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O’Boyle NM, Helesbeux JJ, Meegan MJ, Sasse A, O’Shaughnessy E, Qaisar A, Clancy A, McCarthy F, Marchand P. 30th Annual GP2A Medicinal Chemistry Conference. Pharmaceuticals (Basel) 2023; 16:ph16030432. [PMID: 36986531 PMCID: PMC10056312 DOI: 10.3390/ph16030432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 01/16/2023] [Indexed: 03/14/2023] Open
Abstract
The Group for the Promotion of Pharmaceutical Chemistry in Academia (GP2A) held their 30th annual conference in August 2022 in Trinity College Dublin, Ireland. There were 9 keynote presentations, 10 early career researcher presentations and 41 poster presentations.
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Affiliation(s)
- Niamh M. O’Boyle
- School of Pharmacy and Pharmaceutical Sciences, Panoz Institute and Trinity Biomedical Sciences Institute, Trinity College Dublin, D02 PN40 Dublin, Ireland
- Correspondence: ; Tel.: +353-1896-2524
| | | | - Mary J. Meegan
- School of Pharmacy and Pharmaceutical Sciences, Panoz Institute and Trinity Biomedical Sciences Institute, Trinity College Dublin, D02 PN40 Dublin, Ireland
| | - Astrid Sasse
- School of Pharmacy and Pharmaceutical Sciences, Panoz Institute and Trinity Biomedical Sciences Institute, Trinity College Dublin, D02 PN40 Dublin, Ireland
| | - Elizabeth O’Shaughnessy
- School of Pharmacy and Pharmaceutical Sciences, Panoz Institute and Trinity Biomedical Sciences Institute, Trinity College Dublin, D02 PN40 Dublin, Ireland
| | - Alina Qaisar
- School of Pharmacy and Pharmaceutical Sciences, Panoz Institute and Trinity Biomedical Sciences Institute, Trinity College Dublin, D02 PN40 Dublin, Ireland
| | - Aoife Clancy
- School of Pharmacy and Pharmaceutical Sciences, Panoz Institute and Trinity Biomedical Sciences Institute, Trinity College Dublin, D02 PN40 Dublin, Ireland
| | - Florence McCarthy
- School of Chemistry and ABCRF, University College Cork, T12 K8AF Cork, Ireland
| | - Pascal Marchand
- Cibles et Médicaments des Infections et de l’Immunité, IICiMed, Nantes Université, UR 1155, F-44000 Nantes, France
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Nakano H, Miyao T. Visualization of Topological Pharmacophore Space with Graph Edit Distance. ACS OMEGA 2022; 7:14057-14068. [PMID: 35559135 PMCID: PMC9088954 DOI: 10.1021/acsomega.2c00173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 03/25/2022] [Indexed: 06/15/2023]
Abstract
A topological pharmacophore (TP) is a chemical graph-based pharmacophore representation, where nodes are pharmacophoric features (PF) and edges are topological distances between PFs. Previously proposed sparse pharmacophore graphs (SPhGs) for TPs were shown to be effective in identifying structurally different active compounds while maintaining the interpretability of the graphs. However, one limitation of using SPhGs as queries is that many structurally similar SPhGs can be identified from a set of active compounds, requiring the classification and visualization of SPhGs, followed by an understanding of the pharmacophore hypotheses. In this study, we propose a scheme for SPhG analysis based on dimensionality reduction techniques with the graph edit distance (GED) metric. This metric enables measuring similarities among SPhGs in a quantitative manner. The visualization of SPhGs, which themselves are the graphs shared by active compounds, can help us understand the pharmacophore hypotheses as well as the data set. As a proof-of-concept study, we generated two-dimensional SPhG-maps using three dimensionality reduction techniques for six biological targets. A comparison with other pharmacophore representations was also conducted. We demonstrated knowledge extraction (interpretation of the data set) from the generated maps. Our findings include a suitable mapping algorithm as well as a pharmacophore hypothesis analysis procedure using an SPhG-map.
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Affiliation(s)
- Hiroshi Nakano
- Graduate
School of Science and Technology, Nara Institute
of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan
| | - Tomoyuki Miyao
- Graduate
School of Science and Technology, Nara Institute
of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan
- Data
Science Center, Nara Institute of Science
and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan
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3
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Phuong Vu L, Zyulina M, Hingst A, Schnakenburg G, Gütschow M. Combinatorial Assembly, Traceless Generation and In Situ Evaluation of Inhibitors for Therapeutically Relevant Serine Proteases. Bioorg Chem 2022; 121:105676. [DOI: 10.1016/j.bioorg.2022.105676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 01/24/2022] [Accepted: 02/08/2022] [Indexed: 11/02/2022]
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Nakano H, Miyao T, Swarit J, Funatsu K. Sparse Topological Pharmacophore Graphs for Interpretable Scaffold Hopping. J Chem Inf Model 2021; 61:3348-3360. [PMID: 34264667 DOI: 10.1021/acs.jcim.1c00409] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The aim of scaffold hopping (SH) is to find compounds consisting of different scaffolds from those in already known active compounds, giving an opportunity for unexplored regions of chemical space. We previously demonstrated the usefulness of pharmacophore graphs (PhGs) for this purpose through proof-of-concept virtual screening experiments. PhGs consist of nodes and edges corresponding to pharmacophoric features (PFs) and their topological distances. Although PhGs were effective in SH, they are hard to interpret as they are complete graphs. Herein, we introduce an intuitive representation of a molecule, termed as sparse pharmacophore graphs (SPhG) by keeping the topological distances among PFs as much as possible while reducing the number of edges in the graphs. Several benchmark calculations quantitatively confirmed the sparseness of the graphs and the preservation of topological distances among pharmacophoric points. As proof-of-concept applications, virtual screening (VS) trials for SH were conducted using active and inactive compounds from ChEMBL and PubChem databases for three biological targets: thrombin, tyrosine kinase ABL1, and κ-opioid receptor. The performances of VS were comparable with using fully connected PhGs. Furthermore, highly ranked SPhGs were interpretable for the three biological targets, in particular for thrombin, for which selected SPhGs were in agreement with the structure-based interpretation.
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Affiliation(s)
- Hiroshi Nakano
- Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan
| | - Tomoyuki Miyao
- Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan.,Data Science Center, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan
| | - Jasial Swarit
- Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan.,Data Science Center, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan
| | - Kimito Funatsu
- Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan.,Data Science Center, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan.,Department of Chemical System Engineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
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5
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Nakano H, Miyao T, Funatsu K. Exploring Topological Pharmacophore Graphs for Scaffold Hopping. J Chem Inf Model 2020; 60:2073-2081. [DOI: 10.1021/acs.jcim.0c00098] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Hiroshi Nakano
- Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan
| | - Tomoyuki Miyao
- Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan
- Data Science Center, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan
| | - Kimito Funatsu
- Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan
- Data Science Center, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan
- Department of Chemical System Engineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
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6
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Hüfner-Wulsdorf T, Klebe G. Protein–Ligand Complex Solvation Thermodynamics: Development, Parameterization, and Testing of GIST-Based Solvent Functionals. J Chem Inf Model 2020; 60:1409-1423. [DOI: 10.1021/acs.jcim.9b01109] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Tobias Hüfner-Wulsdorf
- Institut für Pharmazeutische Chemie, Philipps Universität Marburg, Marbacher Weg 6, 35037 Marburg, Germany
| | - Gerhard Klebe
- Institut für Pharmazeutische Chemie, Philipps Universität Marburg, Marbacher Weg 6, 35037 Marburg, Germany
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7
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Endreas W, Brüßler J, Vornicescu D, Keusgen M, Bakowsky U, Steinmetzer T. Thrombin-Inhibiting Anticoagulant Liposomes: Development and Characterization. ChemMedChem 2015; 11:340-9. [DOI: 10.1002/cmdc.201500489] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Indexed: 11/07/2022]
Affiliation(s)
- Wegderes Endreas
- Institute of Pharmaceutical Chemistry; Philipps University; Marbacher Weg 6 35032 Marburg Germany
| | - Jana Brüßler
- Institute of Pharmaceutical Technology & Biopharmacy; Philipps University; Ketzerbach 63 35032 Marburg Germany
| | - Doru Vornicescu
- Institute of Pharmaceutical Chemistry; Philipps University; Marbacher Weg 6 35032 Marburg Germany
| | - Michael Keusgen
- Institute of Pharmaceutical Chemistry; Philipps University; Marbacher Weg 6 35032 Marburg Germany
| | - Udo Bakowsky
- Institute of Pharmaceutical Technology & Biopharmacy; Philipps University; Ketzerbach 63 35032 Marburg Germany
| | - Torsten Steinmetzer
- Institute of Pharmaceutical Chemistry; Philipps University; Marbacher Weg 6 35032 Marburg Germany
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8
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Biela A, Sielaff F, Terwesten F, Heine A, Steinmetzer T, Klebe G. Ligand Binding Stepwise Disrupts Water Network in Thrombin: Enthalpic and Entropic Changes Reveal Classical Hydrophobic Effect. J Med Chem 2012; 55:6094-110. [DOI: 10.1021/jm300337q] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Adam Biela
- Department
of Pharmaceutical Chemistry, Philipps University
Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Frank Sielaff
- Department
of Pharmaceutical Chemistry, Philipps University
Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Felix Terwesten
- Department
of Pharmaceutical Chemistry, Philipps University
Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Andreas Heine
- Department
of Pharmaceutical Chemistry, Philipps University
Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Torsten Steinmetzer
- Department
of Pharmaceutical Chemistry, Philipps University
Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Gerhard Klebe
- Department
of Pharmaceutical Chemistry, Philipps University
Marburg, Marbacher Weg 6, 35032 Marburg, Germany
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