Prediction of n-octanol/water partition coefficients and acidity constants (pKa) in the SAMPL7 blind challenge with the IEFPCM-MST model.

Antonio Viayna; Silvana Pinheiro; Carles Curutchet; F Javier Luque; William J Zamora

doi:10.1007/s10822-021-00394-6

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Prediction of n-octanol/water partition coefficients and acidity constants (pKa) in the SAMPL7 blind challenge with the IEFPCM-MST model.

Authors

Viayna, Antonio¹
Pinheiro, Silvana²
Curutchet, Carles³
Luque, F Javier⁴
Zamora, William J^{5, 6}

¹ Department of Nutrition, Food Sciences and Gastronomy, Faculty of Pharmacy and Food Sciences, Institute of Biomedicine (IBUB), and Institute of Theoretical and Computational Chemistry (IQTC-UB), University of Barcelona (UB), Avda. Prat de La Riba, 171, 08921, Santa Coloma de Gramenet, Spain. [email protected] , (Spain)
² Institute of Exact and Natural Sciences, Federal University of Pará, Belém, Pará, 66075-110, Brazil. , (Brazil)
³ Department of Pharmacy and Pharmaceutical Technology and Physical Chemistry, Faculty of Pharmacy and Food Sciences, and Institute of Theoretical and Computational Chemistry (IQTC-UB), University of Barcelona, Av. de Joan XXIII, 27-31, 08028, Barcelona, Spain. , (Spain)
⁴ Department of Nutrition, Food Sciences and Gastronomy, Faculty of Pharmacy and Food Sciences, Institute of Biomedicine (IBUB), and Institute of Theoretical and Computational Chemistry (IQTC-UB), University of Barcelona (UB), Avda. Prat de La Riba, 171, 08921, Santa Coloma de Gramenet, Spain. , (Spain)
⁵ School of Chemistry and Faculty of Pharmacy, University of Costa Rica, San Pedro, San José, Costa Rica. , (Costa Rica)
⁶ Advanced Computing Lab (CNCA), National High Technology Center (CeNAT), Pavas, San José, Costa Rica. , (Costa Rica)

Type

Published Article

Journal

Journal of Computer-Aided Molecular Design

Publisher

Springer-Verlag

Publication Date

Jul 01, 2021

Volume

35

Issue

7

Pages

803–811

Identifiers

DOI: 10.1007/s10822-021-00394-6

PMID: 34244905

Source

Medline

Keywords

Language

English

License

Unknown

Abstract

Within the scope of SAMPL7 challenge for predicting physical properties, the Integral Equation Formalism of the Miertus-Scrocco-Tomasi (IEFPCM/MST) continuum solvation model has been used for the blind prediction of n-octanol/water partition coefficients and acidity constants of a set of 22 and 20 sulfonamide-containing compounds, respectively. The log P and pKa were computed using the B3LPYP/6-31G(d) parametrized version of the IEFPCM/MST model. The performance of our method for partition coefficients yielded a root-mean square error of 1.03 (log P units), placing this method among the most accurate theoretical approaches in the comparison with both globally (rank 8th) and physical (rank 2nd) methods. On the other hand, the deviation between predicted and experimental pKa values was 1.32 log units, obtaining the second best-ranked submission. Though this highlights the reliability of the IEFPCM/MST model for predicting the partitioning and the acid dissociation constant of drug-like compounds compound, the results are discussed to identify potential weaknesses and improve the performance of the method. © 2021. The Author(s).

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. This record was last updated on 01/04/2022 and may not reflect the most current and accurate biomedical/scientific data available from NLM. The corresponding record at NLM can be accessed at https://www.ncbi.nlm.nih.gov/pubmed/34244905

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Abstract

Prediction of n -octanol/water partition coefficients and acidity constants ( pK a ) in the SAMPL7 blind challenge with the IEFPCM-MST model

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