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Wang S, König G, Roth HJ, Fouché M, Rodde S, Riniker S. Effect of Flexibility, Lipophilicity, and the Location of Polar Residues on the Passive Membrane Permeability of a Series of Cyclic Decapeptides. J Med Chem 2021; 64:12761-12773. [PMID: 34406766 DOI: 10.1021/acs.jmedchem.1c00775] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Cyclic peptides have received increasing attention over the recent years as potential therapeutics for "undruggable" targets. One major obstacle is, however, their often relatively poor bioavailability. Here, we investigate the structure-permeability relationship of 24 cyclic decapeptides that share the same backbone N-methylation pattern but differ in their side chains. The peptides cover a large range of values for passive membrane permeability as well as lipophilicity and solubility. To rationalize the observed differences in permeability, we extracted for each peptide the population of the membrane-permeable conformation in water from extensive explicit-solvent molecular dynamics simulations and used this as a metric for conformational rigidity or "prefolding." The insights from the simulations together with lipophilicity measurements highlight the intricate interplay between polarity/lipophilicity and flexibility/rigidity and the possible compensating effects on permeability. The findings allow us to better understand the structure-permeability relationship of cyclic peptides and extract general guiding principles.
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Affiliation(s)
- Shuzhe Wang
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Gerhard König
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Hans-Jörg Roth
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Novartis Campus, 4056 Basel, Switzerland
| | - Marianne Fouché
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Novartis Campus, 4056 Basel, Switzerland
| | - Stephane Rodde
- Novartis Institutes for BioMedical Research, Novartis Pharma AG, Novartis Campus, 4056 Basel, Switzerland
| | - Sereina Riniker
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
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Prasad S, Brooks BR. A deep learning approach for the blind logP prediction in SAMPL6 challenge. J Comput Aided Mol Des 2020; 34:535-542. [PMID: 32002779 PMCID: PMC8689685 DOI: 10.1007/s10822-020-00292-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 01/17/2020] [Indexed: 12/14/2022]
Abstract
Water octanol partition coefficient serves as a measure for the lipophilicity of a molecule and is important in the field of drug discovery. A novel method for computational prediction of logarithm of partition coefficient (logP) has been developed using molecular fingerprints and a deep neural network. The machine learning model was trained on a dataset of 12,000 molecules and tested on 2000 molecules. In this article, we present our results for the blind prediction of logP for the SAMPL6 challenge. While the best submission achieved a RMSE of 0.41 logP units, our submission had a RMSE of 0.61 logP units. Overall, we ranked in the top quarter out of the 92 submissions that were made. Our results show that the deep learning model can be used as a fast, accurate and robust method for high throughput prediction of logP of small molecules.
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Affiliation(s)
- Samarjeet Prasad
- Biophysics and Biophysical Chemistry, The Johns Hopkins University, School of Medicine, Baltimore, MD, 21205, USA.
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, 20814, USA.
| | - Bernard R Brooks
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, 20814, USA
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Wang Y, Jafari M, Tang Y, Tang J. Predicting Meridian in Chinese traditional medicine using machine learning approaches. PLoS Comput Biol 2019; 15:e1007249. [PMID: 31765369 PMCID: PMC6876772 DOI: 10.1371/journal.pcbi.1007249] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 10/20/2019] [Indexed: 12/26/2022] Open
Abstract
Plant-derived nature products, known as herb formulas, have been commonly used in Traditional Chinese Medicine (TCM) for disease prevention and treatment. The herbs have been traditionally classified into different categories according to the TCM Organ systems known as Meridians. Despite the increasing knowledge on the active components of the herbs, the rationale of Meridian classification remains poorly understood. In this study, we took a machine learning approach to explore the classification of Meridian. We determined the molecule features for 646 herbs and their active components including structure-based fingerprints and ADME properties (absorption, distribution, metabolism and excretion), and found that the Meridian can be predicted by machine learning approaches with a top accuracy of 0.83. We also identified the top compound features that were important for the Meridian prediction. To the best of our knowledge, this is the first time that molecular properties of the herb compounds are associated with the TCM Meridians. Taken together, the machine learning approach may provide novel insights for the understanding of molecular evidence of Meridians in TCM.
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Affiliation(s)
- Yinyin Wang
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Mohieddin Jafari
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Yun Tang
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Jing Tang
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
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Influence of LAR and VAR on Para-Aminopyridine Antimalarials Targetting Haematin in Chloroquine-Resistance. PLoS One 2016; 11:e0160091. [PMID: 27483471 PMCID: PMC4970729 DOI: 10.1371/journal.pone.0160091] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 07/13/2016] [Indexed: 11/23/2022] Open
Abstract
Antimalarial chloroquine (CQ) prevents haematin detoxication when CQ-base concentrates in the acidic digestive vacuole through protonation of its p-aminopyridine (pAP) basic aromatic nitrogen and sidechain diethyl-N. CQ export through the variant vacuolar membrane export channel, PFCRT, causes CQ-resistance in Plasmodium falciparum but 3-methyl CQ (sontochin SC), des-ethyl amodiaquine (DAQ) and bis 4-aminoquinoline piperaquine (PQ) are still active. This is determined by changes in drug accumulation ratios in parasite lipid (LAR) and in vacuolar water (VAR). Higher LAR may facilitate drug binding to and blocking PFCRT and also aid haematin in lipid to bind drug. LAR for CQ is only 8.3; VAR is 143,482. More hydrophobic SC has LAR 143; VAR remains 68,523. Similarly DAQ with a phenol substituent has LAR of 40.8, with VAR 89,366. In PQ, basicity of each pAP is reduced by distal piperazine N, allowing very high LAR of 973,492, retaining VAR of 104,378. In another bis quinoline, dichlorquinazine (DCQ), also active but clinically unsatisfactory, each pAP retains basicity, being insulated by a 2-carbon chain from a proximal nitrogen of the single linking piperazine. While LAR of 15,488 is still high, the lowest estimate of VAR approaches 4.9 million. DCQ may be expected to be very highly lysosomotropic and therefore potentially hepatotoxic. In 11 pAP antimalarials a quadratic relationship between logLAR and logResistance Index (RI) was confirmed, while log (LAR/VAR) vs logRI for 12 was linear. Both might be used to predict the utility of structural modifications.
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Sugano K, Kansy M, Artursson P, Avdeef A, Bendels S, Di L, Ecker GF, Faller B, Fischer H, Gerebtzoff G, Lennernaes H, Senner F. Coexistence of passive and carrier-mediated processes in drug transport. Nat Rev Drug Discov 2010; 9:597-614. [PMID: 20671764 DOI: 10.1038/nrd3187] [Citation(s) in RCA: 435] [Impact Index Per Article: 31.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The permeability of biological membranes is one of the most important determinants of the pharmacokinetic processes of a drug. Although it is often accepted that many drug substances are transported across biological membranes by passive transcellular diffusion, a recent hypothesis speculated that carrier-mediated mechanisms might account for the majority of membrane drug transport processes in biological systems. Based on evidence of the physicochemical characteristics and of in vitro and in vivo findings for marketed drugs, as well as results from real-life discovery and development projects, we present the view that both passive transcellular processes and carrier-mediated processes coexist and contribute to drug transport activities across biological membranes.
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Affiliation(s)
- Kiyohiko Sugano
- Pfizer, Research Formulation, Sandwich Laboratories, Ramsgate Road, Sandwich, Kent CT13 9NJ, UK.
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Warhurst DC, Craig JC, Adagu IS, Meyer DJ, Lee SY. The relationship of physico-chemical properties and structure to the differential antiplasmodial activity of the cinchona alkaloids. Malar J 2003; 2:26. [PMID: 14505493 PMCID: PMC201021 DOI: 10.1186/1475-2875-2-26] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2003] [Accepted: 09/01/2003] [Indexed: 11/28/2022] Open
Abstract
Background The 8-amino and 9-hydroxy substituents of antimalarial cinchona alkaloids have the erythro orientation while their inactive 9-epimers are threo. From the X-ray structures a 90° difference in torsion angle between the N1-H1 and C9-O12 bonds in the two series is believed to be important. In order to kill the malaria parasite, alkaloids must cross the erythrocyte and parasite membranes to accumulate in the acid digestive vacuole where they prevent detoxication of haematin produced during haemoglobin breakdown. Methods Ionization constants, octanol/water distribution and haematin interaction are examined for eight alkaloids to explain the influence of small structural differences on activity. Results Erythro isomers have a high distribution ratio of 55:1 from plasma to the erythrocyte membrane, while for the more basic threo epimers this is only 4.5:1. This gives an increased transfer rate of the erythro drugs into the erythrocyte and thence into the parasite vacuole where their favourable conformation allows interaction with haematin, inhibiting its dimerization strongly (90 ± 7%) and thereby killing the parasite. The threo compounds not only enter more slowly but are then severely restricted from binding to haematin by the gauche alignment of their N1-H1 and C9-O12 bonds. Confirmatory molecular models allowed measurement of angles and bond lengths and computation of the electronic spectrum of a quinine-haematin complex. Conclusion Differences in the antiplasmodial activity of the erythro and threo cinchona alkaloids may therefore be attributed to the cumulative effects of lipid/aqueous distribution ratio and drug-haematin interaction. Possible insights into the mechanism of chloroquine-resistance are discussed.
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Affiliation(s)
- David C Warhurst
- Pathogen Molecular Biology Unit, Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel St., London WC1E 7HT, UK
| | - John C Craig
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California, CA 94143-00446 USA
| | - Ipemida S Adagu
- Pathogen Molecular Biology Unit, Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel St., London WC1E 7HT, UK
| | - David J Meyer
- Pathogen Molecular Biology Unit, Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel St., London WC1E 7HT, UK
| | - Sylvia Y Lee
- Pathogen Molecular Biology Unit, Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel St., London WC1E 7HT, UK
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The influence of physico-chemical properties of homologous nicotinic acid esters on the permeability and maximum flux through an octanol membrane. Int J Pharm 1998. [DOI: 10.1016/s0378-5173(97)00286-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Neef C, Meijer DK. Structure-pharmacokinetics relationship of quaternary ammonium compounds. Correlation of physicochemical and pharmacokinetic parameters. NAUNYN-SCHMIEDEBERG'S ARCHIVES OF PHARMACOLOGY 1984; 328:111-8. [PMID: 6527701 DOI: 10.1007/bf00512059] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Correlations between lipophilicity or molecular weight and some pharmacokinetic parameters such as clearance (Cl), elimination rate constant (k10), volume of distribution (V), and terminal half life (lambda z) are presented for a series of structurally related quaternary ammonium cations (QACs). The structure-pharmacokinetics relations were fitted using the computer program NONLIN and were represented by linear, parabolic or S-shaped curves. The relationship between total plasma clearance or hepatic, renal and intestinal clearance and lipophilicity for the present set of data could be described most properly by the equation Y = 1/(aXb + c), where Y stands for the logarithm of the pharmacokinetic parameters and X represents the logarithm of the values of some physicochemical parameters, such as the partition coefficient (P), the (HPLC) capacity factor k' (another lipophilicity parameter) and molecular weight (MW). On the basis of this relationship, correlations of the hepatic or intestinal clearances with the lipophilicity parameters were good (r = 0.98 and r = 0.95 respectively). Curves relating values for partition coefficients and clearance via liver and intestine (expressed relative to the most simple QAC tetramethyl ammonium) showed S-shaped correlation patterns, in contrast to the renal clearance, which correlated poorly (r = 0.54) with lipophilicity. The extent of biliary output of the organic cations shows a threshold phenomenon, sharply increasing at log P greater than 1.5 to a maximum at P greater than 2.5. This pattern was less pronounced in the case of intestinal elimination and absent in the case of renal clearance. The apparent maximum in the hepatic and intestinal clearance for the most lipophilic organic cations is probably due to limitation by organ blood-flow and/or plasma protein binding.(ABSTRACT TRUNCATED AT 250 WORDS)
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Relationships between Octanol-Water Partition Data, Chromatographic Indices and Their Dependence on pH in a Set of Nonsteroidal Anti-Inflammatory Drugs. ACTA ACUST UNITED AC 1983. [DOI: 10.1002/qsar.19830020405] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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