, Vellore, Tamil Nadu 632014 India
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94
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Stone VN, Parikh HI, El-rami F, Ge X, Chen W, Zhang Y, Kellogg GE, Xu P. Identification of Small-Molecule Inhibitors against Meso-2, 6-Diaminopimelate Dehydrogenase from Porphyromonas gingivalis. PLoS One 2015; 10:e0141126. [PMID: 26544875 PMCID: PMC4636305 DOI: 10.1371/journal.pone.0141126] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 10/05/2015] [Indexed: 01/03/2023] Open
Abstract
Species-specific antimicrobial therapy has the potential to combat the increasing threat of antibiotic resistance and alteration of the human microbiome. We therefore set out to demonstrate the beginning of a pathogen-selective drug discovery method using the periodontal pathogen Porphyromonas gingivalis as a model. Through our knowledge of metabolic networks and essential genes we identified a “druggable” essential target, meso-diaminopimelate dehydrogenase, which is found in a limited number of species. We adopted a high-throughput virtual screen method on the ZINC chemical library to select a group of potential small-molecule inhibitors. Meso-diaminopimelate dehydrogenase from P. gingivalis was first expressed and purified in Escherichia coli then characterized for enzymatic inhibitor screening studies. Several inhibitors with similar structural scaffolds containing a sulfonamide core and aromatic substituents showed dose-dependent inhibition. These compounds were further assayed showing reasonable whole-cell activity and the inhibition mechanism was determined. We conclude that the establishment of this target and screening strategy provides a model for the future development of new antimicrobials.
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Affiliation(s)
- Victoria N. Stone
- Philips Institute for Oral Health Research, Virginia Commonwealth University, Richmond, Virginia, United States of America
- Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Hardik I. Parikh
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Fadi El-rami
- Philips Institute for Oral Health Research, Virginia Commonwealth University, Richmond, Virginia, United States of America
- Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Xiuchun Ge
- Philips Institute for Oral Health Research, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Weihau Chen
- Philips Institute for Oral Health Research, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Yan Zhang
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Glen E. Kellogg
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, Virginia, United States of America
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Ping Xu
- Philips Institute for Oral Health Research, Virginia Commonwealth University, Richmond, Virginia, United States of America
- Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, Virginia, United States of America
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, Virginia, United States of America
- * E-mail:
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95
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Talevi A. Multi-target pharmacology: possibilities and limitations of the "skeleton key approach" from a medicinal chemist perspective. Front Pharmacol 2015; 6:205. [PMID: 26441661 PMCID: PMC4585027 DOI: 10.3389/fphar.2015.00205] [Citation(s) in RCA: 215] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2015] [Accepted: 09/04/2015] [Indexed: 11/23/2022] Open
Abstract
Multi-target drugs have raised considerable interest in the last decade owing to their advantages in the treatment of complex diseases and health conditions linked to drug resistance issues. Prospective drug repositioning to treat comorbid conditions is an additional, overlooked application of multi-target ligands. While medicinal chemists usually rely on some version of the lock and key paradigm to design novel therapeutics, modern pharmacology recognizes that the mid- and long-term effects of a given drug on a biological system may depend not only on the specific ligand-target recognition events but also on the influence of the repeated administration of a drug on the cell gene signature. The design of multi-target agents usually imposes challenging restrictions on the topology or flexibility of the candidate drugs, which are briefly discussed in the present article. Finally, computational strategies to approach the identification of novel multi-target agents are overviewed.
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Affiliation(s)
- Alan Talevi
- Medicinal Chemistry, Department of Biological Sciences, Faculty of Exact Sciences, National University of La Plata , La Plata, Argentina
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96
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Abstract
The dramatic rise in microbial drug resistance in recent years has led to ongoing searches for novel drugs to add to the armory against infectious disease. Nevertheless, a paucity of new antibacterial drugs in discovery and development pipelines using traditional approaches has prompted a variety of unconventional and disruptive strategies for antibacterial drug discovery. Herein, we review recent nontraditional approaches that have been piloted for early drug discovery efforts. These unique methodologies open new avenues for finding the next generation of antimicrobials.
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Affiliation(s)
- Maya A Farha
- M.G. DeGroote Institute for Infectious Disease Research, and Department of Biochemistry and Biomedical Sciences, McMaster University, Ontario, Canada
| | - Eric D Brown
- M.G. DeGroote Institute for Infectious Disease Research, and Department of Biochemistry and Biomedical Sciences, McMaster University, Ontario, Canada
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97
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Nazarshodeh E, Shiri F, Ghasemi JB. 3D-QSAR and virtual screening studies in identification of new Rho kinase inhibitors with different scaffolds. JOURNAL OF THE IRANIAN CHEMICAL SOCIETY 2015. [DOI: 10.1007/s13738-015-0669-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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98
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Kang CM, Liu DQ, Wang XY, Yu RL, Lv YT. The unbinding studies of vascular endothelial growth factor receptor-2 protein tyrosine kinase type II inhibitors. J Mol Graph Model 2015; 59:130-5. [PMID: 25989626 DOI: 10.1016/j.jmgm.2015.04.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Revised: 04/17/2015] [Accepted: 04/20/2015] [Indexed: 01/16/2023]
Abstract
Vascular endothelial growth factor receptor-2 (VEGFR-2) tyrosine kinase has two conformations, active and inactive conformations. Type II inhibitors bind to inactive conformation. It has two possible binding/unbinding paths. To explore the unbinding path of inhibitor 01-435 that was generated by fragment build in the binding pocket of VEGFR-2, molecular dynamics (MD) simulation was performed on the crystal structure of VEGFR-2 in complex with 01-435, then steered molecular dynamics (SMD) simulation was executed on the crystal structure of VEGFR-2 in complex with 01-435. Pull force, van der Waals and electrostatic interaction along the two paths were calculated by using SMD simulation. The SMD simulation results indicate that the more favorable path for inhibitor dissociation is along with the traditional ATP-channel rather than the allosteric-pocket-channel, which is mainly due to the less electrostatic interaction that the ligand suffers during dissociation process along the traditional ATP-channel.
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Affiliation(s)
- Cong-min Kang
- College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao 266042, PR China
| | - Dong-qing Liu
- College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao 266042, PR China
| | - Xin-ying Wang
- College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao 266042, PR China
| | - Ri-lei Yu
- School of Pharmacy, Ocean University of China, Qingdao 266003, PR China
| | - Ying-tao Lv
- College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao 266042, PR China.
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99
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In silico identification of targets for a novel scaffold, 2-thiazolylimino-5-benzylidin-thiazolidin-4-one. Mol Divers 2015; 19:855-70. [PMID: 25894361 DOI: 10.1007/s11030-015-9578-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2013] [Accepted: 03/12/2015] [Indexed: 11/27/2022]
Abstract
Thiazolidinone derivatives have been found to exhibit a wide range of pharmacological activities. 2-Thiazolylimino-5-benzylidene-thiazolidin-4-one derivatives show antibacterial activity in in vitro tests which are comparable to marketed drugs. However, the target for this scaffold remains yet to be identified. In our work, we identified seven putative targets for this scaffold using web servers such as DRAR-CPI, PharmMapper, and TarFisDock and databases such as BindingDB and ChEMBL. Each of these servers used different algorithms and scoring functions for protein target identification. Further, these targets are substantiated by molecular docking analysis. Based on the docking studies, scaffold 2-thiazolylimino-5-benzylidene-thiazolidin-4-one is observed to exhibit affinity against diverse targets, particularly, towards COX-2, acetylcholinesterase, aldose reductase, and thyroid hormone receptor alpha. This study describes an initial probability that these proteins may be targeted by this scaffold.
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100
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Salunke SB, Azad AK, Kapuriya NP, Balada-Llasat JM, Pancholi P, Schlesinger LS, Chen CS. Design and synthesis of novel anti-tuberculosis agents from the celecoxib pharmacophore. Bioorg Med Chem 2015; 23:1935-43. [PMID: 25818768 DOI: 10.1016/j.bmc.2015.03.041] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Revised: 03/03/2015] [Accepted: 03/15/2015] [Indexed: 11/15/2022]
Abstract
The identification of compounds with anti-mycobacterial activity within classes of molecules that have been developed for other purposes is a fruitful approach for the development of anti-tuberculosis (TB) agents. In this study we used the scaffold of celecoxib which exhibits several activities against different pathogens, for the design and focused synthesis of a library of 64 compounds. For the primary screen, we used a bioluminescence-based method by constructing a luciferase-expressing reporter M.tb strain which contains the entire bacterial Lux operon cloned in a mycobacterial integrative expression vector. Through the screening of this library, we identified 6 hit compounds with high in vitro anti-mycobacterial activity (IC₅₀ ∼0.18-0.48 μM). In particular, compounds 41, 51 and 53 were capable of inhibiting M.tb as effectively as the anti-TB drug isoniazid (INH) at 5 μM over a 72-h period, as analyzed by both bioluminescence- and colony forming unit (CFU)-based assays. All hit compounds also showed anti-M.tb activities against several multi-drug-resistant (MDR) strains. Most of the hit compounds showed no cytotoxicity for human macrophages at concentrations as high as 40 μM, setting the stage for further optimization and development of these anti-TB hit compounds both ex vivo and in vivo.
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Affiliation(s)
- Santosh B Salunke
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, 500 West 12th Avenue, Columbus, OH 43210, United States
| | - Abul K Azad
- Center for Microbial Interface Biology, The Ohio State University, 460 W 12th Avenue, Columbus, OH 43210, United States; Department of Microbial Infection and Immunity, The Ohio State University College of Medicine, Wexner Medical Center, 460 W 12th Avenue, Columbus, OH 43210, United States
| | - Naval P Kapuriya
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, 500 West 12th Avenue, Columbus, OH 43210, United States; Division of Pharmaceutical and Organic Chemistry, M. & N. Virani Science College, Saurashtra University, Rajkot 360005, Gujarat, India
| | - Joan-Miquel Balada-Llasat
- Department of Pathology, The Ohio State University, 410 W. 10th Avenue, Columbus, OH 43210, United States
| | - Preeti Pancholi
- Department of Pathology, The Ohio State University, 410 W. 10th Avenue, Columbus, OH 43210, United States
| | - Larry S Schlesinger
- Center for Microbial Interface Biology, The Ohio State University, 460 W 12th Avenue, Columbus, OH 43210, United States; Department of Microbial Infection and Immunity, The Ohio State University College of Medicine, Wexner Medical Center, 460 W 12th Avenue, Columbus, OH 43210, United States.
| | - Ching-Shih Chen
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, 500 West 12th Avenue, Columbus, OH 43210, United States; Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan.
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