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Šegan S, Krunić MJ, Andrić DB, Šukalović VB, Penjišević JZ, Jevtić II. Evaluation of lipophilicity and drug-likeness of donepezil-like compounds using reversed-phase thin-layer chromatography. Biomed Chromatogr 2024:e5867. [PMID: 38558037 DOI: 10.1002/bmc.5867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 02/08/2024] [Accepted: 03/07/2024] [Indexed: 04/04/2024]
Abstract
Fourteen donepezil-like acetylcholinesterase (AChE) inhibitors from our library were analyzed using reversed-phase thin-layer chromatography to assess their lipophilicity and blood-brain barrier permeability. Compounds possessed N-benzylpiperidine and N,N-diarylpiperazine moieties connected via a short carboxamide or amine linker. Retention parameters RM 0, b, and C0 were considered as the measures of lipophilicity. Besides, logD of the investigated compounds was determined chromatographically using standard compounds with known logPow and logD values at pH 11. Experimentally obtained lipophilicity parameters correlated well with in silico generated results, and the effect of the nature of the linker between two pharmacophores and substituents on the arylpiperazine part of the molecule was observed. As a result of drug-likeness analysis, both Lipinski's rule of five and Veber's rule parameters were determined, suggesting that examined compounds could be potential candidates for further drug development. Principal component analysis was performed to obtain an insight into a grouping of compounds based on calculated structural descriptors, experimentally obtained values of lipophilicity, and AChE inhibitory activity.
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Affiliation(s)
- Sandra Šegan
- Department of Chemistry, Institute of Chemistry, Technology and Metallurgy, University of Belgrade, Belgrade, Republic of Serbia
| | - Mihajlo J Krunić
- Department of Chemistry, Institute of Chemistry, Technology and Metallurgy, University of Belgrade, Belgrade, Republic of Serbia
| | - Deana B Andrić
- Department of Organic Chemistry, Faculty of Chemistry, University of Belgrade, Belgrade, Republic of Serbia
| | - Vladimir B Šukalović
- Department of Chemistry, Institute of Chemistry, Technology and Metallurgy, University of Belgrade, Belgrade, Republic of Serbia
| | - Jelena Z Penjišević
- Department of Chemistry, Institute of Chemistry, Technology and Metallurgy, University of Belgrade, Belgrade, Republic of Serbia
| | - Ivana I Jevtić
- Department of Chemistry, Institute of Chemistry, Technology and Metallurgy, University of Belgrade, Belgrade, Republic of Serbia
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2
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Kohl Y, William N, Elje E, Backes N, Rothbauer M, Srancikova A, Rundén-Pran E, El Yamani N, Korenstein R, Madi L, Barbul A, Kozics K, Sramkova M, Steenson K, Gabelova A, Ertl P, Dusinska M, Nelson A. Rapid identification of in vitro cell toxicity using an electrochemical membrane screening platform. Bioelectrochemistry 2023; 153:108467. [PMID: 37244203 DOI: 10.1016/j.bioelechem.2023.108467] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 04/28/2023] [Accepted: 05/15/2023] [Indexed: 05/29/2023]
Abstract
This study compares the performance and output of an electrochemical phospholipid membrane platform against respective in vitro cell-based toxicity testing methods using three toxicants of different biological action (chlorpromazine (CPZ), colchicine (COL) and methyl methanesulphonate (MMS)). Human cell lines from seven different tissues (lung, liver, kidney, placenta, intestine, immune system) were used to validate this physicochemical testing system. For the cell-based systems, the effective concentration at 50 % cell death (EC50) values are calculated. For the membrane sensor, a limit of detection (LoD) value was extracted as a quantitative parameter describing the minimum concentration of toxicant which significantly affects the structure of the phospholipid sensor membrane layer. LoD values were found to align well with the EC50 values when acute cell viability was used as an end-point and showed a similar toxicity ranking of the tested toxicants. Using the colony forming efficiency (CFE) or DNA damage as end-point, a different order of toxicity ranking was observed. The results of this study showed that the electrochemical membrane sensor generates a parameter relating to biomembrane damage, which is the predominant factor in decreasing cell viability when in vitro models are acutely exposed to toxicants. These results lead the way to using electrochemical membrane-based sensors for rapid relevant preliminary toxicity screens.
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Affiliation(s)
- Yvonne Kohl
- Fraunhofer Institute for Biomedical Engineering IBMT, Joseph-von-Fraunhofer-Weg 1, Sulzbach 66280, Germany.
| | - Nicola William
- School of Chemistry and Faculty of Engineering and Physical Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom.
| | - Elisabeth Elje
- NILU-Norwegian Institute for Air Research, Department for Environmental Chemistry, Health Effects Laboratory, Instituttveien 18, Kjeller 2007, Norway; Faculty of Medicine, Institute of Basic Medical Sciences Department of Molecular Medicine, University of Oslo, Sognsvannsveien 9, Oslo 0372, Norway.
| | - Nadine Backes
- Fraunhofer Institute for Biomedical Engineering IBMT, Joseph-von-Fraunhofer-Weg 1, Sulzbach 66280, Germany
| | - Mario Rothbauer
- Institute of Applied Synthetic Chemistry, Vienna University of Technology, Getreidemarkt 9, 1060 Vienna, Austria.
| | - Annamaria Srancikova
- Department of Nanobiology, Cancer Research Institute, Biomedical Research Center of the Slovak Academy of Sciences, Dubravska Cesta 9, Bratislava 84505, Slovakia.
| | - Elise Rundén-Pran
- NILU-Norwegian Institute for Air Research, Department for Environmental Chemistry, Health Effects Laboratory, Instituttveien 18, Kjeller 2007, Norway.
| | - Naouale El Yamani
- NILU-Norwegian Institute for Air Research, Department for Environmental Chemistry, Health Effects Laboratory, Instituttveien 18, Kjeller 2007, Norway
| | - Rafi Korenstein
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, 69978, Israel.
| | - Lea Madi
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, 69978, Israel.
| | - Alexander Barbul
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, 69978, Israel.
| | - Katarina Kozics
- Department of Nanobiology, Cancer Research Institute, Biomedical Research Center of the Slovak Academy of Sciences, Dubravska Cesta 9, Bratislava 84505, Slovakia.
| | - Monika Sramkova
- Department of Nanobiology, Cancer Research Institute, Biomedical Research Center of the Slovak Academy of Sciences, Dubravska Cesta 9, Bratislava 84505, Slovakia.
| | - Karen Steenson
- School of Chemistry and Faculty of Engineering and Physical Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom.
| | - Alena Gabelova
- Department of Nanobiology, Cancer Research Institute, Biomedical Research Center of the Slovak Academy of Sciences, Dubravska Cesta 9, Bratislava 84505, Slovakia.
| | - Peter Ertl
- Institute of Applied Synthetic Chemistry, Vienna University of Technology, Getreidemarkt 9, 1060 Vienna, Austria; Institute of Chemical Technologies and Analytics, Vienna University of Technology, Getreidemarkt 9, 1060 Vienna, Austria.
| | - Maria Dusinska
- NILU-Norwegian Institute for Air Research, Department for Environmental Chemistry, Health Effects Laboratory, Instituttveien 18, Kjeller 2007, Norway.
| | - Andrew Nelson
- School of Chemistry and Faculty of Engineering and Physical Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom.
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3
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Seo H, Jackl MK, Kalaj M, Cohen SM. Developing Metal-Binding Isosteres of 8-Hydroxyquinoline as Metalloenzyme Inhibitor Scaffolds. Inorg Chem 2022; 61:7631-7641. [PMID: 35507007 PMCID: PMC9912809 DOI: 10.1021/acs.inorgchem.2c00891] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The use of metal-binding pharmacophores (MBPs) in fragment-based drug discovery has proven effective for targeted metalloenzyme drug development. However, MBPs can still suffer from pharmacokinetic liabilities. Bioisostere replacement is an effective strategy utilized by medicinal chemists to navigate these issues during the drug development process. The quinoline pharmacophore and its bioisosteres, such as quinazoline, are important building blocks in the design of new therapeutics. More relevant to metalloenzyme inhibition, 8-hydroxyquinoline (8-HQ) and its derivatives can serve as MBPs for metalloenzyme inhibition. In this report, 8-HQ isosteres are designed and the coordination chemistry of the resulting metal-binding isosteres (MBIs) is explored using a bioinorganic model complex. In addition, the physicochemical properties and metalloenzyme inhibition activity of these MBIs were investigated to establish drug-like profiles. This report provides a new group of 8-HQ-derived MBIs that can serve as novel scaffolds for metalloenzyme inhibitor development with tunable, and potentially improved, physicochemical properties.
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4
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Manley PW, Huth F, Moussaoui S, Schoepfer J. A kinase inhibitor which specifically targets the ABL myristate pocket (STAMP), but unlike asciminib crosses the blood–brain barrier. Bioorg Med Chem Lett 2022; 59:128577. [DOI: 10.1016/j.bmcl.2022.128577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 01/03/2022] [Accepted: 01/15/2022] [Indexed: 11/25/2022]
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5
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Jackl MK, Seo H, Karges J, Kalaj M, Cohen SM. Salicylate metal-binding isosteres as fragments for metalloenzyme inhibition. Chem Sci 2022; 13:2128-2136. [PMID: 35308862 PMCID: PMC8849047 DOI: 10.1039/d1sc06011b] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 01/12/2022] [Indexed: 01/22/2023] Open
Abstract
Metalloenzyme inhibitors typically share a common need to possess a metal-binding pharmacophore (MBP) for binding the active site metal ions. However, MBPs can suffer from physicochemical liabilities, impeding the pharmacological properties and drug-likeliness of inhibitors. To circumvent this, problematic features of the MBP can be identified and exchanged with isosteric replacements. Herein, the carboxylic and hydroxyl group of the salicylic acid MBP were replaced and a total of 27 salicylate metal-binding isosteres (MBIs) synthesized. Of these 27 MBIs, at least 12 represent previously unreported compounds, and the metal-binding abilities of >20 of the MBIs have not been previously reported. These salicylate MBIs were examined for their metal-binding features in model complexes, physicochemical properties, and biological activity. It was observed that salicylate MBIs can demonstrate a range of attractive physicochemical properties and bind to the metal in a variety of expected and unexpected binding modes. The biological activity of these novel MBIs was evaluated by measuring inhibition against two Zn2+-dependent metalloenzymes, human glyoxalase 1 (GLO1) and matrix metalloproteinase 3 (MMP-3), as well as a dinuclear Mn2+-dependent metalloenzyme, influenza H1N1 N-terminal endonuclease (PAN). It was observed that salicylate MBIs could maintain or improve enzyme inhibition and selectivity. To probe salicylate MBIs as fragments for fragment-based drug discovery (FBDD), an MBI that showed good inhibitory activity against GLO1 was derivatized and a rudimentary structure-activity relationship was developed. The resulting elaborated fragments showed GLO1 inhibition with low micromolar activity.
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Affiliation(s)
- Moritz K Jackl
- Department of Chemistry and Biochemistry, University of California San Diego 9500 Gilman Drive La Jolla CA 92093-0358 USA
| | - Hyeonglim Seo
- Department of Chemistry and Biochemistry, University of California San Diego 9500 Gilman Drive La Jolla CA 92093-0358 USA
| | - Johannes Karges
- Department of Chemistry and Biochemistry, University of California San Diego 9500 Gilman Drive La Jolla CA 92093-0358 USA
| | - Mark Kalaj
- Department of Chemistry and Biochemistry, University of California San Diego 9500 Gilman Drive La Jolla CA 92093-0358 USA
| | - Seth M Cohen
- Department of Chemistry and Biochemistry, University of California San Diego 9500 Gilman Drive La Jolla CA 92093-0358 USA
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6
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Fındık V, Ruiz-López MF, Erdem SS. Mechanistic insights into lysine-targeting covalent inhibition through a theoretical study of ester aminolysis. Org Biomol Chem 2021; 19:9996-10004. [PMID: 34755747 DOI: 10.1039/d1ob01963e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Development of targeted covalent inhibitors in drug design has a broad and important interest and many efforts are currently being made in this direction. Targeted covalent inhibitors have special relevance in oncology due to the possibilities they offer to overcome the problems of acquired resistance. In recent experiments, lysine-targeting has been envisaged for the irreversible inhibition of the heterodimeric lipid kinase phosphoinositide 3-kinase delta (PI3Kδ). Activated esters have been evaluated and shown to be promising inhibitors of this enzyme, but the reaction mechanisms display specificities that are not yet fully understood. In the present work, we have carried out a theoretical study of the aminolysis reaction of model esters in aqueous solution to gain insights into the corresponding biological processes. We have found that phenolic esters bearing electron-withdrawing groups are particularly reactive. The predicted mechanism involves the formation of a tetrahedral zwitterionic intermediate, which dissociates into an alkoxide and a protonated amide, this charge separation being the driving force for the subsequent proton transfer and final product formation. Structure-reactivity relationships are reported and shown to be a useful tool for evaluating potential inhibitor candidates.
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Affiliation(s)
- Volkan Fındık
- LPCT, UMR 7019, University of Lorraine, CNRS, BP 70239, 54506 Vandoeuvre-les-Nancy, France. .,Department of Chemistry, Faculty of Arts and Sciences, Marmara University, 34722 Istanbul, Turkey.
| | - Manuel F Ruiz-López
- LPCT, UMR 7019, University of Lorraine, CNRS, BP 70239, 54506 Vandoeuvre-les-Nancy, France.
| | - Safiye Sag Erdem
- Department of Chemistry, Faculty of Arts and Sciences, Marmara University, 34722 Istanbul, Turkey.
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7
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Hashimoto Y, Hosokawa S, Liang F, Suzuki Y, Dai N, Tana G, Eda K, Kakiuchi T, Okazoe T, Harada H, Tsuda A. Photo-on-Demand Base-Catalyzed Phosgenation Reactions with Chloroform: Synthesis of Arylcarbonate and Halocarbonate Esters. J Org Chem 2021; 86:9811-9819. [PMID: 34182754 DOI: 10.1021/acs.joc.1c01210] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Carbonate esters are utilized as solvents and reagents for C1 building blocks in organic synthesis. This study reports a novel photo-on-demand in situ synthesis of carbonate esters with CHCl3 solutions containing a mixture of an aromatic or haloalkyl alcohol having relatively high acidity, and an organic base. We found that the acid-base interaction of the alcohol and base in the CHCl3 solution plays a key role in enabling the photochemical reaction. This reaction allows practical syntheses of diphenyl carbonate derivatives, haloalkyl carbonates, and polycarbonates, which are important chemicals and materials in industry.
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Affiliation(s)
- Yuka Hashimoto
- Department of Chemistry, Graduate School of Science, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe 657-8501, Japan
| | - Sasuga Hosokawa
- Department of Chemistry, Graduate School of Science, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe 657-8501, Japan
| | - Fengying Liang
- Department of Chemistry, Graduate School of Science, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe 657-8501, Japan
| | - Yuto Suzuki
- Department of Chemistry, Graduate School of Science, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe 657-8501, Japan
| | - Namin Dai
- Department of Chemistry, Graduate School of Science, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe 657-8501, Japan
| | - Gegen Tana
- Department of Chemistry, Graduate School of Science, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe 657-8501, Japan
| | - Kazuo Eda
- Department of Chemistry, Graduate School of Science, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe 657-8501, Japan
| | - Toshifumi Kakiuchi
- Innovative Technology Laboratories, AGC Inc., Suehiro 1-1 Tsurumi-ku, Yokohama City, Kanagawa 230-0045, Japan
| | - Takashi Okazoe
- Materials Integration Laboratories, AGC Inc., Suehiro 1-1 Tsurumi-ku, Yokohama City, Kanagawa 230-0045, Japan
| | - Hidefumi Harada
- Tokyo Research Laboratory, Mitsubishi Gas Chemical Company, Inc., Nijyuku 6-1-1 Katsushika-ku, Tokyo 125-8601, Japan
| | - Akihiko Tsuda
- Department of Chemistry, Graduate School of Science, Kobe University, 1-1 Rokkodai-cho, Nada-ku, Kobe 657-8501, Japan
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8
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Dick BL, Patel A, Cohen SM. Effect of heterocycle content on metal binding isostere coordination. Chem Sci 2020; 11:6907-6914. [PMID: 33209243 PMCID: PMC7597899 DOI: 10.1039/d0sc02717k] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 06/16/2020] [Indexed: 11/21/2022] Open
Abstract
Bioisostere replacement is a core concept in modern medicinal chemistry and in this work new metal-binding isosteres (MBIs) are synthesized and evaluated for use in metalloenzyme inhibitors.
Bioisostere replacement is a core concept in modern medicinal chemistry and has proven an invaluable strategy to address pharmacodynamic and pharmacokinetic limitations of therapeutics. The success of bioisostere replacement is often dependent on the scaffold that is being modified (i.e., “context dependence”). The application of bioisostere replacement to a picolinic acid fragment was recently demonstrated as a means to expand a library of metal-binding pharmacophores (MBPs) to modulate their physicochemical properties, while retaining their metal binding and metalloenzyme inhibitory activity. Here, metal binding isosteres (MBIs) with different nitrogen-containing heteroarenes is explored. This resulted in a number of new MBIs that were evaluated for their physicochemical properties and metal binding features. It was observed that the coordination behavior of an MBI is dependent on the identity and arrangement of the heteroatoms within each heteroarene. To further understand the observed coordination chemistry trends, density functional theory (DFT) calculations were performed. Theory indicates that preferences in coordination geometry are largely determined by the electronic character of the heteroarene scaffold. These results provide important insights into the development of novel MBI scaffolds that can serve to broaden the scope of scaffolds for metalloenzyme inhibitor development.
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Affiliation(s)
- Benjamin L Dick
- Department of Chemistry and Biochemistry , University of California San Diego , 9500 Gilman Drive, La Jolla , CA 92093-0358 , USA .
| | - Ashay Patel
- Department of Chemistry and Biochemistry , University of California San Diego , 9500 Gilman Drive, La Jolla , CA 92093-0358 , USA .
| | - Seth M Cohen
- Department of Chemistry and Biochemistry , University of California San Diego , 9500 Gilman Drive, La Jolla , CA 92093-0358 , USA .
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9
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Fundamental aspects of DMPK optimization of targeted protein degraders. Drug Discov Today 2020; 25:969-982. [PMID: 32298797 DOI: 10.1016/j.drudis.2020.03.012] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 03/03/2020] [Accepted: 03/16/2020] [Indexed: 12/30/2022]
Abstract
Targeted protein degraders are an emerging modality. Their properties fall outside the traditional small-molecule property space and are in the 'beyond rule of 5' space. Consequently, drug discovery programs focused on developing orally bioavailable degraders are expected to face complex drug metabolism and pharmacokinetics (DMPK) challenges compared with traditional small molecules. Nevertheless, little information is available on the DMPK optimization of oral degraders. Therefore, in this review, we discuss our experience of these DMPK optimization challenges and present methodologies and strategies to overcome the hurdles dealing with this new small-molecule modality, specifically in developing oral degraders to treat cancer.
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10
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Işık M, Bergazin TD, Fox T, Rizzi A, Chodera JD, Mobley DL. Assessing the accuracy of octanol-water partition coefficient predictions in the SAMPL6 Part II log P Challenge. J Comput Aided Mol Des 2020; 34:335-370. [PMID: 32107702 PMCID: PMC7138020 DOI: 10.1007/s10822-020-00295-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 01/24/2020] [Indexed: 12/12/2022]
Abstract
The SAMPL Challenges aim to focus the biomolecular and physical modeling community on issues that limit the accuracy of predictive modeling of protein-ligand binding for rational drug design. In the SAMPL5 log D Challenge, designed to benchmark the accuracy of methods for predicting drug-like small molecule transfer free energies from aqueous to nonpolar phases, participants found it difficult to make accurate predictions due to the complexity of protonation state issues. In the SAMPL6 log P Challenge, we asked participants to make blind predictions of the octanol-water partition coefficients of neutral species of 11 compounds and assessed how well these methods performed absent the complication of protonation state effects. This challenge builds on the SAMPL6 p[Formula: see text] Challenge, which asked participants to predict p[Formula: see text] values of a superset of the compounds considered in this log P challenge. Blind prediction sets of 91 prediction methods were collected from 27 research groups, spanning a variety of quantum mechanics (QM) or molecular mechanics (MM)-based physical methods, knowledge-based empirical methods, and mixed approaches. There was a 50% increase in the number of participating groups and a 20% increase in the number of submissions compared to the SAMPL5 log D Challenge. Overall, the accuracy of octanol-water log P predictions in SAMPL6 Challenge was higher than cyclohexane-water log D predictions in SAMPL5, likely because modeling only the neutral species was necessary for log P and several categories of method benefited from the vast amounts of experimental octanol-water log P data. There were many highly accurate methods: 10 diverse methods achieved RMSE less than 0.5 log P units. These included QM-based methods, empirical methods, and mixed methods with physical modeling supported with empirical corrections. A comparison of physical modeling methods showed that QM-based methods outperformed MM-based methods. The average RMSE of the most accurate five MM-based, QM-based, empirical, and mixed approach methods based on RMSE were 0.92 ± 0.13, 0.48 ± 0.06, 0.47 ± 0.05, and 0.50 ± 0.06, respectively.
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Affiliation(s)
- Mehtap Işık
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.
- Tri-Institutional PhD Program in Chemical Biology, Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, NY, 10065, USA.
| | | | - Thomas Fox
- Computational Chemistry, Medicinal Chemistry, Boehringer Ingelheim Pharma GmbH & Co KG, 88397, Biberach, Germany
| | - Andrea Rizzi
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
- Tri-Institutional Training Program in Computational Biology and Medicine, New York, NY, 10065, USA
| | - John D Chodera
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - David L Mobley
- Department of Pharmaceutical Sciences, University of California, Irvine, CA, 92697, USA
- Department of Chemistry, University of California, Irvine, CA, 92697, USA
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11
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Işık M, Levorse D, Mobley DL, Rhodes T, Chodera JD. Octanol-water partition coefficient measurements for the SAMPL6 blind prediction challenge. J Comput Aided Mol Des 2019; 34:405-420. [PMID: 31858363 DOI: 10.1007/s10822-019-00271-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Accepted: 12/07/2019] [Indexed: 11/24/2022]
Abstract
Partition coefficients describe the equilibrium partitioning of a single, defined charge state of a solute between two liquid phases in contact, typically a neutral solute. Octanol-water partition coefficients ([Formula: see text]), or their logarithms (log P), are frequently used as a measure of lipophilicity in drug discovery. The partition coefficient is a physicochemical property that captures the thermodynamics of relative solvation between aqueous and nonpolar phases, and therefore provides an excellent test for physics-based computational models that predict properties of pharmaceutical relevance such as protein-ligand binding affinities or hydration/solvation free energies. The SAMPL6 Part II octanol-water partition coefficient prediction challenge used a subset of kinase inhibitor fragment-like compounds from the SAMPL6 [Formula: see text] prediction challenge in a blind experimental benchmark. Following experimental data collection, the partition coefficient dataset was kept blinded until all predictions were collected from participating computational chemistry groups. A total of 91 submissions were received from 27 participating research groups. This paper presents the octanol-water log P dataset for this SAMPL6 Part II partition coefficient challenge, which consisted of 11 compounds (six 4-aminoquinazolines, two benzimidazole, one pyrazolo[3,4-d]pyrimidine, one pyridine, one 2-oxoquinoline substructure containing compounds) with log P values in the range of 1.95-4.09. We describe the potentiometric log P measurement protocol used to collect this dataset using a Sirius T3, discuss the limitations of this experimental approach, and share suggestions for future log P data collection efforts for the evaluation of computational methods.
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Affiliation(s)
- Mehtap Işık
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
- Tri-Institutional PhD Program in Chemical Biology, Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, NY, 10065, USA
| | - Dorothy Levorse
- Pharmaceutical Sciences, MRL, Merck & Co., Inc., 126 East Lincoln Avenue, Rahway, NJ, 07065, USA
| | - David L Mobley
- Department of Pharmaceutical Sciences and Department of Chemistry, University of California, Irvine, Irvine, CA, 92697, USA
| | - Timothy Rhodes
- Pharmaceutical Sciences, MRL, Merck & Co., Inc., 126 East Lincoln Avenue, Rahway, NJ, 07065, USA.
| | - John D Chodera
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.
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12
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Loschen C, Reinisch J, Klamt A. COSMO-RS based predictions for the SAMPL6 logP challenge. J Comput Aided Mol Des 2019; 34:385-392. [PMID: 31773462 DOI: 10.1007/s10822-019-00259-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 11/19/2019] [Indexed: 12/15/2022]
Abstract
Within the framework of the 6th physical property blind challenge (SAMPL6) the authors have participated in predicting the octanol-water partition coefficients (logP) for several small drug like molecules. Those logP values where experimentally known by the organizers but only revealed after the submissions of the predictions. Two different sets of predictions were submitted by the authors, both based on the COSMOtherm implementation of COSMO-RS theory. COSMOtherm predictions using the FINE parametrization level (hmz0n) obtained the highest accuracy among all submissions as measured by the root mean squared error. COSMOquick predictions using a fast algorithm to estimate σ-profiles and an a posterio machine learning correction on top of the COSMOtherm results (3vqbi) scored 3rd out of 91 submissions. Both results underline the high quality of COSMO-RS derived molecular free energies in solution.
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Affiliation(s)
| | | | - Andreas Klamt
- Dassault Systèmes, BIOVIA, Leverkusen, Germany.,Institute of Physical and Theoretical Chemistry, University of Regensburg, Regensburg, Germany
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13
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David V, Moldoveanu SC. Variation with temperature of octanol/water partition coefficient for the homologous series from benzene to propylbenzene. SEPARATION SCIENCE PLUS 2019. [DOI: 10.1002/sscp.201900033] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Victor David
- University of Bucharest, Faculty of ChemistryDepartment of Analytical Chemistry Romania
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14
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Fernández-Pumarega A, Amézqueta S, Fuguet E, Rosés M. Determination of the retention factor of ionizable compounds in microemulsion electrokinetic chromatography. Anal Chim Acta 2019; 1078:221-230. [DOI: 10.1016/j.aca.2019.06.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 05/30/2019] [Accepted: 06/02/2019] [Indexed: 10/26/2022]
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15
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Abstract
The principle of isosteres or bioisosteres in medicinal chemistry is a central and essential concept in modern drug discovery. For example, carboxylic acids are often replaced by bioisosteres to mitigate issues related to lipophilicity or acidity while retaining acidic characteristics in addition to hydrogen bond donor/acceptor abilities. Separately, the development of metal-binding pharmacophores (MBPs) for binding to the active site metal ion in metalloenzymes of therapeutic interest is an emerging area in the realm of fragment-based drug discovery (FBDD). The direct application of the bioisostere concept to MBPs has not been well-described or systematically investigated. Herein, the picolinic acid MBP is used as a case study for the development of MBP isosteres (so-called MBIs). Many of these isosteres are novel compounds, and data on their physicochemical properties, metal binding capacity, and metalloenzyme inhibition characteristics are presented. The results show that MBIs of picolinic acid generally retain metal coordinating properties and exhibit predictable metalloenzyme inhibitory activity while possessing a broad range of physicochemical properties (e.g., p Ka, log P). These findings demonstrate the use of bioisosteres results in an untapped source of metal binding functional groups suitable for metalloenzyme FBDD. These MBIs provide a previously unexplored route for modulating the physicochemical properties of metalloenzyme inhibitors and improving their drug-likeness.
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Affiliation(s)
- Benjamin L. Dick
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, 92093, USA
| | - Seth M. Cohen
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, 92093, USA
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16
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Adamek RN, Credille CV, Dick BL, Cohen SM. Isosteres of hydroxypyridinethione as drug-like pharmacophores for metalloenzyme inhibition. J Biol Inorg Chem 2018; 23:1129-1138. [PMID: 30003339 DOI: 10.1007/s00775-018-1593-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 06/28/2018] [Indexed: 12/18/2022]
Abstract
Hydroxypyridinethiones (HOPTOs) are strong ligands for metal ions and potentially useful pharmacophores for inhibiting metalloenzymes relevant to human disease. However, HOPTOs have been sparingly used in drug discovery efforts due, in part, to concerns that this scaffold will act as a promiscuous, non-selective metalloenzyme inhibitor, as well as possess poor pharmacokinetics (PK), which may undermine drug candidates containing this functional group. To advance HOPTOs as a useful pharmacophore for metalloenzyme inhibitors, a library of 22 HOPTO isostere compounds has been synthesized and investigated. This library demonstrates that it is possible to maintain the core metal-binding pharmacophore (MBP) while generating diversity in structure, electronics, and PK properties. This HOPTO library has been screened against a set of four different metalloenzymes, demonstrating that while the same metal-binding donor atoms are maintained, there is a wide range of activity between metalloenzyme targets. Overall, this work shows that HOPTO isosteres are useful MBPs and valuable scaffolds for metalloenzyme inhibitors.
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Affiliation(s)
- Rebecca N Adamek
- Department of Chemistry and Biochemistry, University of California, La Jolla, San Diego, CA, 92093, USA
| | - Cy V Credille
- Department of Chemistry and Biochemistry, University of California, La Jolla, San Diego, CA, 92093, USA
| | - Benjamin L Dick
- Department of Chemistry and Biochemistry, University of California, La Jolla, San Diego, CA, 92093, USA
| | - Seth M Cohen
- Department of Chemistry and Biochemistry, University of California, La Jolla, San Diego, CA, 92093, USA.
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17
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Investigation of Solution pKa and Thermodynamic Values of Lamivudine and Pefloxacin Drugs by Ab initio and DFT Methods. J SOLUTION CHEM 2018. [DOI: 10.1007/s10953-018-0775-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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18
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Shiung YC, Chen CY, Wu JC, Chang SW, Lin CH. Determination of the pK
a
of Benzophenones by Capillary Zone Electrophoresis. J CHIN CHEM SOC-TAIP 2017. [DOI: 10.1002/jccs.201700254] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Yuan-Chi Shiung
- Department of Chemistry; National Taiwan University; Taipei 10617 Taiwan
| | - Chih-Yu Chen
- Department of Environmental Engineering and Science; Fooyin University; Kaohsiung City 83102 Taiwan
| | - Jong-Chang Wu
- Department of Applied Chemistry and Material Science; Fooyin University; Kaohsiung City 83102 Taiwan
| | - Shu-Wen Chang
- Department of Applied Chemistry and Material Science; Fooyin University; Kaohsiung City 83102 Taiwan
| | - Chen-Hsing Lin
- Department of Applied Chemistry and Material Science; Fooyin University; Kaohsiung City 83102 Taiwan
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19
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Volná T, Motyka K, Hlaváč J. RP-HPLC determination of dissociation constant using solely aqueous mobile phase. J Pharm Biomed Anal 2017; 134:143-148. [PMID: 27915191 DOI: 10.1016/j.jpba.2016.11.038] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 11/14/2016] [Accepted: 11/15/2016] [Indexed: 11/18/2022]
Abstract
The proposed HPLC method using solely or nearly 100% aqueous mobile buffer as mobile phase offers fast determination of dissociation constant for compounds in relatively wide range of lipophilicity (log P from -2.26 to 2.26). The dissociation constant value for simpler chemical compounds can be determined via only 8 chromatographic runs. The number of needed chromatographic separations depends on the structural complexity of the tested compound. Moreover, the proposed method does not require a measurement of Yasuda-Shedlovsky extrapolation that includes several pKa determinations in solutions with different methanol content which speeds up considerably the procedure. The methodology is suitable for evaluation of large series of drug candidates, which can be present as complex mixtures and in small amounts.
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Affiliation(s)
- Tereza Volná
- Department of Organic Chemistry, Faculty of Science, Palacký University in Olomouc, 17. listopadu 12, 771 46 Olomouc, Czech Republic
| | - Kamil Motyka
- Department of Organic Chemistry, Faculty of Science, Palacký University in Olomouc, 17. listopadu 12, 771 46 Olomouc, Czech Republic.
| | - Jan Hlaváč
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacký University in Olomouc, Hněvotínská 5, 779 00 Olomouc, Czech Republic
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20
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Begnaud F, Larcinese JP, Fankhauser P, Maddalena U. LogP measurement of a highly hydrophobic properfume: evaluation of extrapolation of RP-HPLC results and impact of chemical moieties on accuracy. FLAVOUR FRAG J 2016. [DOI: 10.1002/ffj.3309] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- F. Begnaud
- Firmenich SA; Corporate R&D Division; Route des Jeunes 1 1211 Geneva
| | - J.-P. Larcinese
- Firmenich SA; Corporate R&D Division; Route des Jeunes 1 1211 Geneva
| | - P. Fankhauser
- Firmenich SA; Corporate R&D Division; Route des Jeunes 1 1211 Geneva
| | - U. Maddalena
- Firmenich SA; Corporate R&D Division; Route des Jeunes 1 1211 Geneva
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21
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Colclough N, Wenlock MC. Interpreting physicochemical experimental data sets. J Comput Aided Mol Des 2015; 29:779-94. [PMID: 26054297 DOI: 10.1007/s10822-015-9850-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Accepted: 05/29/2015] [Indexed: 12/01/2022]
Abstract
With the wealth of experimental physicochemical data available to chemoinformaticians from the literature, commercial, and company databases an increasing challenge is the interpretation of such datasets. Subtle differences in experimental methodology used to generate these datasets can give rise to variations in physicochemical property values. Such methodology nuances will be apparent to an expert experimentalist but not necessarily to the data analyst and modeller. This paper describes the differences between common methodologies for measuring the four most important physicochemical properties namely aqueous solubility, octan-1-ol/water distribution coefficient, pK(a) and plasma protein binding highlighting key factors that can lead to systematic differences. Insight is given into how to identify datasets suitable for combining.
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Affiliation(s)
- Nicola Colclough
- Oncology and Drug Safety and Metabolism, Innovative Medicines, Mereside, AstraZeneca, Alderley Park, Macclesfield, Cheshire, SK10 4TG, UK.
| | - Mark C Wenlock
- Oncology and Drug Safety and Metabolism, Innovative Medicines, Mereside, AstraZeneca, Alderley Park, Macclesfield, Cheshire, SK10 4TG, UK
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22
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Bergström CA, Holm R, Jørgensen SA, Andersson SB, Artursson P, Beato S, Borde A, Box K, Brewster M, Dressman J, Feng KI, Halbert G, Kostewicz E, McAllister M, Muenster U, Thinnes J, Taylor R, Mullertz A. Early pharmaceutical profiling to predict oral drug absorption: Current status and unmet needs. Eur J Pharm Sci 2014; 57:173-99. [DOI: 10.1016/j.ejps.2013.10.015] [Citation(s) in RCA: 192] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Revised: 10/17/2013] [Accepted: 10/27/2013] [Indexed: 01/17/2023]
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23
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Moldoveanu SC, David V. Dependence of the distribution constant in liquid-liquid partition equilibria on the van der Waals molecular surface area. J Sep Sci 2013; 36:2963-78. [DOI: 10.1002/jssc.201300330] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Revised: 05/13/2013] [Accepted: 06/11/2013] [Indexed: 11/10/2022]
Affiliation(s)
| | - Victor David
- Faculty of Chemistry, Department of Analytical Chemistry; University of Bucharest; Bucharest Romania
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24
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Ma D, Chen L, Lui R. Decrease of antiandrogenic activity in gray water and domestic wastewater treated by the MBR process. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2013; 15:668-676. [PMID: 23738366 DOI: 10.1039/c3em30737a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
In order to figure out the variation of the androgens/antiandrogens in wastewater treatment, androgenic/antiandrogenic activities were investigated in two membrane bioreactors (MBR) treating gray water and domestic wastewater, respectively, in Beijing city, China. The androgens and antiandrogens were extracted from water and solid samples by a solid phase extraction (SPE) method and the androgenic/antiandrogenic activities were detected with a recombined androgen receptor (AR) yeast assay. The results showed that there were no androgenic induction activities either in water or in solid samples, but all samples exhibited obvious antiandrogenic activities. The antiandrogenic activities in the suspended solids contributed to 27.4% of the total antiandrogenic activities in gray water and 37.7% in domestic wastewater. Although the concentration of flutamide equivalent (FEQ) of the domestic wastewater (3.1 mg L(-1)) was about three times higher than that of the gray water (1.1 mg L-(1)) in the liquid phase, the effluent FEQ of the two processes was comparable, and the concentrations were 53.7 ± 2.4 μg L(-1) and 68.9 ± 6.0 μg L(-1), respectively. By mass balance analysis, a total of 1825.2 mg FEQ antiandrogens flowed into the gray water and 4914.1 mg flowed into the domestic wastewater treatment process every day. More than 95% of the influent antiandrogens in the liquid phase was removed in both systems. And only 64.5 mg and 69.0 mg FEQ antiandrogens flowed out of gray water and domestic wastewater treatment processes every day. Biodegradation was considered to be the crucial antiandrogen removal mechanism in MBR, which contributed to 98% of the antiandrogen removal in the gray water treatment plant, and 91% in the domestic wastewater treatment plant.
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Affiliation(s)
- Dehua Ma
- School of Environment, Tsinghua University, Beijing, China.
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25
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Shoemaker CJ, Schornberg KL, Delos SE, Scully C, Pajouhesh H, Olinger GG, Johansen LM, White JM. Multiple cationic amphiphiles induce a Niemann-Pick C phenotype and inhibit Ebola virus entry and infection. PLoS One 2013; 8:e56265. [PMID: 23441171 PMCID: PMC3575416 DOI: 10.1371/journal.pone.0056265] [Citation(s) in RCA: 110] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Accepted: 01/07/2013] [Indexed: 12/11/2022] Open
Abstract
Ebola virus (EBOV) is an enveloped RNA virus that causes hemorrhagic fever in humans and non-human primates. Infection requires internalization from the cell surface and trafficking to a late endocytic compartment, where viral fusion occurs, providing a conduit for the viral genome to enter the cytoplasm and initiate replication. In a concurrent study, we identified clomiphene as a potent inhibitor of EBOV entry. Here, we screened eleven inhibitors that target the same biosynthetic pathway as clomiphene. From this screen we identified six compounds, including U18666A, that block EBOV infection (IC50 1.6 to 8.0 µM) at a late stage of entry. Intriguingly, all six are cationic amphiphiles that share additional chemical features. U18666A induces phenotypes, including cholesterol accumulation in endosomes, associated with defects in Niemann–Pick C1 protein (NPC1), a late endosomal and lysosomal protein required for EBOV entry. We tested and found that all six EBOV entry inhibitors from our screen induced cholesterol accumulation. We further showed that higher concentrations of cationic amphiphiles are required to inhibit EBOV entry into cells that overexpress NPC1 than parental cells, supporting the contention that they inhibit EBOV entry in an NPC1-dependent manner. A previously reported inhibitor, compound 3.47, inhibits EBOV entry by blocking binding of the EBOV glycoprotein to NPC1. None of the cationic amphiphiles tested had this effect. Hence, multiple cationic amphiphiles (including several FDA approved agents) inhibit EBOV entry in an NPC1-dependent fashion, but by a mechanism distinct from that of compound 3.47. Our findings suggest that there are minimally two ways of perturbing NPC1-dependent pathways that can block EBOV entry, increasing the attractiveness of NPC1 as an anti-filoviral therapeutic target.
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Affiliation(s)
- Charles J. Shoemaker
- Departmentof Cell Biology, University of Virginia, Charlottesville, Virginia, United States of America
| | - Kathryn L. Schornberg
- Departmentof Cell Biology, University of Virginia, Charlottesville, Virginia, United States of America
| | - Sue E. Delos
- Departmentof Cell Biology, University of Virginia, Charlottesville, Virginia, United States of America
| | - Corinne Scully
- U.S. Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Maryland, United States of America
| | - Hassan Pajouhesh
- Zalicus Inc., Cambridge, Massachusetts, United States of America
| | - Gene G. Olinger
- U.S. Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Maryland, United States of America
| | - Lisa M. Johansen
- Zalicus Inc., Cambridge, Massachusetts, United States of America
| | - Judith M. White
- Departmentof Cell Biology, University of Virginia, Charlottesville, Virginia, United States of America
- Departmentof Microbiology, University of Virginia, Charlottesville, Virginia, United States of America
- * E-mail:
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26
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Sustained release of the CCR5 inhibitors CMPD167 and maraviroc from vaginal rings in rhesus macaques. Antimicrob Agents Chemother 2012; 56:2251-8. [PMID: 22330914 DOI: 10.1128/aac.05810-11] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Antiretroviral entry inhibitors are now being considered as vaginally administered microbicide candidates for the prevention of the sexual transmission of human immunodeficiency virus. Previous studies testing the entry inhibitors maraviroc and CMPD167 in aqueous gel formulations showed efficacy in the macaque challenge model, although protection was highly dependent on the time period between initial gel application and subsequent challenge. In this paper, we describe the sustained release of maraviroc and CMPD167 from matrix-type silicone elastomer vaginal rings both in vitro and in vivo. Both inhibitors were released continuously during 28 days from rings in vitro at rates of 100 to 2,500 μg/day. In 28-day pharmacokinetic studies in rhesus macaques, the compounds were measured in the vaginal fluid and vaginal tissue; steady-state fluid concentrations were ~10(6)-fold greater than the 50% inhibitory concentrations (IC(50)s) for simian human immunodeficiency virus 162P3 inhibition in macaque lymphocytes in vitro. Plasma concentrations for both compounds were very low. The pretreatment of macaques with Depo-Provera (DP), which is commonly used in macaque challenge studies, was shown to significantly modify the biodistribution of the inhibitors but not the overall amount released. Vaginal fluid and tissue concentrations were significantly decreased while plasma levels increased with DP pretreatment. These observations have implications for designing macaque challenge experiments and also for ring performance during the human female menstrual cycle.
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27
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David S, Timmins P, Conway B. Impact of the counterion on the solubility and physicochemical properties of salts of carboxylic acid drugs. Drug Dev Ind Pharm 2011; 38:93-103. [DOI: 10.3109/03639045.2011.592530] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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28
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Dutta AK, Stodghill SP, Wyandt CM. Physicochemical characterization of NPC 1161C, a novel antimalarial 8-aminoquinoline, in solution and solid state. AAPS PharmSciTech 2011; 12:177-91. [PMID: 21191676 DOI: 10.1208/s12249-010-9578-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2010] [Accepted: 12/16/2010] [Indexed: 11/30/2022] Open
Abstract
NPC 1161C is a novel antimalarial drug of interest because of its superior curative and prophylactic activity, and favorable toxicity profile against in vivo and in vitro models of malaria, pneumocystis carinii pneumonia, and leishmaniasis. The preformulation studies performed included determination of pK(a)s, aqueous and pH solubility, cosolvent solubility, log P, pH stability, thermal analysis, and preliminary hygroscopicity studies. The mean pK(a1), pK(a2), and pK(a3) were determined to be 10.12, 4.07, and 1.88, respectively. The aqueous solubility was found to be 2.4×10(-4) M having a saturated solution pH of 4.3-5.0 and a low intrinsic solubility of 1.6×10(-6) M. A mathematical model of the pH-solubility profile was derived from pH 2.2 to 8.0. An exponential decrease in solubility was observed with increasing pH. The excess solid phase in equilibrium with the solution in aqueous buffers was determined to be the free-base form of the drug. A significant increase in solubility was observed with all the cosolvents studied, in both unbuffered and buffered systems. Mean log P of the salt and the free base were estimated to be 2.18 and 3.70, respectively. The compound had poor stability at pH 7.0 at 37 °C, with a t (90) of 3.58 days. Thermal analysis of the drug using DSC and TGA revealed that the drug is present as a semi-crystalline powder, which transformed into the amorphous state after melting. The drug was also found to sublime at higher temperatures. Determination of physicochemical properties of NPC 1161C provided useful information for the development of a dosage form and preclinical evaluation.
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29
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Wenlock MC, Potter T, Barton P, Austin RP. A Method for Measuring the Lipophilicity of Compounds in Mixtures of 10. ACTA ACUST UNITED AC 2011; 16:348-55. [DOI: 10.1177/1087057110396372] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Lipophilicity is an important parameter for any potential drug candidate. Accurate and efficient lipophilicity measurements facilitate the development of high-quality predictive in silico models that support the design of future drugs. Lipophilicity estimates derived from the traditional 1-octanol/water shake flask techniques have been the most widely employed and are therefore the best understood. This technique can be considered to give a good measure of a compound’s lipophilicity, albeit slower and more labor intensive to run compared with some other methodologies. Herein is described and validated an efficient 1-octanol/water shake flask technique that has sufficient capacity to be run as a primary screen within the drug discovery process. This is achieved by the simultaneous measurement of the distribution coefficients of mixtures of up to 10 compounds using high-performance liquid chromatography and tandem mass spectrometry. Concerns regarding ion pair partitioning that could result in erroneous results due to interactions between compounds within a mixture are discussed.
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Affiliation(s)
- Mark C. Wenlock
- Department of Chemistry, AstraZeneca R&D Charnwood, Loughborough, Leicestershire, UK
| | - Tim Potter
- Department of Chemistry, AstraZeneca R&D Charnwood, Loughborough, Leicestershire, UK
| | - Patrick Barton
- Department of Chemistry, AstraZeneca R&D Charnwood, Loughborough, Leicestershire, UK
| | - Rupert P. Austin
- Department of Chemistry, AstraZeneca R&D Charnwood, Loughborough, Leicestershire, UK
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30
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Kristensen JL, Püschl A, Jensen M, Risgaard R, Christoffersen CT, Bang-Andersen B, Balle T. Exploring the Neuroleptic Substituent in Octoclothepin: Potential Ligands for Positron Emission Tomography with Subnanomolar Affinity for α1-Adrenoceptors. J Med Chem 2010; 53:7021-34. [DOI: 10.1021/jm100652h] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jesper L. Kristensen
- Department of Medicinal Chemistry, The Faculty of Pharmaceutical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | | | - Martin Jensen
- Department of Medicinal Chemistry, The Faculty of Pharmaceutical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
- Medicinal Chemistry Research
| | - Rune Risgaard
- Department of Medicinal Chemistry, The Faculty of Pharmaceutical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
- Medicinal Chemistry Research
| | | | | | - Thomas Balle
- Department of Medicinal Chemistry, The Faculty of Pharmaceutical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
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31
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Computer programs for calculating pKa: A comparative study for 3-[3-(2-nitrophenyl)prop-2-enoyl]-2h-1-benzopyran-2-one. JOURNAL OF THE SERBIAN CHEMICAL SOCIETY 2010. [DOI: 10.2298/jsc1002243s] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Coumarin-based compounds containing a chalcone moiety exhibit antimicrobial activity. These substances are potential drugs and it is important to determine their pKa values. However, they are almost insoluble in water. The dissociation constant was experimentally determined by potentiometric titration for 3-[3-(2-nitrophenyl)prop-2-enoyl]-2H-1-benzopyran-2-one because this compound shows good activity and solubility. A number of different computer programs for the calculation of the dissociation constant of chemical compounds have been developed. The pKa value of the target compound was calculated using three different computer programs, i.e., the ACD/pKa, CSpKaPredictor and ADME/ToxWEB programs, which are based on different theoretical approaches. The analysis demonstrated good agreement between the experimentally observed pKa value of 3-[3-(2-nitrophenyl)prop-2-enoyl]-2H-1-benzopyran- 2-one and the value calculated using the computer program CSpKa.
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32
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Shoghi E, Romero L, Reta M, Ràfols C, Bosch E. Enthalpies and constants of dissociation of several neutral and cationic acids in aqueous and methanol/water solutions at various temperatures. J Pharm Biomed Anal 2009; 49:923-30. [DOI: 10.1016/j.jpba.2009.01.037] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2008] [Accepted: 01/25/2009] [Indexed: 11/29/2022]
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33
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Nishimura I, Hirano A, Yamashita T, Fukami T. Improvement of the high-speed logD assay using an injection marker for the water plug aspiration/injection method. J Chromatogr A 2009; 1216:2984-8. [DOI: 10.1016/j.chroma.2009.02.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2008] [Revised: 01/26/2009] [Accepted: 02/03/2009] [Indexed: 11/16/2022]
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34
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Casoni D, Kot-Wasik A, Namieśnik J, Sârbu C. Lipophilicity data for some preservatives estimated by reversed-phase liquid chromatography and different computation methods. J Chromatogr A 2009; 1216:2456-65. [DOI: 10.1016/j.chroma.2009.01.029] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2008] [Revised: 11/29/2008] [Accepted: 01/12/2009] [Indexed: 11/30/2022]
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35
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Ibatullin FM, Baumann MJ, Greffe L, Brumer H. Kinetic Analyses of Retaining endo-(Xylo)glucanases from Plant and Microbial Sources Using New Chromogenic Xylogluco-Oligosaccharide Aryl Glycosides. Biochemistry 2008; 47:7762-9. [DOI: 10.1021/bi8009168] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Farid M. Ibatullin
- School of Biotechnology, Royal Institute of Technology (KTH), AlbaNova University Centre, SE-106 91 Stockholm, Sweden, and Petersburg Nuclear Physics Institute, Molecular and Radiation Biology Division, Russian Academy of Science, Gatchina, St. Petersburg 188300, Russia
| | - Martin J. Baumann
- School of Biotechnology, Royal Institute of Technology (KTH), AlbaNova University Centre, SE-106 91 Stockholm, Sweden, and Petersburg Nuclear Physics Institute, Molecular and Radiation Biology Division, Russian Academy of Science, Gatchina, St. Petersburg 188300, Russia
| | - Lionel Greffe
- School of Biotechnology, Royal Institute of Technology (KTH), AlbaNova University Centre, SE-106 91 Stockholm, Sweden, and Petersburg Nuclear Physics Institute, Molecular and Radiation Biology Division, Russian Academy of Science, Gatchina, St. Petersburg 188300, Russia
| | - Harry Brumer
- School of Biotechnology, Royal Institute of Technology (KTH), AlbaNova University Centre, SE-106 91 Stockholm, Sweden, and Petersburg Nuclear Physics Institute, Molecular and Radiation Biology Division, Russian Academy of Science, Gatchina, St. Petersburg 188300, Russia
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36
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Polettini A, Gottardo R, Pascali JP, Tagliaro F. Implementation and Performance Evaluation of a Database of Chemical Formulas for the Screening of Pharmaco/Toxicologically Relevant Compounds in Biological Samples Using Electrospray Ionization-Time-of-Flight Mass Spectrometry. Anal Chem 2008; 80:3050-7. [DOI: 10.1021/ac800071n] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Aldo Polettini
- Department of Medicine and Public Health, Unit of Forensic Medicine, University of Verona, Verona, Italy
| | - Rossella Gottardo
- Department of Medicine and Public Health, Unit of Forensic Medicine, University of Verona, Verona, Italy
| | - Jennifer Paola Pascali
- Department of Medicine and Public Health, Unit of Forensic Medicine, University of Verona, Verona, Italy
| | - Franco Tagliaro
- Department of Medicine and Public Health, Unit of Forensic Medicine, University of Verona, Verona, Italy
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37
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Lombardo F, Faller B, Shalaeva M, Tetko I, Tilton S. The Good, the Bad and the Ugly of Distribution Coefficients: Current Status, Views and Outlook. ACTA ACUST UNITED AC 2008. [DOI: 10.1002/9783527621286.ch16] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Sibley SD, Pedersen JA. Interaction of the macrolide antimicrobial clarithromycin with dissolved humic acid. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2008; 42:422-428. [PMID: 18284141 DOI: 10.1021/es071467d] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
The association of the cationic macrolide antimicrobial clarithromycin (CLA) with dissolved Elliot soil humic acid (ESHA) was investigated as a function of solution chemistry. CLA-ESHA association was strongly pH-dependent, reaching a maximum near pH 6.5, and was modeled successfully using FITEQL as a 1:1 complexation reaction between CLA+ and discreet deprotonated acidic functional groups with pKa values of 4 and 6. Approximate order of magnitude increases in ionic strength produced approximately 10-fold decreases in CLA+ -ESHA association. Coefficients for CLA+ -ESHA association were significantly smaller in the presence of K+ vs Na+. Sorption data were well-fit by the Freundlich model; the Freundlich exponent was <1, suggesting CLA+ interacted with sites having a range of binding energies. Sorption appeared largely reversible; little sorption-desorption hysteresis was observed. The affinities of erythromycin and CLA+ for ESHA association sites were indistinguishable, suggesting interaction with specific sorption sites. Comparison of experimentally determined CLA-ESHA association coefficients with those predicted from single-parameter linear free energy relationships based on log Kow suggested limited contribution of hydrophobic interactions to CLA-ESHA association at environmentally relevant pH values. CLA-ESHA association constants were similar in magnitude (10(3.9)-10(4.6) to those of many nonpolar organic contaminants, and macroscopic binding data were consistent with cation exchange dominating CLA+ -ESHA association.
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Affiliation(s)
- Samuel D Sibley
- Environmental Chemistry and Technology Program, and Department of Soil Science, University of Wisconsin, Madison, Wisconsin 53706, USA
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40
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Demare S, Slater B, Lacombe G, Breuzin D, Dini C. Accurate automated logPo/w measurement by gradient-flow liquid–liquid partition chromatography. J Chromatogr A 2007; 1175:16-23. [DOI: 10.1016/j.chroma.2007.09.093] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2007] [Revised: 09/22/2007] [Accepted: 09/27/2007] [Indexed: 10/22/2022]
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41
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Kornhuber J, Tripal P, Reichel M, Terfloth L, Bleich S, Wiltfang J, Gulbins E. Identification of New Functional Inhibitors of Acid Sphingomyelinase Using a Structure−Property−Activity Relation Model. J Med Chem 2007; 51:219-37. [DOI: 10.1021/jm070524a] [Citation(s) in RCA: 153] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Johannes Kornhuber
- Department of Psychiatry and Psychotherapy, University of Erlangen, Germany, Molecular Networks, Erlangen, Germany, and Department of Molecular Biology, University of Duisburg—Essen, Germany
| | - Philipp Tripal
- Department of Psychiatry and Psychotherapy, University of Erlangen, Germany, Molecular Networks, Erlangen, Germany, and Department of Molecular Biology, University of Duisburg—Essen, Germany
| | - Martin Reichel
- Department of Psychiatry and Psychotherapy, University of Erlangen, Germany, Molecular Networks, Erlangen, Germany, and Department of Molecular Biology, University of Duisburg—Essen, Germany
| | - Lothar Terfloth
- Department of Psychiatry and Psychotherapy, University of Erlangen, Germany, Molecular Networks, Erlangen, Germany, and Department of Molecular Biology, University of Duisburg—Essen, Germany
| | - Stefan Bleich
- Department of Psychiatry and Psychotherapy, University of Erlangen, Germany, Molecular Networks, Erlangen, Germany, and Department of Molecular Biology, University of Duisburg—Essen, Germany
| | - Jens Wiltfang
- Department of Psychiatry and Psychotherapy, University of Erlangen, Germany, Molecular Networks, Erlangen, Germany, and Department of Molecular Biology, University of Duisburg—Essen, Germany
| | - Erich Gulbins
- Department of Psychiatry and Psychotherapy, University of Erlangen, Germany, Molecular Networks, Erlangen, Germany, and Department of Molecular Biology, University of Duisburg—Essen, Germany
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42
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Giaginis C, Tsantili‐Kakoulidou A. Current State of the Art in HPLC Methodology for Lipophilicity Assessment of Basic Drugs. A Review. J LIQ CHROMATOGR R T 2007. [DOI: 10.1080/10826070701665626] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Costas Giaginis
- a Department of Pharmaceutical Chemistry , School of Pharmacy, University of Athens , Athens, Greece
| | - Anna Tsantili‐Kakoulidou
- a Department of Pharmaceutical Chemistry , School of Pharmacy, University of Athens , Athens, Greece
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43
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David V, Albu F, Medvedovici A. Structure–Retention Correlation of Some Oxicam Drugs in Reversed‐Phase Liquid Chromatography. J LIQ CHROMATOGR R T 2007. [DOI: 10.1081/jlc-120030172] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Victor David
- a Department of Analytical Chemistry, Faculty of Chemistry , University of Bucharest , Sos. Panduri, No. 90, Bucharest‐5 , Romania
| | - Florin Albu
- b LaborMed Pharma S.A. , Splaiul Independentei , Bucharest , Romania
| | - Andrei Medvedovici
- a Department of Analytical Chemistry, Faculty of Chemistry , University of Bucharest , Sos. Panduri, No. 90, Bucharest‐5 , Romania
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Meloun M, Bordovská S. Benchmarking and validating algorithms that estimate pK a values of drugs based on their molecular structures. Anal Bioanal Chem 2007; 389:1267-81. [PMID: 17676314 DOI: 10.1007/s00216-007-1502-x] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2007] [Revised: 06/04/2007] [Accepted: 07/11/2007] [Indexed: 10/23/2022]
Abstract
The REGDIA regression diagnostics algorithm in S-Plus is introduced in order to examine the accuracy of pK(a) predictions made with four updated programs: PALLAS, MARVIN, ACD/pKa and SPARC. This report reviews the current status of computational tools for predicting the pK(a) values of organic drug-like compounds. Outlier predicted pK(a) values correspond to molecules that are poorly characterized by the pK(a) prediction program concerned. The statistical detection of outliers can fail because of masking and swamping effects. The Williams graph was selected to give the most reliable detection of outliers. Six statistical characteristics (F(exp), R(2), R(P)(2), MEP, AIC, and s(e) in pK(a) units) of the results obtained when four selected pK(a) prediction algorithms were applied to three datasets were examined. The highest values of F(exp), R(2), R(P)(2), the lowest values of MEP and s(e), and the most negative AIC were found using the ACD/pK (a) algorithm for pK(a) prediction, so this algorithm achieves the best predictive power and the most accurate results. The proposed accuracy test performed by the REGDIA program can also be applied to test the accuracy of other predicted values, such as log P, log D, aqueous solubility or certain physicochemical properties of drug molecules.
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Affiliation(s)
- Milan Meloun
- Department of Analytical Chemistry, Faculty of Chemical Technology, Pardubice University, 532 10, Pardubice, Czech Republic.
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45
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Faller B, Ertl P. Computational approaches to determine drug solubility. Adv Drug Deliv Rev 2007; 59:533-45. [PMID: 17588703 DOI: 10.1016/j.addr.2007.05.005] [Citation(s) in RCA: 129] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2007] [Accepted: 05/10/2007] [Indexed: 11/20/2022]
Abstract
Water solubility is an important molecular property for successful drug development as it is a key factor governing drug access to biological membranes. There have been a number of review articles addressing computational models to predict water solubility with emphasis on the accuracy of the various prediction methods. This paper briefly reviews the available models and focuses on the value which can be extracted by comparing calculated and measured solubility, discusses the potential and limitations of the main computational approaches, and provides guidelines as to when to trust the computed value.
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Affiliation(s)
- Bernard Faller
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Basel, Switzerland.
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Warhurst DC, Craig JC, Adagu IS, Guy RK, Madrid PB, Fivelman QL. Activity of piperaquine and other 4-aminoquinoline antiplasmodial drugs against chloroquine-sensitive and resistant blood-stages of Plasmodium falciparum. Biochem Pharmacol 2007; 73:1910-26. [PMID: 17466277 DOI: 10.1016/j.bcp.2007.03.011] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2007] [Revised: 03/05/2007] [Accepted: 03/12/2007] [Indexed: 10/23/2022]
Abstract
Chloroquine (CQ), a 4-aminoquinoline, accumulates in acidic digestive vacuoles of the malaria parasite, preventing conversion of toxic haematin to beta-haematin. We examine how bis 4-aminoquinoline piperaquine (PQ) and its hydroxy-modification (OH-PQ) retain potency on chloroquine-resistant (CQ-R) Plasmodium falciparum. For CQ, PQ, OH-PQ and 4 and 5, representing halves of PQ, beta-haematin inhibitory activity (BHIA) was assayed, while potency was determined in CQ-sensitive (CQ-S) and CQ-R P. falciparum. From measured pK(a)s and the pH-modulated distribution of base between water and lipid (logD), the vacuolar accumulation ratio (VAR) of charged drug from plasma water (pH 7.4) into vacuolar water (pH 4.8) and lipid accumulation ratio (LAR) were calculated. All agents were active in BHIA. In CQ-S, PQ, OH-PQ and CQ were equally potent while 4 and 5 were 100 times less potent. CQ with two basic centres has a VAR of 143,482, while 4 and 5, with two basic centres of lower pK(a)s have VARs of 1287 and 1966. In contrast PQ and OH-PQ have four basic centres and achieve VARs of 104,378 and 19,874. This confirms the importance of VAR for potency against CQ-S parasites. Contrasting results were seen in CQ-R. 5, PQ and OH-PQ with LARs of 693; 973,492 and 398,118 (compared with 8.25 for CQ) showed similar potency in CQ-S and CQ-R. Importance of LAR for potency against CQ-R parasites probably reflects ability to block efflux by hydrophobic interaction with PfCRT but may relate to beta-haematin inhibition in vacuolar lipid.
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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, University of London, Keppel Street, London WC1E 7HT, UK.
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Wiczling P, Kawczak P, Nasal A, Kaliszan R. Simultaneous determination of pKa and lipophilicity by gradient RP HPLC. Anal Chem 2007; 78:239-49. [PMID: 16383333 DOI: 10.1021/ac0512103] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
High-performance methods of testing of drug candidates for properties of pharmacokinetics and pharmacodynamics importance, in particular lipophilicity and acidity, are necessary to overcome innovation stagnation in the pharmaceutical industry. Reversed-phase high-performance liquid chromatography (RP HPLC) might be a unique tool for the determination of both pKa and the apparent (pH-dependent) partition coefficient, applicable in high-throughput analysis of multicomponent mixtures, e.g., samples originating from automated synthesis. In this work, the pH/organic modifier gradient RP HPLC is presented as a means of simultaneous determination of an analyte's acidity and lipophilicity. The approach consists of retention measurements in a series of methanol gradient runs differing in pH range and duration of the gradient. Two different models of the influence of pH on retention in organic modifier gradient RP HPLC are compared regarding the quality of the simultaneously determined lipophilicity and dissociation constants. Advantages of the proposed approach over currently employed procedures are that it can be applied to compound mixtures, it requires only minute amounts of substances, and pKa values can be determined in the range 3-10 units and lipophilicity in the range 0-7 units. Verification of the reliability of the parameters determined by the new method was demonstrated on a series of 93 acidic and basic drug analytes.
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Affiliation(s)
- Paweł Wiczling
- Department of Biopharmaceutics and Pharmacodynamics, Medical University of Gdañsk, Gen. J. Hallera 107, 80-416 Gdañsk, Poland
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Dravid SM, Erreger K, Yuan H, Nicholson K, Le P, Lyuboslavsky P, Almonte A, Murray E, Mosely C, Barber J, French A, Balster R, Murray TF, Traynelis SF. Subunit-specific mechanisms and proton sensitivity of NMDA receptor channel block. J Physiol 2007; 581:107-28. [PMID: 17303642 PMCID: PMC2075223 DOI: 10.1113/jphysiol.2006.124958] [Citation(s) in RCA: 116] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
We have compared the potencies of structurally distinct channel blockers at recombinant NR1/NR2A, NR1/NR2B, NR1/NR2C and NR1/NR2D receptors. The IC50 values varied with stereochemistry and subunit composition, suggesting that it may be possible to design subunit-selective channel blockers. For dizocilpine (MK-801), the differential potency of MK-801 stereoisomers determined at recombinant NMDA receptors was confirmed at native receptors in vitro and in vivo. Since the proton sensor is tightly linked both structurally and functionally to channel gating, we examined whether blocking molecules that interact in the channel pore with the gating machinery can differentially sense protonation of the receptor. Blockers capable of remaining trapped in the pore during agonist unbinding showed the strongest dependence on extracellular pH, appearing more potent at acidic pH values that promote channel closure. Determination of pK(a) values for channel blockers suggests that the ionization of ketamine but not of other blockers can influence its pH-dependent potency. Kinetic modelling and single channel studies suggest that the pH-dependent block of NR1/NR2A by (-)MK-801 but not (+)MK-801 reflects an increase in the MK-801 association rate even though protons reduce channel open probability and thus MK-801 access to its binding site. Allosteric modulators that alter pH sensitivity alter the potency of MK-801, supporting the interpretation that the pH sensitivity of MK-801 binding reflects the changes at the proton sensor rather than a secondary effect of pH. These data suggest a tight coupling between the proton sensor and the ion channel gate as well as unique subunit-specific mechanisms of channel block.
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Affiliation(s)
- Shashank M Dravid
- Department of Pharmacology, Emory University School of Medicine, Rollins Research Centre, 1510 Clifton Road, Atlanta, GA 30322-3090, USA.
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49
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Shimoyama R, Ohkubo T, Sugawara K. CHARACTERISTICS OF INTERACTION BETWEEN BARBITURATE DERIVATIVES AND VARIOUS SORBENTS ON LIQUID CHROMATOGRAPHY AND DETERMINATION OF PHENOBARBITAL IN JAPANESEHUMAN BREAST MILK. J LIQ CHROMATOGR R T 2007. [DOI: 10.1081/jlc-100101475] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Ritsuko Shimoyama
- Department of Pharmacy, Hirosaki University Hospital , Hirosaki, 036-8563, Japan
| | - Tadashi Ohkubo
- Department of Pharmacy, Hirosaki University Hospital , Hirosaki, 036-8563, Japan
| | - Kazunobu Sugawara
- Department of Pharmacy, Hirosaki University Hospital , Hirosaki, 036-8563, Japan
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50
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Sköld C, Winiwarter S, Wernevik J, Bergström F, Engström L, Allen R, Box K, Comer J, Mole J, Hallberg A, Lennernäs H, Lundstedt T, Ungell AL, Karlén A. Presentation of a structurally diverse and commercially available drug data set for correlation and benchmarking studies. J Med Chem 2007; 49:6660-71. [PMID: 17154497 DOI: 10.1021/jm0506219] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A multivariate analysis of drugs on the Swedish market was the basis for the selection of a small, physicochemically diverse set of 24 drug compounds. Factors such as structural diversity, commercial availability, price, and a suitable analytical technique for quantification were considered in the selection. Lipophilicity, pKa, solubility, and permeability across human Caco-2 cell monolayers were measured for the compiled data set. The results show that, by use of a physicochemically diverse data set, experimental responses over a wide range were obtained. The paper also shows how experimental difficulties due to the diversity of the data set can be overcome. We anticipate that this data set can serve as a benchmark set for validation of new experimental techniques or in silico models. It can also be used as a diverse starting data set for the development of new computational models.
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Affiliation(s)
- Christian Sköld
- Division of Organic Pharmaceutical Chemistry, Department of Medicinal Chemistry, BMC, Uppsala University, Sweden
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