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Žuvela P, Liu JJ, Yi M, Pomastowski PP, Sagandykova G, Belka M, David J, Bączek T, Szafrański K, Żołnowska B, Sławiński J, Supuran CT, Wong MW, Buszewski B. Target-based drug discovery through inversion of quantitative structure-drug-property relationships and molecular simulation: CA IX-sulphonamide complexes. J Enzyme Inhib Med Chem 2018; 33:1430-1443. [PMID: 30220229 PMCID: PMC6151961 DOI: 10.1080/14756366.2018.1511551] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
In this work, a target-based drug screening method is proposed exploiting the synergy effect of ligand-based and structure-based computer-assisted drug design. The new method provides great flexibility in drug design and drug candidates with considerably lower risk in an efficient manner. As a model system, 45 sulphonamides (33 training, 12 testing ligands) in complex with carbonic anhydrase IX were used for development of quantitative structure-activity-lipophilicity (property)-relationships (QSPRs). For each ligand, nearly 5,000 molecular descriptors were calculated, while lipophilicity (logkw) and inhibitory activity (logKi) were used as drug properties. Genetic algorithm-partial least squares (GA-PLS) provided a QSPR model with high prediction capability employing only seven molecular descriptors. As a proof-of-concept, optimal drug structure was obtained by inverting the model with respect to reference drug properties. 3509 ligands were ranked accordingly. Top 10 ligands were further validated through molecular docking. Large-scale MD simulations were performed to test the stability of structures of selected ligands obtained through docking complemented with biophysical experiments.
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Affiliation(s)
- Petar Žuvela
- a Department of Chemistry , National University of Singapore , Singapore.,b Department of Environmental Chemistry and Bioanalytics, Faculty of Chemistry , Nicolaus Copernicus University , Toruń , Poland
| | - J Jay Liu
- c Department of Chemical Engineering , Pukyong National University , Busan , Korea
| | - Myunggi Yi
- d Department of Biomedical Engineering , Pukyong National University , Busan , Korea
| | - Paweł P Pomastowski
- b Department of Environmental Chemistry and Bioanalytics, Faculty of Chemistry , Nicolaus Copernicus University , Toruń , Poland
| | - Gulyaim Sagandykova
- e Interdisciplinary Centre for Modern Technologies, Nicolaus Copernicus University , Toruń , Poland
| | - Mariusz Belka
- f Department of Pharmaceutical Chemistry , Medical University of Gdańsk , Gdańsk , Poland
| | - Jonathan David
- a Department of Chemistry , National University of Singapore , Singapore
| | - Tomasz Bączek
- f Department of Pharmaceutical Chemistry , Medical University of Gdańsk , Gdańsk , Poland
| | - Krzysztof Szafrański
- g Department of Organic Chemistry , Medical University of Gdańsk , Gdańsk , Poland
| | - Beata Żołnowska
- g Department of Organic Chemistry , Medical University of Gdańsk , Gdańsk , Poland
| | - Jarosław Sławiński
- g Department of Organic Chemistry , Medical University of Gdańsk , Gdańsk , Poland
| | - Claudiu T Supuran
- h Dipartimento di Chimica, Universita degli Studi di Firenze , Polo Scientifico, Laboratorio di Chimica Bioinorganica , Sesto Fiorentino (Florence) , Italy.,i NEUROFARBA Department, Sezione di Scienze Farmaceutiche , Università degli Studi di Firenze , Sesto Fiorentino (Florence) , Italy
| | - Ming Wah Wong
- a Department of Chemistry , National University of Singapore , Singapore
| | - Bogusław Buszewski
- b Department of Environmental Chemistry and Bioanalytics, Faculty of Chemistry , Nicolaus Copernicus University , Toruń , Poland.,e Interdisciplinary Centre for Modern Technologies, Nicolaus Copernicus University , Toruń , Poland
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A Quantitative Structure-Property Relationship Model Based on Chaos-Enhanced Accelerated Particle Swarm Optimization Algorithm and Back Propagation Artificial Neural Network. APPLIED SCIENCES-BASEL 2018. [DOI: 10.3390/app8071121] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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