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Miao R, Liu D, Mao L, Chen X, Zhang L, Yuan Z, Shi S, Li H, Li S. GR-pKa: a message-passing neural network with retention mechanism for pKa prediction. Brief Bioinform 2024; 25:bbae408. [PMID: 39171986 PMCID: PMC11339865 DOI: 10.1093/bib/bbae408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 07/26/2024] [Accepted: 08/01/2024] [Indexed: 08/23/2024] Open
Abstract
During the drug discovery and design process, the acid-base dissociation constant (pKa) of a molecule is critically emphasized due to its crucial role in influencing the ADMET (absorption, distribution, metabolism, excretion, and toxicity) properties and biological activity. However, the experimental determination of pKa values is often laborious and complex. Moreover, existing prediction methods exhibit limitations in both the quantity and quality of the training data, as well as in their capacity to handle the complex structural and physicochemical properties of compounds, consequently impeding accuracy and generalization. Therefore, developing a method that can quickly and accurately predict molecular pKa values will to some extent help the structural modification of molecules, and thus assist the development process of new drugs. In this study, we developed a cutting-edge pKa prediction model named GR-pKa (Graph Retention pKa), leveraging a message-passing neural network and employing a multi-fidelity learning strategy to accurately predict molecular pKa values. The GR-pKa model incorporates five quantum mechanical properties related to molecular thermodynamics and dynamics as key features to characterize molecules. Notably, we originally introduced the novel retention mechanism into the message-passing phase, which significantly improves the model's ability to capture and update molecular information. Our GR-pKa model outperforms several state-of-the-art models in predicting macro-pKa values, achieving impressive results with a low mean absolute error of 0.490 and root mean square error of 0.588, and a high R2 of 0.937 on the SAMPL7 dataset.
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Affiliation(s)
- Runyu Miao
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, No. 130, Meilong Road, Xuhui District, Shanghai, 200237, China
| | - Danlin Liu
- Innovation Center for AI and Drug Discovery, School of Pharmacy, East China Normal University, No. 3663, Zhongshan North Road, Putuo District, Shanghai, 200062, China
- School of Computer Science and Technology, East China Normal University, No. 3663, Zhongshan North Road, Putuo District, Shanghai, 200062, China
| | - Liyun Mao
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, No. 130, Meilong Road, Xuhui District, Shanghai, 200237, China
| | - Xingyu Chen
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, No. 130, Meilong Road, Xuhui District, Shanghai, 200237, China
| | - Leihao Zhang
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, No. 130, Meilong Road, Xuhui District, Shanghai, 200237, China
| | - Zhen Yuan
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, No. 130, Meilong Road, Xuhui District, Shanghai, 200237, China
| | - Shanshan Shi
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, No. 130, Meilong Road, Xuhui District, Shanghai, 200237, China
| | - Honglin Li
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, No. 130, Meilong Road, Xuhui District, Shanghai, 200237, China
- Innovation Center for AI and Drug Discovery, School of Pharmacy, East China Normal University, No. 3663, Zhongshan North Road, Putuo District, Shanghai, 200062, China
- Lingang Laboratory, No. 319, Yueyang Road, Xuhui District, Shanghai, 200031, China
| | - Shiliang Li
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, No. 130, Meilong Road, Xuhui District, Shanghai, 200237, China
- Innovation Center for AI and Drug Discovery, School of Pharmacy, East China Normal University, No. 3663, Zhongshan North Road, Putuo District, Shanghai, 200062, China
- Department of Pain management, HuaDong Hospital affiliated to Fudan University, No. 221, West Yan'an Road, Jing'an District, Shanghai, 200040, China
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Davies J, Lyonnet JR, Carvalho B, Sahoo B, Day CS, Juliá-Hernández F, Duan Y, Álvaro Velasco-Rubio, Obst M, Norrby PO, Hopmann KH, Martin R. Kinetically-Controlled Ni-Catalyzed Direct Carboxylation of Unactivated Secondary Alkyl Bromides without Chain Walking. J Am Chem Soc 2024; 146:1753-1759. [PMID: 38193812 PMCID: PMC10824404 DOI: 10.1021/jacs.3c11205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 12/19/2023] [Accepted: 12/20/2023] [Indexed: 01/10/2024]
Abstract
Herein, we report the direct carboxylation of unactivated secondary alkyl bromides enabled by the merger of photoredox and nickel catalysis, a previously inaccessible endeavor in the carboxylation arena. Site-selectivity is dictated by a kinetically controlled insertion of CO2 at the initial C(sp3)-Br site by the rapid formation of Ni(I)-alkyl species, thus avoiding undesired β-hydride elimination and chain-walking processes. Preliminary mechanistic experiments reveal the subtleties of stereoelectronic effects for guiding the reactivity and site-selectivity.
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Affiliation(s)
- Jacob Davies
- Institute
of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology, 43007 Tarragona, Spain
| | - Julien R. Lyonnet
- Institute
of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology, 43007 Tarragona, Spain
- Universitat
Rovira i Virgili, Departament de Química
Orgànica, 43007 Tarragona, Spain
| | - Bjørn Carvalho
- Department
of Chemistry, UiT The Arctic University
of Norway, N-9307 Tromsø, Norway
| | - Basudev Sahoo
- Institute
of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology, 43007 Tarragona, Spain
| | - Craig S. Day
- Institute
of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology, 43007 Tarragona, Spain
- Universitat
Rovira i Virgili, Departament de Química
Orgànica, 43007 Tarragona, Spain
| | - Francisco Juliá-Hernández
- Institute
of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology, 43007 Tarragona, Spain
| | - Yaya Duan
- Institute
of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology, 43007 Tarragona, Spain
| | - Álvaro Velasco-Rubio
- Institute
of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology, 43007 Tarragona, Spain
| | - Marc Obst
- Department
of Chemistry, UiT The Arctic University
of Norway, N-9307 Tromsø, Norway
| | - Per-Ola Norrby
- Data
Science & Modelling, Pharmaceutical Sciences, R&D, AstraZeneca Gothenburg, SE-431 83 Mölndal, Sweden
| | - Kathrin H. Hopmann
- Department
of Chemistry, UiT The Arctic University
of Norway, N-9307 Tromsø, Norway
| | - Ruben Martin
- Institute
of Chemical Research of Catalonia (ICIQ), The Barcelona Institute of Science and Technology, 43007 Tarragona, Spain
- ICREA, 08010 Barcelona, Spain
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3
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Popović-Nikolić MR, Nikolić KM, Popović GV. Protolytic equilibria of ACE inhibitors in micellar solution of nonionic surfactant Brij 35. MONATSHEFTE FUR CHEMIE 2023; 154:615-624. [PMID: 37193115 PMCID: PMC10111327 DOI: 10.1007/s00706-023-03059-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 03/21/2023] [Indexed: 05/18/2023]
Abstract
The acid-base equilibria of six ACE inhibitors (ACEIs), captopril, cilazapril, enalapril, lisinopril, quinapril, and ramipril, were investigated in the presence of micelles of nonionic surfactant Brij 35. The pKa values were potentiometrically determined at 25 °C and at a constant ionic strength (0.1 M NaCl). The obtained potentiometric data were evaluated in the computer program Hyperquad. On the basis of the shift in the pKa values (ΔpKa) determined in micellar media in relation to the pKa values previously determined in "pure" water, the effect of Brij 35 micelles on ACEIs ionization was estimated. The presence of nonionic Brij 35 micelles caused a shift in the pKa values of all ionizable groups of the investigated ACEIs (ΔpKa from - 3.44 to + 1.9) while shifting the protolytic equilibria of both acidic and basic groups toward the molecular form. The Brij 35 micelles expressed the most pronounced effect on the ionization of captopril among the investigated ACEIs and stronger effect on the ionization of amino than on the ionization of carboxyl groups. The obtained results suggest that ionizable functional groups of ACEIs are involved in interactions with palisade layer of nonionic Brij 35 micelles, which potentially can be considered in physiological conditions. Distribution diagrams of the investigated ACEIs equilibrium forms as a function of pH indicate that the change in distribution is most strongly expressed in pH range 4-8, which includes biopharmaceutically important pH values. Graphical abstract
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Affiliation(s)
- Marija R. Popović-Nikolić
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Belgrade, Vojvode Stepe 450, 11000 Belgrade, Serbia
| | - Katarina M. Nikolić
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Belgrade, Vojvode Stepe 450, 11000 Belgrade, Serbia
| | - Gordana V. Popović
- Department of General and Inorganic Chemistry, Faculty of Pharmacy, University of Belgrade, Vojvode Stepe 450, 11000 Belgrade, Serbia
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4
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Vincze A, Dékány G, Bicsak R, Formanek A, Moreau Y, Koplányi G, Takács G, Katona G, Balogh-Weiser D, Arany Á, Balogh GT. Natural Lipid Extracts as an Artificial Membrane for Drug Permeability Assay: In Vitro and In Silico Characterization. Pharmaceutics 2023; 15:pharmaceutics15030899. [PMID: 36986760 PMCID: PMC10053807 DOI: 10.3390/pharmaceutics15030899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/04/2023] [Accepted: 03/06/2023] [Indexed: 03/12/2023] Open
Abstract
In vitro non-cellular permeability models such as the parallel artificial membrane permeability assay (PAMPA) are widely applied tools for early-phase drug candidate screening. In addition to the commonly used porcine brain polar lipid extract for modeling the blood–brain barrier’s permeability, the total and polar fractions of bovine heart and liver lipid extracts were investigated in the PAMPA model by measuring the permeability of 32 diverse drugs. The zeta potential of the lipid extracts and the net charge of their glycerophospholipid components were also determined. Physicochemical parameters of the 32 compounds were calculated using three independent forms of software (Marvin Sketch, RDKit, and ACD/Percepta). The relationship between the lipid-specific permeabilities and the physicochemical descriptors of the compounds was investigated using linear correlation, Spearman correlation, and PCA analysis. While the results showed only subtle differences between total and polar lipids, permeability through liver lipids highly differed from that of the heart or brain lipid-based models. Correlations between the in silico descriptors (e.g., number of amide bonds, heteroatoms, and aromatic heterocycles, accessible surface area, and H-bond acceptor–donor balance) of drug molecules and permeability values were also found, which provides support for understanding tissue-specific permeability.
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Affiliation(s)
- Anna Vincze
- Department of Chemical and Environmental Process Engineering, Budapest University of Technology and Economics, Műegyetem rkp. 3, H-1111 Budapest, Hungary
| | - Gergely Dékány
- Department of Chemical and Environmental Process Engineering, Budapest University of Technology and Economics, Műegyetem rkp. 3, H-1111 Budapest, Hungary
| | - Richárd Bicsak
- Department of Chemical and Environmental Process Engineering, Budapest University of Technology and Economics, Műegyetem rkp. 3, H-1111 Budapest, Hungary
| | - András Formanek
- ESAT-STADIUS KU LEUVEN, 3001 Leuven, Belgium
- Department of Measurement and Information Systems, Faculty of Electrical Engineering and Informatics, Budapest University of Technology and Economics, Műegyetem rkp. 3, H-1111 Budapest, Hungary
| | - Yves Moreau
- ESAT-STADIUS KU LEUVEN, 3001 Leuven, Belgium
| | - Gábor Koplányi
- Department of Organic Chemistry and Technology, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, Műegyetem rkp. 3, H-1111 Budapest, Hungary
| | - Gergely Takács
- Department of Chemical and Environmental Process Engineering, Budapest University of Technology and Economics, Műegyetem rkp. 3, H-1111 Budapest, Hungary
- Mcule.com Kft, Bartók Béla út 105-113, H-1115 Budapest, Hungary
| | - Gábor Katona
- Institute of Pharmaceutical Technology and Regulatory Affairs, Faculty of Pharmacy, University of Szeged, Eötvös Str. 6, H-6720 Szeged, Hungary
| | - Diána Balogh-Weiser
- Department of Organic Chemistry and Technology, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, Műegyetem rkp. 3, H-1111 Budapest, Hungary
- Department of Physical Chemistry and Materials Science, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, Műegyetem rkp. 3, H-1111 Budapest, Hungary
| | - Ádám Arany
- ESAT-STADIUS KU LEUVEN, 3001 Leuven, Belgium
| | - György T. Balogh
- Department of Chemical and Environmental Process Engineering, Budapest University of Technology and Economics, Műegyetem rkp. 3, H-1111 Budapest, Hungary
- Institute of Pharmacodynamics and Biopharmacy, Faculty of Pharmacy, University of Szeged, Eötvös u. 6, H-6720 Szeged, Hungary
- Correspondence:
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A New Unnatural Amino Acid Derived from the Modification of 4′-(p-tolyl)-2,2′:6′,2″-terpyridine and Its Mixed-Ligand Complexes with Ruthenium: Synthesis, Characterization, and Photophysical Properties. CHEMISTRY 2023. [DOI: 10.3390/chemistry5010012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The modification of the methyl group of 4′-(p-tolyl)-2,2′:6′,2″-terpyridine produced the novel unnatural amino acid 3-(4-([2,2′:6′,2″-terpyridin]-4′-yl)phenyl)-2-aminopropanoic acid (phet). Mononuclear heteroleptic ruthenium complexes of the general formulae [Ru(L1)(L2)](PF6)2 (L1 = 2-acetylamino-2-(4-[2,2′:6′,2″]terpyridine-4′-yl-benzyl)-malonic acid diethyl ester, (phem), 3-(4-([2,2′:6′,2″-terpyridin]-4′-yl)phenyl)-2-aminopropanoic acid, (phet), and L2 = 2,2′:6′,2″-terpyridine (tpy), 4′-phenyl-2,2′:6′,2″-terpyridine (ptpy), 4′-(p-tolyl)-2,2′:6′,2″-terpyridine (mptpy)), as well as the homoleptic [Ru(phem)2](PF6)2 and [Ru(phet)2](PF6)2, were synthesized and characterized by means of NMR spectroscopic techniques, elemental analysis, and high-resolution mass spectrometry. The photophysical properties of the synthesized complexes were also studied.
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6
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Agarwal P, Huckle J, Newman J, Reid DL. Trends in small molecule drug properties: A developability molecule assessment perspective. Drug Discov Today 2022; 27:103366. [PMID: 36122862 DOI: 10.1016/j.drudis.2022.103366] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 08/10/2022] [Accepted: 09/13/2022] [Indexed: 11/18/2022]
Abstract
Developability molecule assessment is a key interfacial capability across the biopharmaceutical industry, screening and staging molecules discovered by medicinal chemists for successful chemistry manufacturing controls (CMC) development and launch. The breadth of responsibility and expertise such teams possess puts them in a unique position to understand the impact of the physicochemical properties of a drug during its initial discovery and subsequent development. However, most of the publications describing trends in physicochemical properties are written from a medicinal chemistry perspective with the aim to identify molecules with better ADMET profiles that are either lead-like or drug-like, failing to describe the impact these properties have on CMC development. To systematically uncover knowledge obtained from recent trends in physicochemical properties and the corresponding impact on CMC development, a comprehensive analysis was conducted on molecules in the drug repurposing hub dataset. The only physicochemical property that seems to have been preserved in FDA-approved oral molecules over the decades (1900-2020) is a constant H-bond donor count, highlighting the importance this property has on cell permeability and lattice energy. Pharmaceutical attrition analysis suggests that partition-distribution coefficient, H-bond acceptors, polar surface area and the fraction of sp3 carbons are properties that are associated with compound attrition. Looking at pharmaceutical attrition asynchronously with the temporal analysis of FDA-approved oral molecules highlights the opposing trends, risks and diminishing effects some of these physiochemical properties (cLogP, cLogD and Fsp3) have on describing compound attrition during the past decade. Trellising the dataset by target class suggests that certain formulation and drug delivery strategies can be anticipated or put into place based on target class of a molecule. For example, molecules binding to nuclear hormone receptors are amenable to lipid-based drug delivery systems with proven commercial success. Although the poor solubility of kinase inhibitors is a combination of hydrophobicity (due to aromaticity) required to bind to its target and high lattice energy (melting point), they are a challenging target class to formulate. The influence of drug targets on physicochemical properties and the temporal nature of these properties is highlighted when comparing molecules in the drug repurposing dataset to those developed at Amgen. An improved understanding of the impact of molecular properties on performance attributes can accelerate decisions and facilitate risk assessments during candidate selection and development.
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Affiliation(s)
- Prashant Agarwal
- Drug Product Technologies, Process Development, Amgen, One Amgen Center Drive, Thousand Oaks, CA 91320, USA.
| | - James Huckle
- Drug Product Technologies, Process Development, Amgen, One Amgen Center Drive, Thousand Oaks, CA 91320, USA
| | - Jake Newman
- Drug Product Technologies, Process Development, Amgen, One Amgen Center Drive, Thousand Oaks, CA 91320, USA
| | - Darren L Reid
- Drug Product Technologies, Process Development, Amgen, 360 Binney St, Cambridge, MA 02142, USA.
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7
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Meanwell NA, Loiseleur O. Applications of Isosteres of Piperazine in the Design of Biologically Active Compounds: Part 2. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:10972-11004. [PMID: 35675052 DOI: 10.1021/acs.jafc.2c00729] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Applications of piperazine and homopiperazine in drug design are well-established, and these heterocycles have found use as both scaffolding and terminal elements and also as a means of introducing a water-solubilizing element into a molecule. In the accompanying review (10.1021/acs.jafc.2c00726), we summarized applications of piperazine and homopiperazine and their fused ring homologues in bioactive compound design along with illustrations of the use of 4-substituted piperidines and a sulfoximine-based mimetic. In this review, we discuss applications of pyrrolidine- and fused-pyrrolidine-based mimetics of piperazine and homopiperazine and illustrate derivatives of azetidine that include stretched and spirocyclic motifs, along with applications of a series of diaminocycloalkanes.
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Affiliation(s)
- Nicholas A Meanwell
- Small Molecule Drug Discovery, Bristol Myers Squibb Research and Early Development, Post Office Box 4000, Princeton, New Jersey 08543, United States
| | - Olivier Loiseleur
- Syngenta Crop Protection Research, Schaffhauserstrasse, CH-4332 Stein, Switzerland
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8
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Xu C, Li X, Bai L. Direct Aerobic α-Hydroxylation of Arylacetates for the Synthesis of Mandelates. J Org Chem 2022; 87:4298-4304. [PMID: 35245055 DOI: 10.1021/acs.joc.1c03149] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Aerobic α-hydroxylation of α-methylene esters has proven challenging due to overoxidation and hydrolysis of the materials. In this article, KOtBu-promoted TBAB-catalyzed α-hydroxylation of α-methylene aryl esters using O2 as the oxygen source has been developed. Both low reaction temperature and catalyst TBAB are keys to success. This reaction provides an environmentally friendly and low-cost approach to mandelates, which are valuable building blocks and widely present in pharmaceuticals.
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Affiliation(s)
- Changming Xu
- School of Chemistry and Chemical Engineering, Lanzhou Jiaotong University, Lanzhou 730070, China
| | - Xiangfan Li
- School of Chemistry and Chemical Engineering, Lanzhou Jiaotong University, Lanzhou 730070, China
| | - Lei Bai
- College of Chemistry and Chemical Engineering, Northwest Normal University, Lanzhou 730070, China
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9
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Muthuraja P, Usman R, Sajeev R, Gopinath P. Controlled meta-Selective C-H Mono- and Di-Olefination of Mandelic Acid Derivatives. Org Lett 2021; 23:6014-6018. [PMID: 34279109 DOI: 10.1021/acs.orglett.1c02080] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Mandelic acids represent a key structural motif present in many drug molecules. Herein, we report the controlled meta-selective mono- and diolefination of mandelic acids by the careful design of the substrate and oxidant. Furthermore, free meta-functionalized mandelic acid was generated by selectively removing the template under mild basic conditions. The synthesis of functionalized homatropine and cyclandelate drug derivatives was demonstrated. Kinetic isotope effects revealed C-H activation as the rate-limiting step.
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Affiliation(s)
- Perumal Muthuraja
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati 517507, India
| | - Rahamdil Usman
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati 517507, India
| | - Revathy Sajeev
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati 517507, India
| | - Purushothaman Gopinath
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati 517507, India
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10
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Santibáñez-Morán MG, Medina-Franco JL. The Acid/Base Characterization of Molecules with Epigenetic Activity. ChemMedChem 2021; 16:1744-1753. [PMID: 33594823 DOI: 10.1002/cmdc.202001009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 02/08/2021] [Indexed: 12/12/2022]
Abstract
The acidic and basic functional groups in a molecule strongly influence its physicochemical properties, affinity for a macromolecule, pharmacokinetics, and toxicity. For instance, basicity has been correlated with molecular promiscuity, hERG blockade, and phospholipidosis. Nonetheless, no systematic characterization of the acid/base profile of epigenomic databases has been reported. This study describes an analysis of the acidic ionization constant distribution of a library of 7820 compounds with reported activity against epigenetic targets. Furthermore, the epigenomics database's acid/base profile was compared to the reference libraries of food chemicals, natural products, and approved drugs. It was found that the acid/base profile of histone lysine demethylase ligands is more similar to previously approved drugs, and histone acetyltransferase ligands have acidic and basic functional groups largely found in food chemicals and natural products; this support the potential of these libraries for finding new epigenetic inhibitors.
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Affiliation(s)
- Marisa G Santibáñez-Morán
- DIFACQUIM Research Group, School of Chemistry, Universidad Nacional Autónoma de México, Avenida Universidad 3000, Mexico City, 04510, Mexico.,School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - José L Medina-Franco
- DIFACQUIM Research Group, School of Chemistry, Universidad Nacional Autónoma de México, Avenida Universidad 3000, Mexico City, 04510, Mexico
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11
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Veale CGL. Into the Fray! A Beginner's Guide to Medicinal Chemistry. ChemMedChem 2021; 16:1199-1225. [PMID: 33591595 DOI: 10.1002/cmdc.202000929] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Indexed: 12/31/2022]
Abstract
Modern medicinal chemistry is a complex, multidimensional discipline that operates at the interface of the chemical and biological sciences. The medicinal chemistry contribution to drug discovery is typically described in the context of the well-recited linear progression of the drug discovery pipeline. However, compound optimization is idiosyncratic to each project, and clear definitions of hit and lead molecules and the subsequent progress along the pipeline becomes easily blurred. In addition, this description lacks insight into the entangled relationship between chemical and pharmacological properties, and thus provides limited guidance on how innovative medicinal chemistry strategies can be applied to solve optimization problems, regardless of the stage in the pipeline. Through discussion and illustrative examples, this article seeks to provide insights into the finesse of medicinal chemistry and the subtlety of balancing chemical properties pharmacology. In so doing, it aims to serve as an accessible and simple-to-digest guide for anyone who wishes to learn about the underlying principles of medicinal chemistry, in a context that has been decoupled from the pipeline description.
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Affiliation(s)
- Clinton G L Veale
- School of Chemistry and Physics, Pietermaritzburg Campus, University of KwaZulu-Natal, Private Bag X01, Pietermaritzburg, Scottsville, 3209, South Africa
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12
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Işık M, Rustenburg AS, Rizzi A, Gunner MR, Mobley DL, Chodera JD. Overview of the SAMPL6 pK a challenge: evaluating small molecule microscopic and macroscopic pK a predictions. J Comput Aided Mol Des 2021; 35:131-166. [PMID: 33394238 PMCID: PMC7904668 DOI: 10.1007/s10822-020-00362-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 11/17/2020] [Indexed: 01/01/2023]
Abstract
The prediction of acid dissociation constants (pKa) is a prerequisite for predicting many other properties of a small molecule, such as its protein-ligand binding affinity, distribution coefficient (log D), membrane permeability, and solubility. The prediction of each of these properties requires knowledge of the relevant protonation states and solution free energy penalties of each state. The SAMPL6 pKa Challenge was the first time that a separate challenge was conducted for evaluating pKa predictions as part of the Statistical Assessment of Modeling of Proteins and Ligands (SAMPL) exercises. This challenge was motivated by significant inaccuracies observed in prior physical property prediction challenges, such as the SAMPL5 log D Challenge, caused by protonation state and pKa prediction issues. The goal of the pKa challenge was to assess the performance of contemporary pKa prediction methods for drug-like molecules. The challenge set was composed of 24 small molecules that resembled fragments of kinase inhibitors, a number of which were multiprotic. Eleven research groups contributed blind predictions for a total of 37 pKa distinct prediction methods. In addition to blinded submissions, four widely used pKa prediction methods were included in the analysis as reference methods. Collecting both microscopic and macroscopic pKa predictions allowed in-depth evaluation of pKa prediction performance. This article highlights deficiencies of typical pKa prediction evaluation approaches when the distinction between microscopic and macroscopic pKas is ignored; in particular, we suggest more stringent evaluation criteria for microscopic and macroscopic pKa predictions guided by the available experimental data. Top-performing submissions for macroscopic pKa predictions achieved RMSE of 0.7-1.0 pKa units and included both quantum chemical and empirical approaches, where the total number of extra or missing macroscopic pKas predicted by these submissions were fewer than 8 for 24 molecules. A large number of submissions had RMSE spanning 1-3 pKa units. Molecules with sulfur-containing heterocycles or iodo and bromo groups were less accurately predicted on average considering all methods evaluated. For a subset of molecules, we utilized experimentally-determined microstates based on NMR to evaluate the dominant tautomer predictions for each macroscopic state. Prediction of dominant tautomers was a major source of error for microscopic pKa predictions, especially errors in charged tautomers. The degree of inaccuracy in pKa predictions observed in this challenge is detrimental to the protein-ligand binding affinity predictions due to errors in dominant protonation state predictions and the calculation of free energy corrections for multiple protonation states. Underestimation of ligand pKa by 1 unit can lead to errors in binding free energy errors up to 1.2 kcal/mol. The SAMPL6 pKa Challenge demonstrated the need for improving pKa prediction methods for drug-like molecules, especially for challenging moieties and multiprotic molecules.
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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.
| | - Ariën S Rustenburg
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
- Graduate Program in Physiology, Biophysics, and Systems Biology, Weill Cornell Medical College, New York, NY, 10065, USA
| | - Andrea Rizzi
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
- Tri-Institutional PhD Program in Computational Biology and Medicine, Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, NY, 10065, USA
| | - M R Gunner
- Department of Physics, City College of New York, New York, NY, 10031, USA
| | - David L Mobley
- Department of Pharmaceutical Sciences and Department of Chemistry, University of California, Irvine, Irvine, CA, 92697, 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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13
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Elezović A, Marić A, Biščević A, Hadžiabdić J, Škrbo S, Špirtović-Halilović S, Rahić O, Vranić E, Elezović A. In vitro pH dependent passive transport of ketoprofen and metformin. ADMET AND DMPK 2020; 9:57-68. [PMID: 35299877 PMCID: PMC8923306 DOI: 10.5599/admet.916] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 12/02/2020] [Indexed: 11/18/2022] Open
Abstract
The kinetics of passive transport of ketoprofen and metformin, as model substances for high and low permeability, respectively, across the artificial membrane under the influence of the pH of donor solution was investigated. There was an upward trend in the apparent permeation coefficient (P app) of ketoprofen with the decrease in pH to a value close to pKa. At the pH value below pKa the permeation coefficient had lower value, due to the higher retention of ketoprofen in the artificial membrane. Metformin is a low permeable compound, and the highest permeation values were recorded at pH 7.4. Two dissociation constants determine that metformin at physiological pH exists as a hydrophilic cationic molecule, i.e. predominantly in ionized form. At pH values below 2.8, metformin mainly exists in diprotonated form, and it was, thus, very poorly permeable. The highest retention, i.e. affinity of both ketoprofen and metformin to the membrane, was at the lowest pH values, which is explained by different mechanisms. At higher pH values of donor compartment the substances showed significantly less affinity to the membrane. The obtained values of apparent permeation coefficients at studied pH values showed good correlation with the obtained experimental values by other in vitro methods.
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Affiliation(s)
- Alisa Elezović
- Department of Pharmaceutical Technology, Faculty of Pharmacy, University of Sarajevo, Zmaja od Bosne 8, 71000 Sarajevo, Bosnia and Herzegovina
| | - Amina Marić
- Department of Pharmaceutical Technology, Faculty of Pharmacy, University of Sarajevo, Zmaja od Bosne 8, 71000 Sarajevo, Bosnia and Herzegovina
| | - Amila Biščević
- Department of Pharmaceutical Technology, Faculty of Pharmacy, University of Sarajevo, Zmaja od Bosne 8, 71000 Sarajevo, Bosnia and Herzegovina
| | - Jasmina Hadžiabdić
- Department of Pharmaceutical Technology, Faculty of Pharmacy, University of Sarajevo, Zmaja od Bosne 8, 71000 Sarajevo, Bosnia and Herzegovina
| | - Selma Škrbo
- Department of Clinical Pharmacy, Faculty of Pharmacy, University of Sarajevo, Zmaja od Bosne 8, 71000 Sarajevo
| | - Selma Špirtović-Halilović
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Sarajevo, Zmaja od Bosne 8, 71000 Sarajevo, Bosnia and Herzegovina
| | - Ognjenka Rahić
- Department of Pharmaceutical Technology, Faculty of Pharmacy, University of Sarajevo, Zmaja od Bosne 8, 71000 Sarajevo, Bosnia and Herzegovina
| | - Edina Vranić
- Department of Pharmaceutical Technology, Faculty of Pharmacy, University of Sarajevo, Zmaja od Bosne 8, 71000 Sarajevo, Bosnia and Herzegovina
| | - Amar Elezović
- Control Laboratory of the Agency for Medicinal Products and Medical Devices, Titova 9, 71000 Sarajevo
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14
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Yang Q, Li Y, Yang J, Liu Y, Zhang L, Luo S, Cheng J. Holistic Prediction of the p
K
a
in Diverse Solvents Based on a Machine‐Learning Approach. Angew Chem Int Ed Engl 2020; 59:19282-19291. [DOI: 10.1002/anie.202008528] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 07/13/2020] [Indexed: 12/12/2022]
Affiliation(s)
- Qi Yang
- Center of Basic Molecular Science Department of Chemistry Tsinghua University 100084 Beijing China
| | - Yao Li
- Center of Basic Molecular Science Department of Chemistry Tsinghua University 100084 Beijing China
| | - Jin‐Dong Yang
- Center of Basic Molecular Science Department of Chemistry Tsinghua University 100084 Beijing China
| | - Yidi Liu
- Center of Basic Molecular Science Department of Chemistry Tsinghua University 100084 Beijing China
| | - Long Zhang
- Center of Basic Molecular Science Department of Chemistry Tsinghua University 100084 Beijing China
| | - Sanzhong Luo
- Center of Basic Molecular Science Department of Chemistry Tsinghua University 100084 Beijing China
| | - Jin‐Pei Cheng
- Center of Basic Molecular Science Department of Chemistry Tsinghua University 100084 Beijing China
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15
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Yang Q, Li Y, Yang J, Liu Y, Zhang L, Luo S, Cheng J. Holistic Prediction of the p
K
a
in Diverse Solvents Based on a Machine‐Learning Approach. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202008528] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Qi Yang
- Center of Basic Molecular Science Department of Chemistry Tsinghua University 100084 Beijing China
| | - Yao Li
- Center of Basic Molecular Science Department of Chemistry Tsinghua University 100084 Beijing China
| | - Jin‐Dong Yang
- Center of Basic Molecular Science Department of Chemistry Tsinghua University 100084 Beijing China
| | - Yidi Liu
- Center of Basic Molecular Science Department of Chemistry Tsinghua University 100084 Beijing China
| | - Long Zhang
- Center of Basic Molecular Science Department of Chemistry Tsinghua University 100084 Beijing China
| | - Sanzhong Luo
- Center of Basic Molecular Science Department of Chemistry Tsinghua University 100084 Beijing China
| | - Jin‐Pei Cheng
- Center of Basic Molecular Science Department of Chemistry Tsinghua University 100084 Beijing China
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16
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Xi Y, Yang X, Zhang H, Liu H, Watson P, Yang F. Binding interactions of halo-benzoic acids, halo-benzenesulfonic acids and halo-phenylboronic acids with human transthyretin. CHEMOSPHERE 2020; 242:125135. [PMID: 31669991 DOI: 10.1016/j.chemosphere.2019.125135] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 10/15/2019] [Accepted: 10/16/2019] [Indexed: 06/10/2023]
Abstract
The anionic form-dependent binding interaction of halo-phenolic substances with human transthyretin (hTTR) has been observed previously. This indicates that ionizable compounds should be the primary focus in screening potential hTTR disruptors. Here, the potential binding potency of halo-benzoic acids, halo-benzenesulfonic acids/sulfates and halo-phenylboronic acids with hTTR was determined and analyzed by competitive fluorescence displacement assay integrated with computational methods. The laboratorial results indicated that the three test groups of model compounds exhibited a distinct binding affinity to hTTR. All the tested halo-phenylboronic acids, some of the tested halo-benzoic acids and halo-benzenesulfonic acids/sulfates were shown to be inactive with hTTR. Other halo-benzoic acids and halo-benzenesulfonic acids/sulfates were moderate and/or weak hTTR binders. The binding affinity of halo-benzoic acids and halo-benzenesulfonic acids/sulfates with hTTR was similar. The low distribution ability of the model compounds from water to hTTR may be the reason why they exhibited the binding potency observed with hTTR. By introducing other highly hydrophobic compounds, we observed that the binding affinity between compounds and hTTR increased with increasing molecular hydrophobicity. Those results indicated that the highly hydrophobic halo-benzoic acids and halo-benzenesulfonic acids/sulfates may be high-priority hTTR disruptors. Finally, a binary classification model was constructed employing three predictive variables. The sensitivity (Sn), specificity (Sp), predictive accuracy (Q) values of the training set and validation set were >0.83, indicating that the model had good classification performance. Thus, the binary classification model developed here could be used to distinguish whether a given ionizable compound is a potential hTTR binder or not.
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Affiliation(s)
- Yue Xi
- Jiangsu Key Laboratory of Chemical Pollution Control and Resources Reuse, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, 210094, China
| | - Xianhai Yang
- Jiangsu Key Laboratory of Chemical Pollution Control and Resources Reuse, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, 210094, China.
| | - Hongyu Zhang
- Jiangsu Key Laboratory of Chemical Pollution Control and Resources Reuse, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, 210094, China
| | - Huihui Liu
- Jiangsu Key Laboratory of Chemical Pollution Control and Resources Reuse, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, 210094, China.
| | - Peter Watson
- Department of Civil and Environmental Engineering, University of Connecticut, Storrs, 06268, CT, United States
| | - Feifei Yang
- Department of Civil and Environmental Engineering, University of Connecticut, Storrs, 06268, CT, United States
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17
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Lu Y, Anand S, Shirley W, Gedeck P, Kelley BP, Skolnik S, Rodde S, Nguyen M, Lindvall M, Jia W. Prediction of pKa Using Machine Learning Methods with Rooted Topological Torsion Fingerprints: Application to Aliphatic Amines. J Chem Inf Model 2019; 59:4706-4719. [DOI: 10.1021/acs.jcim.9b00498] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Yipin Lu
- Novartis Institutes for Biomedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Shankara Anand
- Novartis Institutes for Biomedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - William Shirley
- Novartis Institutes for Biomedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Peter Gedeck
- Novartis Institutes for Biomedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Brian P. Kelley
- Novartis Institutes for Biomedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Suzanne Skolnik
- Novartis Institutes for Biomedical Research, 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Stephane Rodde
- Novartis Institutes for Biomedical Research, Postfach, CH-4002 Basel, Switzerland
| | - Mai Nguyen
- Novartis Institutes for Biomedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Mika Lindvall
- Novartis Institutes for Biomedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
| | - Weiping Jia
- Novartis Institutes for Biomedical Research, 5300 Chiron Way, Emeryville, California 94608, United States
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18
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Santibáñez-Morán MG, Medina-Franco JL. Analysis of the Acid/Base Profile of Natural Products from Different Sources. Mol Inform 2019; 39:e1900099. [PMID: 31556481 DOI: 10.1002/minf.201900099] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 09/17/2019] [Indexed: 11/09/2022]
Abstract
For many years drug discovery and other areas in chemistry have successfully relied on natural products. Recent advances in computational methods have made possible to study the chemical space of natural products from different sources. Ionizable acidic and basic functional groups heavily influence physicochemical properties and thus a molecule's absorption, distribution, metabolism, excretion, and toxicity characteristics as well as their affinity for biological targets. This work reports the generation and critical comparison of the acid/base profiles of ten chemical databases including seven natural products sets from different origins, a set of semisynthetic compounds, a collection of approved drugs, and a compendium of food chemicals. Similarities were found in the proportion of the main charge state categories among the natural products databases with few differences in their pKa distributions. Clear differences were observed between natural products and the approved drugs and semi-synthetic natural products databases, whereas natural products share some trends with the food chemical database. We noted that the natural products collections comprise around 45 % of neutral compounds. The proportion of single acids was approximately twice that found for FDA drugs, and they demonstrated a similar distribution of pKa values. In contrast to drugs, only 5 % of compounds among the natural products sets had a single basic group. Likewise, simple ampholytes were less prevalent in the natural products databases relative to drugs.
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Affiliation(s)
- Marisa G Santibáñez-Morán
- Department of Pharmacy, School of Chemistry, Universidad Nacional Autónoma de México, A, venida Universidad 3000, Mexico City, 04510, Mexico
| | - José L Medina-Franco
- Department of Pharmacy, School of Chemistry, Universidad Nacional Autónoma de México, A, venida Universidad 3000, Mexico City, 04510, Mexico
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19
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Meloun M, Pilařová L, Pfeiferová A, Pekárek T. Method of UV-Metric and pH-Metric Determination of Dissociation Constants of Ionizable Drugs: Valsartan. J SOLUTION CHEM 2019. [DOI: 10.1007/s10953-019-00913-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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20
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Yue Z, Li C, Voth GA, Swanson JMJ. Dynamic Protonation Dramatically Affects the Membrane Permeability of Drug-like Molecules. J Am Chem Soc 2019; 141:13421-13433. [PMID: 31382734 DOI: 10.1021/jacs.9b04387] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Permeability (Pm) across biological membranes is of fundamental importance and a key factor in drug absorption, distribution, and development. Although the majority of drugs will be charged at some point during oral delivery, our understanding of membrane permeation by charged species is limited. The canonical model assumes that only neutral molecules partition into and passively permeate across membranes, but there is mounting evidence that these processes are also facile for certain charged species. However, it is unknown whether such ionizable permeants dynamically neutralize at the membrane surface or permeate in their charged form. To probe protonation-coupled permeation in atomic detail, we herein apply continuous constant-pH molecular dynamics along with free energy sampling to study the permeation of a weak base propranolol (PPL), and evaluate the impact of including dynamic protonation on Pm. The simulations reveal that PPL dynamically neutralizes at the lipid-tail interface, which dramatically influences the permeation free energy landscape and explains why the conventional model overestimates the assigned intrinsic permeability. We demonstrate how fixed-charge-state simulations can account for this effect, and propose a revised model that better describes pH-coupled partitioning and permeation. Our results demonstrate how dynamic changes in protonation state may play a critical role in the permeation of ionizable molecules, including pharmaceuticals and drug-like molecules, thus requiring a revision of the standard picture.
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Affiliation(s)
- Zhi Yue
- Department of Chemistry, James Frank Institute, and Institute for Biophysical Dynamics , The University of Chicago , Chicago , Illinois 60637 , United States
| | - Chenghan Li
- Department of Chemistry, James Frank Institute, and Institute for Biophysical Dynamics , The University of Chicago , Chicago , Illinois 60637 , United States
| | - Gregory A Voth
- Department of Chemistry, James Frank Institute, and Institute for Biophysical Dynamics , The University of Chicago , Chicago , Illinois 60637 , United States
| | - Jessica M J Swanson
- Department of Chemistry, James Frank Institute, and Institute for Biophysical Dynamics , The University of Chicago , Chicago , Illinois 60637 , United States
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21
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Abstract
This Review illustrates the evaluation of permeability of lipid membranes from molecular dynamics (MD) simulation primarily using water and oxygen as examples. Membrane entrance, translocation, and exit of these simple permeants (one hydrophilic and one hydrophobic) can be simulated by conventional MD, and permeabilities can be evaluated directly by Fick's First Law, transition rates, and a global Bayesian analysis of the inhomogeneous solubility-diffusion model. The assorted results, many of which are applicable to simulations of nonbiological membranes, highlight the limitations of the homogeneous solubility diffusion model; support the utility of inhomogeneous solubility diffusion and compartmental models; underscore the need for comparison with experiment for both simple solvent systems (such as water/hexadecane) and well-characterized membranes; and demonstrate the need for microsecond simulations for even simple permeants like water and oxygen. Undulations, subdiffusion, fractional viscosity dependence, periodic boundary conditions, and recent developments in the field are also discussed. Last, while enhanced sampling methods and increasingly sophisticated treatments of diffusion add substantially to the repertoire of simulation-based approaches, they do not address directly the critical need for force fields with polarizability and multipoles, and constant pH methods.
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Affiliation(s)
- Richard M Venable
- Laboratory of Computational Biology, National Lung, Heart, and Blood Institute , National Institutes of Health , Bethesda , Maryland 20892 , United States
| | - Andreas Krämer
- Laboratory of Computational Biology, National Lung, Heart, and Blood Institute , National Institutes of Health , Bethesda , Maryland 20892 , United States
| | - Richard W Pastor
- Laboratory of Computational Biology, National Lung, Heart, and Blood Institute , National Institutes of Health , Bethesda , Maryland 20892 , United States
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22
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Santibáñez‐Morán MG, Rico‐Hidalgo MP, Manallack DT, Medina‐Franco JL. The Acid/Base Profile of a Large Food Chemical Database. Mol Inform 2019; 38:e1800171. [DOI: 10.1002/minf.201800171] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 02/23/2019] [Indexed: 11/09/2022]
Affiliation(s)
- Marisa G. Santibáñez‐Morán
- Department of PharmacySchool of ChemistryUniversidad Nacional Autónoma de México Avenida Universidad 3000 Mexico City 04510 Mexico
| | - Mariel P. Rico‐Hidalgo
- Department of PharmacySchool of ChemistryUniversidad Nacional Autónoma de México Avenida Universidad 3000 Mexico City 04510 Mexico
| | - David T. Manallack
- Monash Institute of Pharmaceutical SciencesMonash University (Parkville Campus) 381 Royal Parade Parkville, VIC 3052 Australia
| | - José L. Medina‐Franco
- Department of PharmacySchool of ChemistryUniversidad Nacional Autónoma de México Avenida Universidad 3000 Mexico City 04510 Mexico
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23
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Manallack DT, Yuriev E, Chalmers DK. The influence and manipulation of acid/base properties in drug discovery. DRUG DISCOVERY TODAY. TECHNOLOGIES 2018; 27:41-47. [PMID: 30103862 DOI: 10.1016/j.ddtec.2018.04.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 04/06/2018] [Accepted: 04/10/2018] [Indexed: 06/08/2023]
Abstract
There is a growing awareness of the importance of acid/base properties in medicinal chemistry research. In many drug classes, ionisable groups are present that make critical interactions with the receptor and are essential for potency. Yet the presence of these groups may cause problems with oral bioavailability, pharmacokinetics, or toxicity. Manipulating pKa values during drug development or applying pro-drug techniques are strategies that can overcome potential deficits in a variety of these areas. Knowledge of drug ionisation states coupled with a consideration of pH-specific cellular environments can be used advantageously to target chemoresistance. As modern drug research ventures into drug candidates that exceed the rule of 5, such exploration requires an understanding of drug acid/base properties and how these factors affect ADMET characteristics.
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Affiliation(s)
- David T Manallack
- Faculty of Pharmacy and Pharmaceutical Sciences, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia.
| | - Elizabeth Yuriev
- Faculty of Pharmacy and Pharmaceutical Sciences, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - David K Chalmers
- Faculty of Pharmacy and Pharmaceutical Sciences, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
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24
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Popović-Nikolić MR, Popović GV, Grujić M, Nikolić KM, Agbaba DD. А theoretical study on ionization of sartans in aqueous media and on interactions with surfactant micelles. J Mol Graph Model 2018; 82:67-73. [PMID: 29704812 DOI: 10.1016/j.jmgm.2018.04.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 04/18/2018] [Accepted: 04/18/2018] [Indexed: 11/30/2022]
Abstract
The ionization order of sartans in aqueous media and possible way of interactions between their equilibrium forms and surfactant micelles have been theoretically investigated. The examined sartans are ampholytes (irbesartan and losartan) and a diacid (valsartan) with the close values of ionization constants. In order to get a better insight in the overlapped protolytic equilibria of sartans and to predict an affinity of the equilibrium forms interacting with micelles as biomembrane mimetic systems, the theoretical study was performed. Energy calculation of the optimized structures of the equilibrium forms was performed at the B3LYP/6-31G (d,p) level of the Density Functional Theory (DFT). The results of the theoretical study helped to assign the experimentally determined pKa values to the corresponding ionizable centers and confirmed that in all examined compounds, the higher pKa values can be attributed to ionization of tetrazole. The molecular descriptor values showed that sartans interact predominantly with the micelle surfaces. The equilibrium forms of ampholytes demonstrate higher affinity to the micelles, as compared to the forms of the diprotic acid. Additionally, it was shown that the uncharged molecular forms of ampholytes are more lipophylic then their zwitterionic forms.
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Affiliation(s)
- Marija R Popović-Nikolić
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Belgrade, Vojvode Stepe 450, 11000, Belgrade, Serbia.
| | - Gordana V Popović
- Department of General and Inorganic Chemistry, Faculty of Pharmacy, University of Belgrade, Vojvode Stepe 450, 11000, Belgrade, Serbia
| | - Maja Grujić
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Belgrade, Vojvode Stepe 450, 11000, Belgrade, Serbia
| | - Katarina M Nikolić
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Belgrade, Vojvode Stepe 450, 11000, Belgrade, Serbia
| | - Danica D Agbaba
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Belgrade, Vojvode Stepe 450, 11000, Belgrade, Serbia
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25
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Zeng W, Nukeyeva M, Wang Q, Jiang C. Synthesis of unnatural α-amino acid derivatives via selective o-C–H functionalization. Org Biomol Chem 2018; 16:598-608. [DOI: 10.1039/c7ob02921g] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Selective o-C–H functionalization of aryl based amino acids including arylation, alkylation, alkynylation, halogenation, alkoxylation, and acyloxylation were developed.
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Affiliation(s)
- Wanting Zeng
- School of Chemical Engineering
- Nanjing University of Science and Technology
- Nanjing 210094
- China
| | - Moldir Nukeyeva
- School of Chemical Engineering
- Nanjing University of Science and Technology
- Nanjing 210094
- China
| | - Qiumei Wang
- School of Chemical Engineering
- Nanjing University of Science and Technology
- Nanjing 210094
- China
| | - Chao Jiang
- School of Chemical Engineering
- Nanjing University of Science and Technology
- Nanjing 210094
- China
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26
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Proton dissociation properties of arylphosphonates: Determination of accurate Hammett equation parameters. J Pharm Biomed Anal 2017; 143:101-109. [PMID: 28578253 DOI: 10.1016/j.jpba.2017.05.038] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 05/19/2017] [Accepted: 05/21/2017] [Indexed: 11/23/2022]
Abstract
Determination of the proton dissociation constants of several arylphosphonic acid derivatives was carried out to investigate the accuracy of the Hammett equations available for this family of compounds. For the measurement of the pKa values modern, accurate methods, such as the differential potentiometric titration and NMR-pH titration were used. We found our results significantly different from the pKa values reported before (pKa1: MAE = 0.16 pKa2: MAE=0.59). Based on our recently measured pKa values, refined Hammett equations were determined that might be used for predicting highly accurate ionization constants of newly synthesized compounds (pKa1=1.70-0.894σ, pKa2=6.92-0.934σ).
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27
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Manallack DT. The acid/base profile of agrochemicals. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2017; 28:621-628. [PMID: 28799807 DOI: 10.1080/1062936x.2017.1359666] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 07/21/2017] [Indexed: 06/07/2023]
Abstract
Drug-likeness has long been studied in the pursuit of finding new medicines. Similarly, in the agrochemical field there is value in exploring the properties of the chemicals involved. Patterns that emerge can potentially influence future discovery campaigns to improve the probability of commercial success. In this study we investigate the acid/base properties and physicochemical characteristics of three classes of compounds: fungicides, herbicides and insecticides. In comparison with FDA-approved drugs, it was noted that the pesticides were generally smaller, possessed a neutral charge state and were more lipophilic. The results are discussed in the light of their intended targets.
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Affiliation(s)
- D T Manallack
- a Faculty of Pharmacy and Pharmaceutical Sciences , Monash Institute of Pharmaceutical Sciences, Monash University , Australia
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28
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Caron G, Vallaro M, Ermondi G. High throughput methods to measure the propensity of compounds to form intramolecular hydrogen bonding. MEDCHEMCOMM 2017; 8:1143-1151. [PMID: 30108824 PMCID: PMC6071820 DOI: 10.1039/c7md00101k] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 04/25/2017] [Indexed: 12/18/2022]
Abstract
Implementation of IMHB considerations in drug discovery needs robust and validated descriptors to experimentally verify the propensity of compounds to exhibit IMHBs. The first part of the paper presents an overview of the most common techniques to measure the propensity of compounds to form IMHBs. Then we review and discuss recently proposed high throughput (HT) physicochemical descriptors (i.e. Δlog Poct-tol, EPSA and log k'80 PLRP-S) which provide the same information. Analysis of the available data enabled us to extract guidelines for the application of these descriptors in drug discovery programs.
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Affiliation(s)
- Giulia Caron
- Molecular Biotechnology and Health Sciences Dept. , University of Torino , Quarello, 15 , 10135 Torino , Italy . ; Tel: +39 011 6708337
| | - Maura Vallaro
- Molecular Biotechnology and Health Sciences Dept. , University of Torino , Quarello, 15 , 10135 Torino , Italy . ; Tel: +39 011 6708337
| | - Giuseppe Ermondi
- Molecular Biotechnology and Health Sciences Dept. , University of Torino , Quarello, 15 , 10135 Torino , Italy . ; Tel: +39 011 6708337
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29
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Sezer D, Oruç T. Protonation Kinetics Compromise Liposomal Fluorescence Assay of Membrane Permeation. J Phys Chem B 2017; 121:5218-5227. [DOI: 10.1021/acs.jpcb.7b01881] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Deniz Sezer
- Faculty of Engineering and
Natural Sciences, Sabancı University, Orhanlı-Tuzla, 34956 Istanbul, Turkey
| | - Tuğçe Oruç
- Faculty of Engineering and
Natural Sciences, Sabancı University, Orhanlı-Tuzla, 34956 Istanbul, Turkey
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30
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Grujić M, Popović M, Popović G, Nikolic K, Agbaba D. Protolytic Equilibria of Sartans in Micellar Solutions of Differently Charged Surfactants. J Pharm Sci 2016; 105:2444-52. [DOI: 10.1016/j.xphs.2016.06.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 05/20/2016] [Accepted: 06/07/2016] [Indexed: 11/27/2022]
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31
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Oruç T, Küçük SE, Sezer D. Lipid bilayer permeation of aliphatic amine and carboxylic acid drugs: rates of insertion, translocation and dissociation from MD simulations. Phys Chem Chem Phys 2016; 18:24511-25. [DOI: 10.1039/c6cp05278a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The overabundance of drugs containing aliphatic amine and carboxylic acid groups is rationalized in terms of their membrane permeability.
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Affiliation(s)
- Tuğçe Oruç
- Faculty of Engineering and Natural Sciences
- Sabanc University
- 34956 Istanbul
- Turkey
| | - Sami Emre Küçük
- Faculty of Engineering and Natural Sciences
- Sabanc University
- 34956 Istanbul
- Turkey
| | - Deniz Sezer
- Faculty of Engineering and Natural Sciences
- Sabanc University
- 34956 Istanbul
- Turkey
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32
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Dastbaravardeh N, Toba T, Farmer ME, Yu JQ. Monoselective o-C-H Functionalizations of Mandelic Acid and α-Phenylglycine. J Am Chem Soc 2015; 137:9877-84. [PMID: 26162456 PMCID: PMC4538457 DOI: 10.1021/jacs.5b04324] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2015] [Indexed: 01/31/2023]
Abstract
Pd-catalyzed C-H functionalization of mandelic acid and α-phenylglycine is reported. We have developed different protocols for the arylation, iodination, acetoxylation, and olefination of these substrates based on two different (Pd(II)/Pd(IV) and Pd(II)/Pd(0)) catalytic cycles. Four crucial features of these protocols are advantageous for practical applications. First, the α-hydroxyl and amino groups are protected with simple protecting groups such as acetates (Ac, Piv) and carbamates (Boc, Fmoc), respectively. Second, these protocols do not involve installation and removal of a directing group. Third, monoselectivity is accomplished. Fourth, no epimerization occurs at the vulnerable α-chiral centers.
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Affiliation(s)
- Navid Dastbaravardeh
- Department of Chemistry, The
Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, California 92037, United States
| | - Tetsuya Toba
- Department of Chemistry, The
Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, California 92037, United States
| | - Marcus E. Farmer
- Department of Chemistry, The
Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, California 92037, United States
| | - Jin-Quan Yu
- Department of Chemistry, The
Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, California 92037, United States
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33
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Wang CK, Northfield SE, Swedberg JE, Colless B, Chaousis S, Price DA, Liras S, Craik DJ. Exploring experimental and computational markers of cyclic peptides: Charting islands of permeability. Eur J Med Chem 2015; 97:202-13. [PMID: 25974856 DOI: 10.1016/j.ejmech.2015.04.049] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Revised: 04/23/2015] [Accepted: 04/24/2015] [Indexed: 12/25/2022]
Abstract
An increasing number of macrocyclic peptides that cross biological membranes are being reported, suggesting that it might be possible to develop peptides into orally bioavailable therapeutics; however, current understanding of what makes macrocyclic peptides cell permeable is still limited. Here, we synthesized 62 cyclic hexapeptides and characterized their permeability using in vitro assays commonly used to predict in vivo absorption rates, i.e. the Caco-2 and PAMPA assays. We correlated permeability with experimentally measured parameters of peptide conformation obtained using rapid methods based on chromatography and nuclear magnetic resonance spectroscopy. Based on these correlations, we propose a model describing the interplay between peptide permeability, lipophilicity and hydrogen bonding potential. Specifically, peptides with very high permeability have high lipophilicity and few solvent hydrogen bond interactions, whereas peptides with very low permeability have low lipophilicity or many solvent interactions. Our model is supported by molecular dynamics simulations of the cyclic peptides calculated in explicit solvent, providing a structural basis for the observed correlations. This prospective exploration into biomarkers of peptide permeability has the potential to unlock wider opportunities for development of peptides into drugs.
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Affiliation(s)
- Conan K Wang
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Susan E Northfield
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Joakim E Swedberg
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Barbara Colless
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Stephanie Chaousis
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - David A Price
- Worldwide Medicinal Chemistry, CVMED, Pfizer, 610 Main Street, Cambridge, MA 02139, USA
| | - Spiros Liras
- Worldwide Medicinal Chemistry, CVMED, Pfizer, 610 Main Street, Cambridge, MA 02139, USA
| | - David J Craik
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia.
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34
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Kayastha S, de la Vega de León A, Dimova D, Bajorath J. Target-based analysis of ionization states of bioactive compounds. MEDCHEMCOMM 2015. [DOI: 10.1039/c5md00051c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ionization states within a chemical neighborhood. Shown are an acidic and a basic analog of a neutral compound.
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Affiliation(s)
- Shilva Kayastha
- Department of Life Science Informatics
- Bonn-Aachen International Center for Information Technology
- Rheinische Friedrich-Wilhelms-Universität Bonn
- D-53113 Bonn
- Germany
| | - Antonio de la Vega de León
- Department of Life Science Informatics
- Bonn-Aachen International Center for Information Technology
- Rheinische Friedrich-Wilhelms-Universität Bonn
- D-53113 Bonn
- Germany
| | - Dilyana Dimova
- Department of Life Science Informatics
- Bonn-Aachen International Center for Information Technology
- Rheinische Friedrich-Wilhelms-Universität Bonn
- D-53113 Bonn
- Germany
| | - Jürgen Bajorath
- Department of Life Science Informatics
- Bonn-Aachen International Center for Information Technology
- Rheinische Friedrich-Wilhelms-Universität Bonn
- D-53113 Bonn
- Germany
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35
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Mathias SL, Hines-Kay J, Yang JJ, Zahoransky-Kohalmi G, Bologa CG, Ursu O, Oprea TI. The CARLSBAD database: a confederated database of chemical bioactivities. Database (Oxford) 2013; 2013:bat044. [PMID: 23794735 PMCID: PMC3689437 DOI: 10.1093/database/bat044] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Revised: 05/12/2013] [Accepted: 05/21/2013] [Indexed: 11/30/2022]
Abstract
Many bioactivity databases offer information regarding the biological activity of small molecules on protein targets. Information in these databases is often hard to resolve with certainty because of subsetting different data in a variety of formats; use of different bioactivity metrics; use of different identifiers for chemicals and proteins; and having to access different query interfaces, respectively. Given the multitude of data sources, interfaces and standards, it is challenging to gather relevant facts and make appropriate connections and decisions regarding chemical-protein associations. The CARLSBAD database has been developed as an integrated resource, focused on high-quality subsets from several bioactivity databases, which are aggregated and presented in a uniform manner, suitable for the study of the relationships between small molecules and targets. In contrast to data collection resources, CARLSBAD provides a single normalized activity value of a given type for each unique chemical-protein target pair. Two types of scaffold perception methods have been implemented and are available for datamining: HierS (hierarchical scaffolds) and MCES (maximum common edge subgraph). The 2012 release of CARLSBAD contains 439 985 unique chemical structures, mapped onto 1,420 889 unique bioactivities, and annotated with 277 140 HierS scaffolds and 54 135 MCES chemical patterns, respectively. Of the 890 323 unique structure-target pairs curated in CARLSBAD, 13.95% are aggregated from multiple structure-target values: 94 975 are aggregated from two bioactivities, 14 544 from three, 7 930 from four and 2214 have five bioactivities, respectively. CARLSBAD captures bioactivities and tags for 1435 unique chemical structures of active pharmaceutical ingredients (i.e. 'drugs'). CARLSBAD processing resulted in a net 17.3% data reduction for chemicals, 34.3% reduction for bioactivities, 23% reduction for HierS and 25% reduction for MCES, respectively. The CARLSBAD database supports a knowledge mining system that provides non-specialists with novel integrative ways of exploring chemical biology space to facilitate knowledge mining in drug discovery and repurposing. Database URL: http://carlsbad.health.unm.edu/carlsbad/.
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Affiliation(s)
| | | | | | | | | | | | - Tudor I. Oprea
- Department of Internal Medicine, Translational Informatics Division, University of New Mexico School of Medicine, 1 University of New Mexico, MSC09 5025, Albuquerque, NM 87131, USA
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