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Ivanova E, Osipova M, Vasilieva T, Eremkin A, Markova S, Zazhivihina E, Smirnova S, Mitrasov Y, Nasakin O. The Recycling of Substandard Rocket Fuel N,N-Dimethylhydrazine via the Involvement of Its Hydrazones Derived from Glyoxal, Acrolein, Metacrolein, Crotonaldehyde, and Formaldehyde in Organic Synthesis. Int J Mol Sci 2023; 24:17196. [PMID: 38139025 PMCID: PMC10742919 DOI: 10.3390/ijms242417196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 11/05/2023] [Accepted: 12/01/2023] [Indexed: 12/24/2023] Open
Abstract
"Heptil" (unsymmetrical dimethylhydrazine-UDMH) is extensively employed worldwide as a propellant for rocket engines. However, UDMH constantly loses its properties as a result of its continuous and uncontrolled absorption of moisture, which cannot be rectified. This situation threatens its long-term usability. UDMH is an exceedingly toxic compound (Hazard Class 1), which complicates its transportation and disposal. Incineration is currently the only method used for its disposal, but this process generates oxidation by-products that are even more toxic than the original UDMH. A more benign approach involves its immediate reaction with a formalin solution to form 1,1-dimethyl-2-methylene hydrazone (MDH), which is significantly less toxic by an order of magnitude. MDH can then be polymerized under acidic conditions, and the resulting product can be burned, yielding substantial amounts of nitrogen oxides. This review seeks to shift the focus of MDH from incineration towards its application in the synthesis of relatively non-toxic and readily available analogs of various pharmaceutical substances. We aim to bring the attention of the international chemical community to the distinctive properties of MDH, as well as other hydrazones (such as glyoxal, acrolein, crotonal, and meta-crolyl), wherein each structural fragment can initiate unique transformations that have potential applications in molecular design, pharmaceutical research, and medicinal chemistry.
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Affiliation(s)
- Elizaveta Ivanova
- Organic and Pharmaceutical Chemistry Department, Ulyanov Chuvash State University, Moskovsky Prospect, 15, 428015 Cheboksary, Russia; (E.I.); (M.O.); (T.V.); (A.E.); (S.M.); (E.Z.); (S.S.)
| | - Margarita Osipova
- Organic and Pharmaceutical Chemistry Department, Ulyanov Chuvash State University, Moskovsky Prospect, 15, 428015 Cheboksary, Russia; (E.I.); (M.O.); (T.V.); (A.E.); (S.M.); (E.Z.); (S.S.)
| | - Tatyana Vasilieva
- Organic and Pharmaceutical Chemistry Department, Ulyanov Chuvash State University, Moskovsky Prospect, 15, 428015 Cheboksary, Russia; (E.I.); (M.O.); (T.V.); (A.E.); (S.M.); (E.Z.); (S.S.)
| | - Alexey Eremkin
- Organic and Pharmaceutical Chemistry Department, Ulyanov Chuvash State University, Moskovsky Prospect, 15, 428015 Cheboksary, Russia; (E.I.); (M.O.); (T.V.); (A.E.); (S.M.); (E.Z.); (S.S.)
| | - Svetlana Markova
- Organic and Pharmaceutical Chemistry Department, Ulyanov Chuvash State University, Moskovsky Prospect, 15, 428015 Cheboksary, Russia; (E.I.); (M.O.); (T.V.); (A.E.); (S.M.); (E.Z.); (S.S.)
| | - Ekaterina Zazhivihina
- Organic and Pharmaceutical Chemistry Department, Ulyanov Chuvash State University, Moskovsky Prospect, 15, 428015 Cheboksary, Russia; (E.I.); (M.O.); (T.V.); (A.E.); (S.M.); (E.Z.); (S.S.)
| | - Svetlana Smirnova
- Organic and Pharmaceutical Chemistry Department, Ulyanov Chuvash State University, Moskovsky Prospect, 15, 428015 Cheboksary, Russia; (E.I.); (M.O.); (T.V.); (A.E.); (S.M.); (E.Z.); (S.S.)
| | - Yurii Mitrasov
- Organic and Pharmaceutical Chemistry Department, Yakovlev Chuvash State Pedagogical University, K. Marx Street, 38, 428000 Cheboksary, Russia;
| | - Oleg Nasakin
- Organic and Pharmaceutical Chemistry Department, Ulyanov Chuvash State University, Moskovsky Prospect, 15, 428015 Cheboksary, Russia; (E.I.); (M.O.); (T.V.); (A.E.); (S.M.); (E.Z.); (S.S.)
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Kumar A, Zhang KYJ. Advances in the Development of Shape Similarity Methods and Their Application in Drug Discovery. Front Chem 2018; 6:315. [PMID: 30090808 PMCID: PMC6068280 DOI: 10.3389/fchem.2018.00315] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 07/09/2018] [Indexed: 12/21/2022] Open
Abstract
Molecular similarity is a key concept in drug discovery. It is based on the assumption that structurally similar molecules frequently have similar properties. Assessment of similarity between small molecules has been highly effective in the discovery and development of various drugs. Especially, two-dimensional (2D) similarity approaches have been quite popular due to their simplicity, accuracy and efficiency. Recently, the focus has been shifted toward the development of methods involving the representation and comparison of three-dimensional (3D) conformation of small molecules. Among the 3D similarity methods, evaluation of shape similarity is now gaining attention for its application not only in virtual screening but also in molecular target prediction, drug repurposing and scaffold hopping. A wide range of methods have been developed to describe molecular shape and to determine the shape similarity between small molecules. The most widely used methods include atom distance-based methods, surface-based approaches such as spherical harmonics and 3D Zernike descriptors, atom-centered Gaussian overlay based representations. Several of these methods demonstrated excellent virtual screening performance not only retrospectively but also prospectively. In addition to methods assessing the similarity between small molecules, shape similarity approaches have been developed to compare shapes of protein structures and binding pockets. Additionally, shape comparisons between atomic models and 3D density maps allowed the fitting of atomic models into cryo-electron microscopy maps. This review aims to summarize the methodological advances in shape similarity assessment highlighting advantages, disadvantages and their application in drug discovery.
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Affiliation(s)
| | - Kam Y. J. Zhang
- Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, Yokohama, Japan
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3
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Pigné S, Zykwinska A, Janod E, Cuenot S, Kerkoud M, Raulo R, Bataillé-Simoneau N, Marchi M, Kwasiborski A, N'Guyen G, Mabilleau G, Simoneau P, Guillemette T. A flavoprotein supports cell wall properties in the necrotrophic fungus Alternaria brassicicola. Fungal Biol Biotechnol 2017; 4:1. [PMID: 28955470 PMCID: PMC5611651 DOI: 10.1186/s40694-016-0029-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 12/21/2016] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Flavin-dependent monooxygenases are involved in key biological processes as they catalyze a wide variety of chemo-, regio- and enantioselective oxygenation reactions. Flavoprotein monooxygenases are frequently encountered in micro-organisms, most of which require further functional and biocatalytic assessment. Here we investigated the function of the AbMak1 gene, which encodes a group A flavin monooxygenase in the plant pathogenic fungus Alternaria brassicicola, by generating a deficient mutant and examining its phenotype. RESULTS Functional analysis indicates that the AbMak1 protein is involved in cell wall biogenesis and influences the melanization process. We documented a significant decrease in melanin content in the Δabmak1 strain compared to the wild-type and complemented strains. We investigated the cell wall morphology and physical properties in the wild-type and transformants using electron and atomic force microscopy. These approaches confirmed the aberrant morphology of the conidial wall structure in the Δabmak1 strain which had an impact on hydrophilic adhesion and conidial surface stiffness. However, there was no significant impairment in growth, conidia formation, pathogenicity or susceptibility to various environmental stresses in the Δabmak1 strain. CONCLUSION This study sheds new light on the function of a fungal flavin-dependent monooxygenase, which plays an important role in melanization.
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Affiliation(s)
- Sandrine Pigné
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, 49071 Beaucouzé, France
| | - Agata Zykwinska
- UMR 6502, Institut des Matériaux Jean Rouxel, 2, Rue de la Houssinière, BP 32229, 44322 Nantes Cedex 3, France.,Present Address: Laboratoire Ecosystèmes Microbiens et Molécules Marines pour les Biotechnologies, IFREMER, Rue de l'île d'Yeu, BP 21105, 44311 Nantes Cedex 3, France
| | - Etienne Janod
- UMR 6502, Institut des Matériaux Jean Rouxel, 2, Rue de la Houssinière, BP 32229, 44322 Nantes Cedex 3, France
| | - Stéphane Cuenot
- UMR 6502, Institut des Matériaux Jean Rouxel, 2, Rue de la Houssinière, BP 32229, 44322 Nantes Cedex 3, France
| | - Mohammed Kerkoud
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, 49071 Beaucouzé, France
| | - Roxane Raulo
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, 49071 Beaucouzé, France
| | | | - Muriel Marchi
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, 49071 Beaucouzé, France
| | - Anthony Kwasiborski
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, 49071 Beaucouzé, France
| | - Guillaume N'Guyen
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, 49071 Beaucouzé, France
| | - Guillaume Mabilleau
- Plateforme SCIAM, Institut de Biologie en Santé, CHU, Université d'Angers, 4, Rue Larrey, 49933 Angers Cedex, France
| | - Philippe Simoneau
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, 49071 Beaucouzé, France
| | - Thomas Guillemette
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, 49071 Beaucouzé, France
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Ali SM, Siddiqui R, Ong SK, Shah MR, Anwar A, Heard PJ, Khan NA. Identification and characterization of antibacterial compound(s) of cockroaches (Periplaneta americana). Appl Microbiol Biotechnol 2016; 101:253-286. [PMID: 27743045 DOI: 10.1007/s00253-016-7872-2] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Revised: 08/21/2016] [Accepted: 09/16/2016] [Indexed: 12/20/2022]
Abstract
Infectious diseases remain a significant threat to human health, contributing to more than 17 million deaths, annually. With the worsening trends of drug resistance, there is a need for newer and more powerful antimicrobial agents. We hypothesized that animals living in polluted environments are potential sources of antimicrobials. Under polluted milieus, organisms such as cockroaches encounter different types of microbes, including superbugs. Such creatures survive the onslaught of superbugs and are able to ward off disease by producing antimicrobial substances. Here, we characterized antibacterial properties in extracts of various body organs of cockroaches (Periplaneta americana) and showed potent antibacterial activity in crude brain extract against methicillin-resistant Staphylococcus aureus and neuropathogenic Escherichia coli K1. The size-exclusion spin columns revealed that the active compound(s) are less than 10 kDa in molecular mass. Using cytotoxicity assays, it was observed that pre-treatment of bacteria with lysates inhibited bacteria-mediated host cell cytotoxicity. Using spectra obtained with LC-MS on Agilent 1290 infinity liquid chromatograph, coupled with an Agilent 6460 triple quadruple mass spectrometer, tissues lysates were analysed. Among hundreds of compounds, only a few homologous compounds were identified that contained the isoquinoline group, chromene derivatives, thiazine groups, imidazoles, pyrrole-containing analogs, sulfonamides, furanones, and flavanones and known to possess broad-spectrum antimicrobial properties and anti-inflammatory, anti-tumour, and analgesic properties. Further identification, characterization, and functional studies using individual compounds can act as a breakthrough in developing novel therapeutics against various pathogens including superbugs.
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Affiliation(s)
- Salwa Mansur Ali
- Department of Biological Sciences, Faculty of Science and Technology, Sunway University, 47500, Subang Jaya, Selangor, Malaysia
| | - Ruqaiyyah Siddiqui
- Department of Biological Sciences, Faculty of Science and Technology, Sunway University, 47500, Subang Jaya, Selangor, Malaysia
| | - Seng-Kai Ong
- Department of Biological Sciences, Faculty of Science and Technology, Sunway University, 47500, Subang Jaya, Selangor, Malaysia
| | - Muhammad Raza Shah
- International Center for Chemical and Biological Sciences, H.E.J. Research Institute of Chemistry, University of Karachi, Karachi, Pakistan
| | - Ayaz Anwar
- International Center for Chemical and Biological Sciences, H.E.J. Research Institute of Chemistry, University of Karachi, Karachi, Pakistan
| | - Peter J Heard
- Department of Biological Sciences, Faculty of Science and Technology, Sunway University, 47500, Subang Jaya, Selangor, Malaysia
| | - Naveed Ahmed Khan
- Department of Biological Sciences, Faculty of Science and Technology, Sunway University, 47500, Subang Jaya, Selangor, Malaysia.
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Chen H, Han X, Qin N, Wei L, Yang Y, Rao L, Chi B, Feng L, Ren Y, Wan J. Synthesis and biological evaluation of novel inhibitors against 1,3,8-trihydroxynaphthalene reductase from Magnaporthe grisea. Bioorg Med Chem 2016; 24:1225-30. [DOI: 10.1016/j.bmc.2016.01.053] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Revised: 01/26/2016] [Accepted: 01/27/2016] [Indexed: 10/22/2022]
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Abadio AKR, Kioshima ES, Leroux V, Martins NF, Maigret B, Felipe MSS. Identification of New Antifungal Compounds Targeting Thioredoxin Reductase of Paracoccidioides Genus. PLoS One 2015; 10:e0142926. [PMID: 26569405 PMCID: PMC4646694 DOI: 10.1371/journal.pone.0142926] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2015] [Accepted: 10/28/2015] [Indexed: 11/27/2022] Open
Abstract
The prevalence of invasive fungal infections worldwide has increased in the last decades. The development of specific drugs targeting pathogenic fungi without producing collateral damage to mammalian cells is a daunting pharmacological challenge. Indeed, many of the toxicities and drug interactions observed with contemporary antifungal therapies can be attributed to “nonselective” interactions with enzymes or cell membrane systems found in mammalian host cells. A computer-aided screening strategy against the TRR1 protein of Paracoccidioides lutzii is presented here. Initially, a bank of commercially available compounds from Life Chemicals provider was docked to model by virtual screening simulations. The small molecules that interact with the model were ranked and, among the best hits, twelve compounds out of 3,000 commercially-available candidates were selected. These molecules were synthesized for validation and in vitro antifungal activity assays for Paracoccidioides lutzii and P. brasiliensis were performed. From 12 molecules tested, 3 harbor inhibitory activity in antifungal assays against the two pathogenic fungi. Corroborating these findings, the molecules have inhibitory activity against the purified recombinant enzyme TRR1 in biochemical assays. Therefore, a rational combination of molecular modeling simulations and virtual screening of new drugs has provided a cost-effective solution to an early-stage medicinal challenge. These results provide a promising technique to the development of new and innovative drugs.
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Affiliation(s)
| | - Erika Seki Kioshima
- Department of Clinical Analysis and Biomedicine, State University of Maringá, Maringá, Paraná, Brazil
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Dolezal R, Sobeslav V, Hornig O, Balik L, Korabecny J, Kuca K. HPC Cloud Technologies for Virtual Screening in Drug Discovery. INTELLIGENT INFORMATION AND DATABASE SYSTEMS 2015. [DOI: 10.1007/978-3-319-15705-4_43] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Kumar A, Zhang KYJ. Hierarchical virtual screening approaches in small molecule drug discovery. Methods 2015; 71:26-37. [PMID: 25072167 PMCID: PMC7129923 DOI: 10.1016/j.ymeth.2014.07.007] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Revised: 07/16/2014] [Accepted: 07/17/2014] [Indexed: 02/06/2023] Open
Abstract
Virtual screening has played a significant role in the discovery of small molecule inhibitors of therapeutic targets in last two decades. Various ligand and structure-based virtual screening approaches are employed to identify small molecule ligands for proteins of interest. These approaches are often combined in either hierarchical or parallel manner to take advantage of the strength and avoid the limitations associated with individual methods. Hierarchical combination of ligand and structure-based virtual screening approaches has received noteworthy success in numerous drug discovery campaigns. In hierarchical virtual screening, several filters using ligand and structure-based approaches are sequentially applied to reduce a large screening library to a number small enough for experimental testing. In this review, we focus on different hierarchical virtual screening strategies and their application in the discovery of small molecule modulators of important drug targets. Several virtual screening studies are discussed to demonstrate the successful application of hierarchical virtual screening in small molecule drug discovery.
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Affiliation(s)
- Ashutosh Kumar
- Structural Bioinformatics Team, Center for Life Science Technologies, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Kam Y J Zhang
- Structural Bioinformatics Team, Center for Life Science Technologies, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan.
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Ghattas MA, Atatreh N, Bichenkova EV, Bryce RA. Protein tyrosine phosphatases: Ligand interaction analysis and optimisation of virtual screening. J Mol Graph Model 2014; 52:114-23. [PMID: 25038507 DOI: 10.1016/j.jmgm.2014.06.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Revised: 06/23/2014] [Accepted: 06/26/2014] [Indexed: 11/28/2022]
Abstract
Docking-based virtual screening is an established component of structure-based drug discovery. Nevertheless, scoring and ranking of computationally docked ligand libraries still suffer from many false positives. Identifying optimal docking parameters for a target protein prior to virtual screening can improve experimental hit rates. Here, we examine protocols for virtual screening against the important but challenging class of drug target, protein tyrosine phosphatases. In this study, common interaction features were identified from analysis of protein-ligand binding geometries of more than 50 complexed phosphatase crystal structures. It was found that two interactions were consistently formed across all phosphatase inhibitors: (1) a polar contact with the conserved arginine residue, and (2) at least one interaction with the P-loop backbone amide. In order to investigate the significance of these features on phosphatase-ligand binding, a series of seeded virtual screening experiments were conducted on three phosphatase enzymes, PTP1B, Cdc25b and IF2. It was observed that when the conserved arginine and P-loop amide interactions were used as pharmacophoric constraints during docking, enrichment of the virtual screen significantly increased in the three studied phosphatases, by up to a factor of two in some cases. Additionally, the use of such pharmacophoric constraints considerably improved the ability of docking to predict the inhibitor's bound pose, decreasing RMSD to the crystallographic geometry by 43% on average. Constrained docking improved enrichment of screens against both open and closed conformations of PTP1B. Incorporation of an ordered water molecule in PTP1B screening was also found to generally improve enrichment. The knowledge-based computational strategies explored here can potentially inform structure-based design of new phosphatase inhibitors using docking-based virtual screening.
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Affiliation(s)
- Mohammad A Ghattas
- College of Pharmacy, Al Ain University of Science and Technology, Al Ain 64141, United Arab Emirates
| | - Noor Atatreh
- College of Pharmacy, Al Ain University of Science and Technology, Al Ain 64141, United Arab Emirates
| | - Elena V Bichenkova
- Manchester Pharmacy School, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Richard A Bryce
- Manchester Pharmacy School, University of Manchester, Oxford Road, Manchester M13 9PT, UK.
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A linear combination of pharmacophore hypotheses as a new tool in search of new active compounds--an application for 5-HT1A receptor ligands. PLoS One 2013; 8:e84510. [PMID: 24367669 PMCID: PMC3867515 DOI: 10.1371/journal.pone.0084510] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Accepted: 11/22/2013] [Indexed: 11/19/2022] Open
Abstract
This study explores a new approach to pharmacophore screening involving the use of an optimized linear combination of models instead of a single hypothesis. The implementation and evaluation of the developed methodology are performed for a complete known chemical space of 5-HT1AR ligands (3616 active compounds with Ki < 100 nM) acquired from the ChEMBL database. Clusters generated from three different methods were the basis for the individual pharmacophore hypotheses, which were assembled into optimal combinations to maximize the different coefficients, namely, MCC, accuracy and recall, to measure the screening performance. Various factors that influence filtering efficiency, including clustering methods, the composition of test sets (random, the most diverse and cluster population-dependent) and hit mode (the compound must fit at least one or two models from a final combination) were investigated. This method outmatched both single hypothesis and random linear combination approaches.
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Kejžar A, Gobec S, Plemenitaš A, Lenassi M. Melanin is crucial for growth of the black yeast Hortaea werneckii in its natural hypersaline environment. Fungal Biol 2013; 117:368-79. [PMID: 23719222 DOI: 10.1016/j.funbio.2013.03.006] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2013] [Accepted: 03/26/2013] [Indexed: 10/27/2022]
Abstract
Melanin has an important role in the ability of fungi to survive extreme conditions, like the high NaCl concentrations that are typical of hypersaline environments. The black fungus Hortaea werneckii that has been isolated from such environments has 1,8-dihydroxynaphthalene-melanin incorporated into the cell wall, which minimises the loss of glycerol at low NaCl concentrations. To further explore the role of melanin in the extremely halotolerant character of H. werneckii, we studied the effects of several melanin biosynthesis inhibitors on its growth, pigmentation and cell morphology. The most potent inhibitors were a 2,3-dihydrobenzofuran derivative and tricyclazole, which restricted the growth of H. werneckii on high-salinity media, as shown by growth curves and plate-drop assays. These inhibitors promoted release of the pigments from the H. werneckii cell surface and changed the medium colour. Inhibitor-treated H. werneckii cells exposed to high salinity showed both decreased and increased cell lengths. We speculate that this absence of melanin perturbs the integrity of the cell wall in H. werneckii, which affects its cell division and exposes it to the harmful effects of high NaCl concentrations. Surprisingly, melanin had no effect on H. werneckii survival under H₂O₂ oxidative stress.
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Affiliation(s)
- Anja Kejžar
- Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, Vrazov Trg 2, SI-1000 Ljubljana, Slovenia.
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Sidhu PS, Mosier PD, Zhou Q, Desai UR. On scaffold hopping: challenges in the discovery of sulfated small molecules as mimetics of glycosaminoglycans. Bioorg Med Chem Lett 2012; 23:355-9. [PMID: 23164711 DOI: 10.1016/j.bmcl.2012.10.079] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2012] [Revised: 10/04/2012] [Accepted: 10/15/2012] [Indexed: 01/25/2023]
Abstract
The design of sulfated, small, nonsaccharide molecules as modulators of proteins is still in its infancy as standard drug discovery tools such as library of diverse sulfated molecules and in silico docking and scoring protocol have not been firmly established. Databases, such as ZINC, contain too few sulfate-containing nonsaccharide molecules, which severely limits the identification of new hits. Lack of a generally applicable protocol for scaffold hopping limits the development of sulfated small molecules as synthetic mimetics of the highly sulfated glycosaminoglycans. We explored a sequential ligand-based (LBVS) and structure-based virtual screening (SBVS) approach starting from our initial discovery of monosulfated benzofurans to discover alternative scaffolds as allosteric modulators of thrombin, a key coagulation enzyme. Screening the ZINC database containing nearly 1 million nonsulfated small molecules using a pharmacophore developed from the parent sulfated benzofurans followed by a genetic algorithm-based dual-filter docking and scoring screening identified a group of 10 promising hits, of which three top-scoring hits were synthesized. Each was found to selectively inhibit human alpha-thrombin suggesting the possibility of this approach for scaffold hopping. Michaelis-Menten kinetics showed allosteric inhibition mechanism for the best molecule and human plasma studies confirmed good anticoagulation potential as expected. Our simple sequential LBVS and SBVS approach is likely to be useful as a general strategy for identification of sulfated small molecules hits as modulators of glycosaminoglycan-protein interactions.
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Affiliation(s)
- Preetpal S Sidhu
- Department of Medicinal Chemistry and Institute for Structural Biology and Drug Discovery, Virginia Commonwealth University, Richmond, VA 23219, United States
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Cheng T, Li Q, Zhou Z, Wang Y, Bryant SH. Structure-based virtual screening for drug discovery: a problem-centric review. AAPS J 2012; 14:133-41. [PMID: 22281989 PMCID: PMC3282008 DOI: 10.1208/s12248-012-9322-0] [Citation(s) in RCA: 352] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2011] [Accepted: 01/04/2012] [Indexed: 11/30/2022] Open
Abstract
Structure-based virtual screening (SBVS) has been widely applied in early-stage drug discovery. From a problem-centric perspective, we reviewed the recent advances and applications in SBVS with a special focus on docking-based virtual screening. We emphasized the researchers' practical efforts in real projects by understanding the ligand-target binding interactions as a premise. We also highlighted the recent progress in developing target-biased scoring functions by optimizing current generic scoring functions toward certain target classes, as well as in developing novel ones by means of machine learning techniques.
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Affiliation(s)
- Tiejun Cheng
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, Maryland 20894 USA
| | - Qingliang Li
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, Maryland 20894 USA
| | - Zhigang Zhou
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, Maryland 20894 USA
| | - Yanli Wang
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, Maryland 20894 USA
| | - Stephen H. Bryant
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, Maryland 20894 USA
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