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Botha MJ, Kirton SB. In Silico Investigations into the Selectivity of Psychoactive and New Psychoactive Substances in Monoamine Transporters. ACS OMEGA 2022; 7:38311-38321. [PMID: 36340072 PMCID: PMC9631908 DOI: 10.1021/acsomega.2c02714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 10/07/2022] [Indexed: 06/16/2023]
Abstract
New psychoactive substances (NPS) are a group of compounds that mimic the effects of illicit substances. A range of NPS have been shown to interact with the three main classes of monoamine transporters (DAT, NET, and SERT) to differing extents, but it is unclear why these differences arise. To aid in understanding the differences in affinity between the classes of monoamine transporters, several in silico experiments were conducted. Docking experiments showed there was no direct correlation between a range of scoring functions and experimental activity, but Spearman ranking analysis showed a significant correlation (α = 0.1) for DAT, with the affinity ΔG (0.42), αHB (0.40), GoldScore (0.40), and PLP (0.41) scoring functions, and for DAT (0.38) and SERT (0.40) using a consensus scoring approach. Qualitative structure-activity relationship (QSAR) experiments resulted in the generation of robust and predictive three-descriptor models for SERT (r 2 = 0.87, q 2 = 0.8, and test set r 2 = 0.74) and DAT (r 2 = 0.68, q 2 = 0.51, test set r 2 = 0.63). Both QSAR models described similar characteristics for binding, i.e., rigid hydrophobic molecules with a biogenic amine moiety, and were not sufficient to facilitate a deeper understanding of differences in affinity between the monoamine transporters. This contextualizes the observed promiscuity for NPS between the isoforms and highlights the difficulty in the design and development of compounds that are isoform-selective.
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Camara R, Ogbeni D, Gerstmann L, Ostovar M, Hurer E, Scott M, Mahmoud NG, Radon T, Crnogorac-Jurcevic T, Patel P, Mackenzie LS, Chau DYS, Kirton SB, Rossiter S. Discovery of novel small molecule inhibitors of S100P with in vitro anti-metastatic effects on pancreatic cancer cells. Eur J Med Chem 2020; 203:112621. [PMID: 32707527 PMCID: PMC7501730 DOI: 10.1016/j.ejmech.2020.112621] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 06/17/2020] [Accepted: 06/23/2020] [Indexed: 12/30/2022]
Abstract
S100P, a calcium-binding protein, is known to advance tumor progression and metastasis in pancreatic and several other cancers. Herein is described the in silico identification of a putative binding pocket of S100P to identify, synthesize and evaluate novel small molecules with the potential to selectively bind S100P and inhibit its activation of cell survival and metastatic pathways. The virtual screening of a drug-like database against the S100P model led to the identification of over 100 clusters of diverse scaffolds. A representative test set identified a number of structurally unrelated hits that inhibit S100P-RAGE interaction, measured by ELISA, and reduce in vitro cell invasion selectively in S100P-expressing pancreatic cancer cells at 10 μM. This study establishes a proof of concept in the potential for rational design of small molecule S100P inhibitors for drug candidate development.
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Affiliation(s)
- Ramatoulie Camara
- School of Life and Medical Sciences, University of Hertfordshire, Hatfield, AL10 9AB, UK
| | - Deborah Ogbeni
- School of Life and Medical Sciences, University of Hertfordshire, Hatfield, AL10 9AB, UK
| | - Lisa Gerstmann
- School of Life and Medical Sciences, University of Hertfordshire, Hatfield, AL10 9AB, UK
| | - Mehrnoosh Ostovar
- School of Life and Medical Sciences, University of Hertfordshire, Hatfield, AL10 9AB, UK
| | - Ellie Hurer
- School of Life and Medical Sciences, University of Hertfordshire, Hatfield, AL10 9AB, UK
| | - Mark Scott
- School of Life and Medical Sciences, University of Hertfordshire, Hatfield, AL10 9AB, UK
| | - Nasir G Mahmoud
- Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ, UK
| | - Tomasz Radon
- Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ, UK
| | | | - Pryank Patel
- School of Life and Medical Sciences, University of Hertfordshire, Hatfield, AL10 9AB, UK
| | - Louise S Mackenzie
- School of Life and Medical Sciences, University of Hertfordshire, Hatfield, AL10 9AB, UK; School of Pharmacy and Biomolecular Sciences, University of Brighton, Brighton, BN2 4GJ, UK
| | - David Y S Chau
- School of Life and Medical Sciences, University of Hertfordshire, Hatfield, AL10 9AB, UK; Eastman Dental Institute, University College London, 256 Grays Inn Rd, London, WC1X 8LD, UK
| | - Stewart B Kirton
- School of Life and Medical Sciences, University of Hertfordshire, Hatfield, AL10 9AB, UK
| | - Sharon Rossiter
- School of Life and Medical Sciences, University of Hertfordshire, Hatfield, AL10 9AB, UK.
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Gaur AS, Bhardwaj A, Sharma A, John L, Vivek MR, Tripathi N, Bharatam PV, Kumar R, Janardhan S, Mori A, Banerji A, Lynn AM, Hemrom AJ, Passi A, Singh A, Kumar A, Muvva C, Madhuri C, Choudhury C, Kumar DA, Pandit D, Bharti DR, Kumar D, Singam ERA, Raghava GPS, Sailaja H, Jangra H, Raithatha K, Tanneeru K, Chaudhary K, Karthikeyan M, Prasanthi M, Kumar N, Yedukondalu N, Rajput NK, Saranya PS, Narang P, Dutta P, Krishnan RV, Sharma R, Srinithi R, Mishra R, Hemasri S, Singh S, Venkatesan S, Kumar S, Jaleel U, Khedkar V, Joshi Y, Sastry GN. Assessing therapeutic potential of molecules: molecular property diagnostic suite for tuberculosis $$(\mathbf{MPDS}^{\mathbf{TB}})$$ ( MPDS TB ). J CHEM SCI 2017. [DOI: 10.1007/s12039-017-1268-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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Multi-level meta-workflows: new concept for regularly occurring tasks in quantum chemistry. J Cheminform 2016; 8:58. [PMID: 27818709 PMCID: PMC5073744 DOI: 10.1186/s13321-016-0169-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2016] [Accepted: 10/04/2016] [Indexed: 11/10/2022] Open
Abstract
Background
In Quantum Chemistry, many tasks are reoccurring frequently, e.g. geometry optimizations, benchmarking series etc. Here, workflows can help to reduce the time of manual job definition and output extraction. These workflows are executed on computing infrastructures and may require large computing and data resources. Scientific workflows hide these infrastructures and the resources needed to run them. It requires significant efforts and specific expertise to design, implement and test these workflows. Significance Many of these workflows are complex and monolithic entities that can be used for particular scientific experiments. Hence, their modification is not straightforward and it makes almost impossible to share them. To address these issues we propose developing atomic workflows and embedding them in meta-workflows. Atomic workflows deliver a well-defined research domain specific function. Publishing workflows in repositories enables workflow sharing inside and/or among scientific communities. We formally specify atomic and meta-workflows in order to define data structures to be used in repositories for uploading and sharing them. Additionally, we present a formal description focused at orchestration of atomic workflows into meta-workflows. Conclusions We investigated the operations that represent basic functionalities in Quantum Chemistry, developed the relevant atomic workflows and combined them into meta-workflows. Having these workflows we defined the structure of the Quantum Chemistry workflow library and uploaded these workflows in the SHIWA Workflow Repository.Meta-workflows and embedded workflows in the template representation ![]() Electronic supplementary material The online version of this article (doi:10.1186/s13321-016-0169-8) contains supplementary material, which is available to authorized users.
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Römer M, Eichner J, Dräger A, Wrzodek C, Wrzodek F, Zell A. ZBIT Bioinformatics Toolbox: A Web-Platform for Systems Biology and Expression Data Analysis. PLoS One 2016; 11:e0149263. [PMID: 26882475 PMCID: PMC4801062 DOI: 10.1371/journal.pone.0149263] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 01/30/2016] [Indexed: 12/20/2022] Open
Abstract
Bioinformatics analysis has become an integral part of research in biology. However, installation and use of scientific software can be difficult and often requires technical expert knowledge. Reasons are dependencies on certain operating systems or required third-party libraries, missing graphical user interfaces and documentation, or nonstandard input and output formats. In order to make bioinformatics software easily accessible to researchers, we here present a web-based platform. The Center for Bioinformatics Tuebingen (ZBIT) Bioinformatics Toolbox provides web-based access to a collection of bioinformatics tools developed for systems biology, protein sequence annotation, and expression data analysis. Currently, the collection encompasses software for conversion and processing of community standards SBML and BioPAX, transcription factor analysis, and analysis of microarray data from transcriptomics and proteomics studies. All tools are hosted on a customized Galaxy instance and run on a dedicated computation cluster. Users only need a web browser and an active internet connection in order to benefit from this service. The web platform is designed to facilitate the usage of the bioinformatics tools for researchers without advanced technical background. Users can combine tools for complex analyses or use predefined, customizable workflows. All results are stored persistently and reproducible. For each tool, we provide documentation, tutorials, and example data to maximize usability. The ZBIT Bioinformatics Toolbox is freely available at https://webservices.cs.uni-tuebingen.de/.
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Affiliation(s)
- Michael Römer
- Department of Computer Science, University of Tübingen, Tübingen, Germany
- * E-mail:
| | - Johannes Eichner
- Department of Computer Science, University of Tübingen, Tübingen, Germany
| | - Andreas Dräger
- Department of Computer Science, University of Tübingen, Tübingen, Germany
- Department of Bioengineering, University of California, San Diego, San Diego, California, United States of America
| | - Clemens Wrzodek
- Department of Computer Science, University of Tübingen, Tübingen, Germany
| | - Finja Wrzodek
- Department of Computer Science, University of Tübingen, Tübingen, Germany
| | - Andreas Zell
- Department of Computer Science, University of Tübingen, Tübingen, Germany
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