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Kenny PW. Hydrogen-Bond Donors in Drug Design. J Med Chem 2022; 65:14261-14275. [DOI: 10.1021/acs.jmedchem.2c01147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Peter W. Kenny
- Berwick-on-Sea, North Coast Road, Blanchisseuse, Saint George, Trinidad and Tobago
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Erckes V, Steuer C. A story of peptides, lipophilicity and chromatography - back and forth in time. RSC Med Chem 2022; 13:676-687. [PMID: 35800203 PMCID: PMC9215158 DOI: 10.1039/d2md00027j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 03/18/2022] [Indexed: 11/25/2022] Open
Abstract
Peptides, as part of the beyond the rule of 5 (bRo5) chemical space, represent a unique class of pharmaceutical compounds. Because of their exceptional position in the chemical space between traditional small molecules (molecular weight (MW) < 500 Da) and large therapeutic proteins (MW > 5000 Da), peptides became promising candidates for targeting challenging binding sites, including even targets traditionally considered as undruggable - e.g. intracellular protein-protein interactions. However, basic knowledge about physicochemical properties that are important for a drug to be membrane permeable is missing but would enhance the drug discovery process of bRo5 molecules. Consequently, there is a demand for quick and simple lipophilicity determination methods for peptides. In comparison to the traditional lipophilicity determination methods via shake flask and in silico prediction, chromatography-based methods could have multiple benefits such as the requirement of low analyte amount, insensitivity to impurities and high throughput. Herein we elucidate the role of peptide lipophilicity and different lipophilicity values. Further, we summarize peptide analysis via common chromatographic techniques, in specific reversed phase liquid chromatography, hydrophilic interaction liquid chromatography and supercritical fluid chromatography and their role in drug discovery and development process.
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Affiliation(s)
- Vanessa Erckes
- Pharmaceutical Analytics, Institute of Pharmaceutical Sciences, Federal Institute of Technology Zurich 8093 Zurich Switzerland
| | - Christian Steuer
- Pharmaceutical Analytics, Institute of Pharmaceutical Sciences, Federal Institute of Technology Zurich 8093 Zurich Switzerland
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Borges NM, Kenny PW, Montanari CA, Prokopczyk IM, Ribeiro JFR, Rocha JR, Sartori GR. The influence of hydrogen bonding on partition coefficients. J Comput Aided Mol Des 2017; 31:163-181. [PMID: 28054187 DOI: 10.1007/s10822-016-0002-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 12/16/2016] [Indexed: 11/28/2022]
Abstract
This Perspective explores how consideration of hydrogen bonding can be used to both predict and better understand partition coefficients. It is shown how polarity of both compounds and substructures can be estimated from measured alkane/water partition coefficients. When polarity is defined in this manner, hydrogen bond donors are typically less polar than hydrogen bond acceptors. Analysis of alkane/water partition coefficients in conjunction with molecular electrostatic potential calculations suggests that aromatic chloro substituents may be less lipophilic than is generally believed and that some of the effect of chloro-substitution stems from making the aromatic π-cloud less available to hydrogen bond donors. Relationships between polarity and calculated hydrogen bond basicity are derived for aromatic nitrogen and carbonyl oxygen. Aligned hydrogen bond acceptors appear to present special challenges for prediction of alkane/water partition coefficients and this may reflect 'frustration' of solvation resulting from overlapping hydration spheres. It is also shown how calculated hydrogen bond basicity can be used to model the effect of aromatic aza-substitution on octanol/water partition coefficients.
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Affiliation(s)
- Nádia Melo Borges
- Grupo de Estudos em Química Medicinal - NEQUIMED, Instituto de Química de São Carlos - Universidade de São Paulo, Av. Trabalhador Sancarlense, 400, São Carlos, SP, 13566-590, Brazil
| | - Peter W Kenny
- Grupo de Estudos em Química Medicinal - NEQUIMED, Instituto de Química de São Carlos - Universidade de São Paulo, Av. Trabalhador Sancarlense, 400, São Carlos, SP, 13566-590, Brazil.
| | - Carlos A Montanari
- Grupo de Estudos em Química Medicinal - NEQUIMED, Instituto de Química de São Carlos - Universidade de São Paulo, Av. Trabalhador Sancarlense, 400, São Carlos, SP, 13566-590, Brazil
| | - Igor M Prokopczyk
- Grupo de Estudos em Química Medicinal - NEQUIMED, Instituto de Química de São Carlos - Universidade de São Paulo, Av. Trabalhador Sancarlense, 400, São Carlos, SP, 13566-590, Brazil
| | - Jean F R Ribeiro
- Grupo de Estudos em Química Medicinal - NEQUIMED, Instituto de Química de São Carlos - Universidade de São Paulo, Av. Trabalhador Sancarlense, 400, São Carlos, SP, 13566-590, Brazil
| | - Josmar R Rocha
- Grupo de Estudos em Química Medicinal - NEQUIMED, Instituto de Química de São Carlos - Universidade de São Paulo, Av. Trabalhador Sancarlense, 400, São Carlos, SP, 13566-590, Brazil
| | - Geraldo Rodrigues Sartori
- Grupo de Estudos em Química Medicinal - NEQUIMED, Instituto de Química de São Carlos - Universidade de São Paulo, Av. Trabalhador Sancarlense, 400, São Carlos, SP, 13566-590, Brazil
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Volná T, Motyka K, Hlaváč J. Potential of High-Performance Liquid Chromatography for Distribution Coefficient Determination of 3-Hydroxyquinolin-4(1H)-one Derivatives. Chromatographia 2016. [DOI: 10.1007/s10337-016-3129-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Martel S, Begnaud F, Schuler W, Gillerat F, Oberhauser N, Nurisso A, Carrupt PA. Limits of rapid log P determination methods for highly lipophilic and flexible compounds. Anal Chim Acta 2016; 915:90-101. [DOI: 10.1016/j.aca.2016.02.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 01/31/2016] [Accepted: 02/03/2016] [Indexed: 10/22/2022]
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Jensen DA, Gary RK. Estimation of alkane–water logP for neutral, acidic, and basic compounds using an alkylated polystyrene-divinylbenzene high-performance liquid chromatography column. J Chromatogr A 2015; 1417:21-9. [DOI: 10.1016/j.chroma.2015.09.020] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2015] [Revised: 09/05/2015] [Accepted: 09/07/2015] [Indexed: 12/30/2022]
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Tosti T, Šegan S, Milić D, Radoičić A, Tešić Ž, Milojković-Opsenica D. Estimation of Lipophilicity of Some Polyoxygenated Steroids by the Means of Normal-Phase Thin-Layer Chromatography. J LIQ CHROMATOGR R T 2015. [DOI: 10.1080/10826076.2015.1028287] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Tomislav Tosti
- Faculty of Chemistry, University of Belgrade, Belgrade, Serbia
| | - Sandra Šegan
- ICTM – Department of Chemistry, University of Belgrade, Belgrade, Serbia
| | - Dragana Milić
- Faculty of Chemistry, University of Belgrade, Belgrade, Serbia
| | | | - Živoslav Tešić
- Faculty of Chemistry, University of Belgrade, Belgrade, Serbia
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Vagenende V, Ching TJ, Chua RJ, Jiang QZ, Gagnon P. Self-assembly of lipopolysaccharide layers on allantoin crystals. Colloids Surf B Biointerfaces 2014; 120:8-14. [DOI: 10.1016/j.colsurfb.2014.04.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Revised: 03/28/2014] [Accepted: 04/11/2014] [Indexed: 02/07/2023]
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