1
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Ali HS, Henchman RH. Energy-entropy multiscale cell correlation method to predict toluene-water log P in the SAMPL9 challenge. Phys Chem Chem Phys 2023; 25:27524-27531. [PMID: 37800345 DOI: 10.1039/d3cp03076h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/07/2023]
Abstract
The energy-entropy multiscale cell correlation (EE-MCC) method is used to calculate toluene-water log P values of 16 drug molecules in the SAMPL9 physical properties challenge. EE-MCC calculates the free energy, energy and entropy from molecular dynamics (MD) simulations of the water and toluene solutions. Specifically, MCC evaluates entropy by partitioning the system into cells of correlated atoms at multiple length scales and further partitioning the local coordinates into energy wells, yielding vibrational and topographical terms from the energy-well sizes and probabilities. The log P values calculated by EE-MCC using three 200 ns MD simulations have a mean average error of 0.82 and standard error of the mean of 0.97 versus experiment, which is comparable with the best methods entered in SAMPL9. The main contribution to log P is from energy. Less polar drugs have more favourable energies of transfer. The entropy of transfer consists of increased solute vibrational and conformational terms in toluene due to weaker interactions, fewer solute positions in the larger-molecule solvent, reduced water vibrational entropy, negligible change in toluene vibrational entropy, and gains in solvent orientational entropy. The solvent entropy contributions here may be slightly underestimated because software limitations and statistical fluctuations meant that only the first shell could be included while averaged over the whole solution. Nonetheless, such issues will be addressed in future software to offer a general method to calculate entropy directly from MD simulation and to provide molecular understanding or guide system design.
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Affiliation(s)
- Hafiz Saqib Ali
- Chemistry Research Laboratory, Department of Chemistry and the INEOS Oxford Institute for Antimicrobial Research, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK.
| | - Richard H Henchman
- Sydney Medical School, Faculty of Medicine and Health, University of Sydney, Sydney, Australia.
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2
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Nalli M, Di Magno L, Wen Y, Liu X, D’Ambrosio M, Puxeddu M, Parisi A, Sebastiani J, Sorato A, Coluccia A, Ripa S, Di Pastena F, Capelli D, Montanari R, Masci D, Urbani A, Naro C, Sette C, Orlando V, D’Angelo S, Biagioni S, Bigogno C, Dondio G, Pastore A, Stornaiuolo M, Canettieri G, Liu T, Silvestri R, La Regina G. Novel N-(Heterocyclylphenyl)benzensulfonamide Sharing an Unreported Binding Site with T-Cell Factor 4 at the β-Catenin Armadillo Repeats Domain as an Anticancer Agent. ACS Pharmacol Transl Sci 2023; 6:1087-1103. [PMID: 37470018 PMCID: PMC10353061 DOI: 10.1021/acsptsci.3c00092] [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: 05/17/2023] [Indexed: 07/21/2023]
Abstract
Despite intensive efforts, no inhibitors of the Wnt/β-catenin signaling pathway have been approved so far for the clinical treatment of cancer. We synthesized novel N-(heterocyclylphenyl)benzenesulfonamides as β-catenin inhibitors. Compounds 5-10 showed strong inhibition of the luciferase activity. Compounds 5 and 6 inhibited the MDA-MB-231, HCC1806, and HCC1937 TNBC cells. Compound 9 induced in vitro cell death in SW480 and HCT116 cells and in vivo tumorigenicity of a human colorectal cancer line HCT116. In a co-immunoprecipitation study in HCT116 cells transfected with Myc-tagged T-cell factor 4 (Tcf-4), compound 9 abrogated the association between β-catenin and Tcf-4. The crystallographic analysis of the β-catenin Armadillo repeats domain revealed that compound 9 and Tcf-4 share a common binding site within the hotspot binding region close to Lys508. To our knowledge, compound 9 is the first small molecule ligand of this region to be reported. These results highlight the potential of this novel class of β-catenin inhibitors as anticancer agents.
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Affiliation(s)
- Marianna Nalli
- Laboratory
affiliated to Istituto Pasteur Italia—Fondazione Cenci Bolognetti,
Department of Drug Chemistry and Technologies, Sapienza University of Rome, Piazzale Aldo Moro 5, I-00185 Rome, Italy
| | - Laura Di Magno
- Laboratory
affiliated to Istituto Pasteur Italia—Fondazione Cenci Bolognetti,
Department of Molecular Medicine Sapienza, University of Rome, Viale Regina Elena 291, I-00161 Rome, Italy
| | - Yichao Wen
- Shanghai
Geriatric Institute of Chinese Medicine, Shanghai University of Traditional Chinese Medicine, 365 South Xiangyang Road, 200031 Shanghai, China
| | - Xin Liu
- Department
of Dermatology, Yueyang Hospital of Integrated Traditional Chinese
and Western Medicine, Shanghai University
of Traditional Chinese Medicine, 200437 Shanghai, China
| | - Michele D’Ambrosio
- Laboratory
affiliated to Istituto Pasteur Italia—Fondazione Cenci Bolognetti,
Department of Drug Chemistry and Technologies, Sapienza University of Rome, Piazzale Aldo Moro 5, I-00185 Rome, Italy
| | - Michela Puxeddu
- Laboratory
affiliated to Istituto Pasteur Italia—Fondazione Cenci Bolognetti,
Department of Drug Chemistry and Technologies, Sapienza University of Rome, Piazzale Aldo Moro 5, I-00185 Rome, Italy
| | - Anastasia Parisi
- Laboratory
affiliated to Istituto Pasteur Italia—Fondazione Cenci Bolognetti,
Department of Drug Chemistry and Technologies, Sapienza University of Rome, Piazzale Aldo Moro 5, I-00185 Rome, Italy
| | - Jessica Sebastiani
- Laboratory
affiliated to Istituto Pasteur Italia—Fondazione Cenci Bolognetti,
Department of Drug Chemistry and Technologies, Sapienza University of Rome, Piazzale Aldo Moro 5, I-00185 Rome, Italy
| | - Andrea Sorato
- Laboratory
affiliated to Istituto Pasteur Italia—Fondazione Cenci Bolognetti,
Department of Drug Chemistry and Technologies, Sapienza University of Rome, Piazzale Aldo Moro 5, I-00185 Rome, Italy
| | - Antonio Coluccia
- Laboratory
affiliated to Istituto Pasteur Italia—Fondazione Cenci Bolognetti,
Department of Drug Chemistry and Technologies, Sapienza University of Rome, Piazzale Aldo Moro 5, I-00185 Rome, Italy
| | - Silvia Ripa
- Laboratory
affiliated to Istituto Pasteur Italia—Fondazione Cenci Bolognetti,
Department of Molecular Medicine Sapienza, University of Rome, Viale Regina Elena 291, I-00161 Rome, Italy
| | - Fiorella Di Pastena
- Laboratory
affiliated to Istituto Pasteur Italia—Fondazione Cenci Bolognetti,
Department of Molecular Medicine Sapienza, University of Rome, Viale Regina Elena 291, I-00161 Rome, Italy
| | - Davide Capelli
- CNR—Institute
of Crystallography, Via
Salaria—km 29.300, Monterotondo, 00015 Rome, Italy
| | - Roberta Montanari
- CNR—Institute
of Crystallography, Via
Salaria—km 29.300, Monterotondo, 00015 Rome, Italy
| | - Domiziana Masci
- Department
of Basic Biotechnological Sciences, Intensivological and Perioperative
Clinics, Catholic University of the Sacred
Heart, Largo Francesco
Vito 1, 00168 Rome, Italy
| | - Andrea Urbani
- Department
of Basic Biotechnological Sciences, Intensivological and Perioperative
Clinics, Catholic University of the Sacred
Heart, Largo Francesco
Vito 1, 00168 Rome, Italy
| | - Chiara Naro
- Department
of Basic Biotechnological Sciences, Intensivological and Perioperative
Clinics, Catholic University of the Sacred
Heart, Largo Francesco
Vito 1, 00168 Rome, Italy
- GSTeP-Organoids
Research Core Facility, Fondazione Policlinico
Universitario A. Gemelli, IRCCS, 00168 Rome, Italy
| | - Claudio Sette
- Department
of Basic Biotechnological Sciences, Intensivological and Perioperative
Clinics, Catholic University of the Sacred
Heart, Largo Francesco
Vito 1, 00168 Rome, Italy
- GSTeP-Organoids
Research Core Facility, Fondazione Policlinico
Universitario A. Gemelli, IRCCS, 00168 Rome, Italy
| | - Viviana Orlando
- Department
of Biology and Biotechnologies “Charles Darwin”, Piazzale Aldo Moro 5, I-00185 Roma, Italy
| | - Sara D’Angelo
- Department
of Biology and Biotechnologies “Charles Darwin”, Piazzale Aldo Moro 5, I-00185 Roma, Italy
| | - Stefano Biagioni
- Department
of Biology and Biotechnologies “Charles Darwin”, Piazzale Aldo Moro 5, I-00185 Roma, Italy
| | - Chiara Bigogno
- Aphad
SrL, Via della Resistenza
65, 20090 Buccinasco, Italy
| | - Giulio Dondio
- Aphad
SrL, Via della Resistenza
65, 20090 Buccinasco, Italy
| | - Arianna Pastore
- Department
of Pharmacy, University of Naples “Federico
II”, Via Domenico
Montesano, 49, 80131 Naples, Italy
| | - Mariano Stornaiuolo
- Department
of Pharmacy, University of Naples “Federico
II”, Via Domenico
Montesano, 49, 80131 Naples, Italy
| | - Gianluca Canettieri
- Laboratory
affiliated to Istituto Pasteur Italia—Fondazione Cenci Bolognetti,
Department of Molecular Medicine Sapienza, University of Rome, Viale Regina Elena 291, I-00161 Rome, Italy
| | - Te Liu
- Shanghai
Geriatric Institute of Chinese Medicine, Shanghai University of Traditional Chinese Medicine, 365 South Xiangyang Road, 200031 Shanghai, China
| | - Romano Silvestri
- Laboratory
affiliated to Istituto Pasteur Italia—Fondazione Cenci Bolognetti,
Department of Drug Chemistry and Technologies, Sapienza University of Rome, Piazzale Aldo Moro 5, I-00185 Rome, Italy
| | - Giuseppe La Regina
- Laboratory
affiliated to Istituto Pasteur Italia—Fondazione Cenci Bolognetti,
Department of Drug Chemistry and Technologies, Sapienza University of Rome, Piazzale Aldo Moro 5, I-00185 Rome, Italy
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3
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Zamora WJ, Viayna A, Pinheiro S, Curutchet C, Bisbal L, Ruiz R, Ràfols C, Luque FJ. Prediction of toluene/water partition coefficients in the SAMPL9 blind challenge: assessment of machine learning and IEF-PCM/MST continuum solvation models. Phys Chem Chem Phys 2023. [PMID: 37376995 DOI: 10.1039/d3cp01428b] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2023]
Abstract
In recent years the use of partition systems other than the widely used biphasic n-octanol/water has received increased attention to gain insight into the molecular features that dictate the lipophilicity of compounds. Thus, the difference between n-octanol/water and toluene/water partition coefficients has proven to be a valuable descriptor to study the propensity of molecules to form intramolecular hydrogen bonds and exhibit chameleon-like properties that modulate solubility and permeability. In this context, this study reports the experimental toluene/water partition coefficients (log Ptol/w) for a series of 16 drugs that were selected as an external test set in the framework of the Statistical Assessment of the Modeling of Proteins and Ligands (SAMPL) blind challenge. This external set has been used by the computational community to calibrate their methods in the current edition (SAMPL9) of this contest. Furthermore, the study also investigates the performance of two computational strategies for the prediction of log Ptol/w. The first relies on the development of two machine learning (ML) models, which are built up by combining the selection of 11 molecular descriptors in conjunction with either the multiple linear regression (MLR) or the random forest regression (RFR) model to target a dataset of 252 experimental log Ptol/w values. The second consists of the parametrization of the IEF-PCM/MST continuum solvation model from B3LYP/6-31G(d) calculations to predict the solvation free energies of 163 compounds in toluene and benzene. The performance of the ML and IEF-PCM/MST models has been calibrated against external test sets, including the compounds that define the SAMPL9 log Ptol/w challenge. The results are used to discuss the merits and weaknesses of the two computational approaches.
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Affiliation(s)
- William J Zamora
- CBio3 Laboratory, School of Chemistry, University of Costa Rica, San Pedro, San José, Costa Rica.
- Laboratory of Computational Toxicology and Artificial Intelligence (LaToxCIA), Biological Testing Laboratory (LEBi), University of Costa Rica, San Pedro, San José, Costa Rica
- Advanced Computing Lab (CNCA), National High Technology Center (CeNAT), Pavas, San José, Costa Rica
| | - Antonio Viayna
- Departament de Nutrició, Ciències de l'Alimentació i Gastronomia, Facultat de Farmàcia i Ciències de l'Alimentació, Universitat de Barcelona (UB), Av. Prat de la Riba 171, 08921 Santa Coloma de Gramenet, Spain.
- Institut de Biomedicina (IBUB), Universitat de Barcelona (UB), Barcelona, Spain
- Institut de Química Teòrica i Computacional (IQTC-UB), Universitat de Barcelona (UB), Barcelona, Spain
| | - Silvana Pinheiro
- CBio3 Laboratory, School of Chemistry, University of Costa Rica, San Pedro, San José, Costa Rica.
- Laboratory of Computational Toxicology and Artificial Intelligence (LaToxCIA), Biological Testing Laboratory (LEBi), University of Costa Rica, San Pedro, San José, Costa Rica
| | - Carles Curutchet
- Institut de Química Teòrica i Computacional (IQTC-UB), Universitat de Barcelona (UB), Barcelona, Spain
- Departament de Farmàcia i Tecnologia Farmacèutica, i Fisicoquímica, Facultat de Farmàcia i Ciències de l'Alimentació, Universitat de Barcelona (UB), Av. Joan XXIII 27-31, 08028, Barcelona, Spain
| | - Laia Bisbal
- Institut de Biomedicina (IBUB), Universitat de Barcelona (UB), Barcelona, Spain
- Departament d'Enginyeria Química i Química Analítica, Universitat de Barcelona (UB), Martí i Franquès 1-11, 08028 Barcelona, Spain.
| | - Rebeca Ruiz
- Pion Inc., Forest Row Business Park, Forest Row RH18 5DW, UK
| | - Clara Ràfols
- Institut de Biomedicina (IBUB), Universitat de Barcelona (UB), Barcelona, Spain
- Departament d'Enginyeria Química i Química Analítica, Universitat de Barcelona (UB), Martí i Franquès 1-11, 08028 Barcelona, Spain.
| | - F Javier Luque
- Departament de Nutrició, Ciències de l'Alimentació i Gastronomia, Facultat de Farmàcia i Ciències de l'Alimentació, Universitat de Barcelona (UB), Av. Prat de la Riba 171, 08921 Santa Coloma de Gramenet, Spain.
- Institut de Biomedicina (IBUB), Universitat de Barcelona (UB), Barcelona, Spain
- Institut de Química Teòrica i Computacional (IQTC-UB), Universitat de Barcelona (UB), Barcelona, Spain
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4
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Kenny PW. Hydrogen-Bond Donors in Drug Design. J Med Chem 2022; 65:14261-14275. [DOI: 10.1021/acs.jmedchem.2c01147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Peter W. Kenny
- Berwick-on-Sea, North Coast Road, Blanchisseuse, Saint George, Trinidad and Tobago
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5
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Forces Driving a Magic Bullet to Its Target: Revisiting the Role of Thermodynamics in Drug Design, Development, and Optimization. Life (Basel) 2022; 12:life12091438. [PMID: 36143474 PMCID: PMC9504344 DOI: 10.3390/life12091438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 09/02/2022] [Accepted: 09/03/2022] [Indexed: 11/27/2022] Open
Abstract
Drug discovery strategies have advanced significantly towards prioritizing target selectivity to achieve the longstanding goal of identifying “magic bullets” amongst thousands of chemical molecules screened for therapeutic efficacy. A myriad of emerging and existing health threats, including the SARS-CoV-2 pandemic, alarming increase in bacterial resistance, and potentially fatal chronic ailments, such as cancer, cardiovascular disease, and neurodegeneration, have incentivized the discovery of novel therapeutics in treatment regimens. The design, development, and optimization of lead compounds represent an arduous and time-consuming process that necessitates the assessment of specific criteria and metrics derived via multidisciplinary approaches incorporating functional, structural, and energetic properties. The present review focuses on specific methodologies and technologies aimed at advancing drug development with particular emphasis on the role of thermodynamics in elucidating the underlying forces governing ligand–target interaction selectivity and specificity. In the pursuit of novel therapeutics, isothermal titration calorimetry (ITC) has been utilized extensively over the past two decades to bolster drug discovery efforts, yielding information-rich thermodynamic binding signatures. A wealth of studies recognizes the need for mining thermodynamic databases to critically examine and evaluate prospective drug candidates on the basis of available metrics. The ultimate power and utility of thermodynamics within drug discovery strategies reside in the characterization and comparison of intrinsic binding signatures that facilitate the elucidation of structural–energetic correlations which assist in lead compound identification and optimization to improve overall therapeutic efficacy.
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6
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Zhou YL, Li XL, Zhang YM, Shi Y, Li HH, Zhang Z, Iqbal C, Ye DX, Li XS, Zhao YR, Xu WL, Smagghe G, Yang XL. A novel bee-friendly peptidomimetic insecticide: Synthesis, aphicidal activity and 3D-QSAR study of insect kinin analogs at Phe 2 modification. PEST MANAGEMENT SCIENCE 2022; 78:2952-2963. [PMID: 35419934 DOI: 10.1002/ps.6920] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 04/07/2022] [Accepted: 04/14/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND As one of the most abundant and destructive pests in agriculture, aphids cause significant damage to crops due to their sap-taking and as virus vectors. Chemical insecticides are the most effective method to control aphids, but they bring insecticide resistance problems and harm nontarget organisms, especially bees, therefore the search for novel eco-friendly aphid control agents with low bee toxicity is urgent. Insect kinins are a class of small neuropeptides that control important functions in insects. In our previous study, we found insect kinin analog IV-3 has good aphicidal activity and the location of the aromatic ring on the side chain of Phe2 is the key to the formation of the β-turn resulting in the biological activity of insect kinin analogs. However, there are few studies on insect kinin Phe2 substitution and modification, and its structure-activity relationship is still unclear. RESULTS In this project, 44 insect kinin analogs with the Phe2 modification, replacing it with different natural or unnatural amino acids, were designed and synthesized based on the lead IV-3 to explore the role of the Phe2 residues. Bioassays with soybean aphids of Aphis glycines indicated that nine analogs have better aphicidal activity than the lead IV-3. In particular, compound L25 exhibits excellent aphicidal activity (LC50 = 0.0047 mmol L-1 ) and has low toxicity to bees. Furthermore, a reliable three-dimensional quantitative structure-activity relationship (3D-QSAR) was established to produce a helpful clue that introducing hydrophobic groups away from the backbone chain is beneficial to improve aphicidal activity. CONCLUSION The residue Phe2 of insect kinin analogs is the key position and has a significant impact on the activity. L25 has a high toxicity for aphids, while a low toxicity to bees, and therefore can be considered as a lead compound to develop new biosafe aphid control agents. Finally, we provide a useful 3D-QSAR model as theoretical guidance for further structural optimization. © 2022 Society of Chemical Industry.
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Affiliation(s)
- Yuan-Lin Zhou
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Science, China Agricultural University, Beijing, 100193, PR China
| | - Xin-Lu Li
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Science, China Agricultural University, Beijing, 100193, PR China
| | - Yi-Meng Zhang
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Science, China Agricultural University, Beijing, 100193, PR China
| | - Yan Shi
- Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, 9000, Belgium
- College of Plant Health and Medicine, Qingdao Agricultural University, Shandong Province, Qingdao, 266109, China
| | - Hong-Hong Li
- Guangxi Key Laboratory of Agro-Environment and Agro-Product Safety, Agricultural College, Guangxi University, Nanning, Guangxi Province, 530004, China
| | - Zhe Zhang
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Science, China Agricultural University, Beijing, 100193, PR China
| | - Chandni Iqbal
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Science, China Agricultural University, Beijing, 100193, PR China
| | - De-Xing Ye
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Science, China Agricultural University, Beijing, 100193, PR China
| | - Xue-Sheng Li
- Guangxi Key Laboratory of Agro-Environment and Agro-Product Safety, Agricultural College, Guangxi University, Nanning, Guangxi Province, 530004, China
| | - Ying-Ru Zhao
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Science, China Agricultural University, Beijing, 100193, PR China
| | - Wei-Long Xu
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Science, China Agricultural University, Beijing, 100193, PR China
| | - Guy Smagghe
- Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, 9000, Belgium
| | - Xin-Ling Yang
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Science, China Agricultural University, Beijing, 100193, PR China
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7
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Okuno Y, Nishimura T, Sasaki Y, Akiyoshi K. Thermoresponsive Carbohydrate- b-Polypeptoid Polymer Vesicles with Selective Solute Permeability and Permeable Factors for Solutes. Biomacromolecules 2021; 22:3099-3106. [PMID: 34165283 DOI: 10.1021/acs.biomac.1c00530] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Solute-permeable polymer vesicles are structural compartments for nanoreactors/nanofactories in the context of drug delivery and artificial cells. We previously proposed design guidelines for polymers that form solute-permeable vesicles, yet we did not provide enough experimental verification. In addition, the fact that there is no clear factor for identifying permeable solutes necessitates extensive trial and error. Herein, we report solute-permeable polymer vesicles based on an amphiphilic copolymer, thermoresponsive oligosaccharide-block-poly(N-n-propylglycine). The introduction of a thermoresponsive polymer as a hydrophobic segment into amphiphilic polymers is a viable approach to construct solute-permeable polymer vesicles. We also demonstrate that the polymer vesicles are preferentially permeable to cationic and neutral fluorophores and are hardly permeable to anionic fluorophores due to the electrostatic repulsion between the bilayer and anionic fluorophores. In addition, the permeability of neutral fluorophores increases with the increasing log P value of the fluorophores. Thus, the electrical charge and log P value are important factors for membrane permeability. These findings will help researchers develop advanced nanoreactors based on permeable vesicles for a broad range of fundamental and biomedical applications.
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Affiliation(s)
- Yota Okuno
- Department of Polymer Chemistry, Graduate School of Engineering, Kyoto University, Kyoto Daigaku-Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Tomoki Nishimura
- Department of Chemistry and Materials, Faculty of Textile Science and Technology, Shinshu University, 3-15-1, Tokida, Nagano 386-8567, Japan
| | - Yoshihiro Sasaki
- Department of Polymer Chemistry, Graduate School of Engineering, Kyoto University, Kyoto Daigaku-Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Kazunari Akiyoshi
- Department of Polymer Chemistry, Graduate School of Engineering, Kyoto University, Kyoto Daigaku-Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
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8
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Ashworth IW, Curran TT, Ford JG, Tomasi S. Prediction of N-Nitrosamine Partition Coefficients for Derisking Drug Substance Manufacturing Processes. Org Process Res Dev 2021. [DOI: 10.1021/acs.oprd.0c00535] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ian W. Ashworth
- Chemical Development, Pharmaceutical Technology & Development, Operations, AstraZeneca, Macclesfield, U.K
| | - Timothy T. Curran
- Process Chemistry, Vertex Pharmaceuticals, Boston, Massachusetts, United States
| | - J. Gair Ford
- Regulatory CMC, Global Regulatory Excellence, AstraZeneca, Macclesfield, U.K
| | - Simone Tomasi
- Chemical Development, Pharmaceutical Technology & Development, Operations, AstraZeneca, Macclesfield, U.K
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9
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Chen D, Wang Q, Li Y, Li Y, Zhou H, Fan Y. A general linear free energy relationship for predicting partition coefficients of neutral organic compounds. CHEMOSPHERE 2020; 247:125869. [PMID: 31972487 DOI: 10.1016/j.chemosphere.2020.125869] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Revised: 01/03/2020] [Accepted: 01/06/2020] [Indexed: 06/10/2023]
Abstract
Predicting the effects of organic compounds on environments and biological systems is an important objective for environmental chemistry and human health. The logarithm (to base 10) of the n-octanoll-water partition coefficient has been widely used to predict the mentioned properties. However, the suitability of this parameter for the purpose has been questioned, since the environments relating to the properties may be quite different from that of bulk n-octanol. In this study, we used a theoretical derivation approach to develop a model for predicting the partition coefficients of solutes between water and an organic solvent that may be similar to n-octanol or quite different from it. Our model relies on solute descriptors that can be calculated based on solute structures. It was used to predict the n-octanoll-water, hexadecanel-water and chloroforml-water partition coefficients of solutes. The calculated values of the examined parameters agreed well with their experimental counterparts. The model can find application in the accurate prediction of the effects of organic compounds on environments and the physicochemical properties of organic compounds by a full in-silico approach and can provide useful guidance for improving some properties of organic compounds.
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Affiliation(s)
- Deliang Chen
- Jiangxi Key Laboratory of Organo-Pharmaceutical Chemistry, Chemistry and Chemical Engineering College, Gannan Normal University, Ganzhou, Jiangxi, 341000, PR China.
| | - Qingyun Wang
- College of Mathematics and Computer Science, Gannan Normal University, Ganzhou, Jiangxi, 341000, PR China
| | - Yibao Li
- Jiangxi Key Laboratory of Organo-Pharmaceutical Chemistry, Chemistry and Chemical Engineering College, Gannan Normal University, Ganzhou, Jiangxi, 341000, PR China
| | - Yongdong Li
- Jiangxi Key Laboratory of Organo-Pharmaceutical Chemistry, Chemistry and Chemical Engineering College, Gannan Normal University, Ganzhou, Jiangxi, 341000, PR China
| | - Hui Zhou
- Jiangxi Key Laboratory of Organo-Pharmaceutical Chemistry, Chemistry and Chemical Engineering College, Gannan Normal University, Ganzhou, Jiangxi, 341000, PR China
| | - Yulan Fan
- Jiangxi Key Laboratory of Organo-Pharmaceutical Chemistry, Chemistry and Chemical Engineering College, Gannan Normal University, Ganzhou, Jiangxi, 341000, PR China.
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10
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Chen D, Zhao M, Tan W, Li Y, Li X, Li Y, Fan X. Effects of intramolecular hydrogen bonds on lipophilicity. Eur J Pharm Sci 2019; 130:100-106. [DOI: 10.1016/j.ejps.2019.01.020] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Revised: 01/08/2019] [Accepted: 01/18/2019] [Indexed: 12/22/2022]
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11
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Naylor MR, Ly AM, Handford MJ, Ramos DP, Pye CR, Furukawa A, Klein VG, Noland RP, Edmondson Q, Turmon AC, Hewitt WM, Schwochert J, Townsend CE, Kelly CN, Blanco MJ, Lokey RS. Lipophilic Permeability Efficiency Reconciles the Opposing Roles of Lipophilicity in Membrane Permeability and Aqueous Solubility. J Med Chem 2018; 61:11169-11182. [DOI: 10.1021/acs.jmedchem.8b01259] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Matthew R. Naylor
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - Andrew M. Ly
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - Mason J. Handford
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - Daniel P. Ramos
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - Cameron R. Pye
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - Akihiro Furukawa
- Modality Research Laboratories, Daiichi Sankyo Company, Ltd., 1-2-58 Hiromachi, Shingawa-ku, Tokyo 140-8710, Japan
| | - Victoria G. Klein
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - Ryan P. Noland
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - Quinn Edmondson
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - Alexandra C. Turmon
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - William M. Hewitt
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - Joshua Schwochert
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - Chad E. Townsend
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - Colin N. Kelly
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
| | - Maria-Jesus Blanco
- Sage Therapeutics, 215 First Street, Suite 220, Cambridge, Massachusetts 02142, United States
| | - R. Scott Lokey
- Department of Chemistry and Biochemistry, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, United States
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12
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Yu HS, Watson MA, Bochevarov AD. Weighted Averaging Scheme and Local Atomic Descriptor for pK a Prediction Based on Density Functional Theory. J Chem Inf Model 2018; 58:271-286. [PMID: 29356524 DOI: 10.1021/acs.jcim.7b00537] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
As a continuation of our work on developing a density functional theory-based pKa predictor, we present conceptual improvements to our previously published shell model, which is a hierarchical organization of pKa training sets and which, in principle, covers all chemical space. The improvements concern the way the studied chemical compound is associated with the data points from the training sets. By introducing a new descriptor of the local atomic environment which foregoes dependence on chemical bonding and connectivity, we are able to automatically locate molecules from the training set that are most relevant to the proton dissociation equilibrium under study. This new scheme leads to the prediction of a single pKa value weighted across multiple training sets and thus patches a defect disclosed in the formulation of our previous model. Using the new parametrization approach, the pKa prediction gets rid of outliers reported in previous applications of our approach, eliminates ambiguity in interpreting the results, and improves the overall accuracy. Our new treatment accounts for multiple conformations both on the level of energetics and parametrization. Illustrative results are shown for several types of chemical structures containing guanidine, amidine, amine, and phenol functional groups, and which are representative of practically important large and flexible drug-like molecules. Our method's performance is compared to the performance of other previously published pKa prediction methods. Further possible improvements to the organization of the training sets and the potential application of our new local atomic descriptor to other kinds of parametrizations are discussed.
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Affiliation(s)
- Haoyu S Yu
- Schrödinger, Inc. , 120 West 45th St., New York, New York 10036, United States
| | - Mark A Watson
- Schrödinger, Inc. , 120 West 45th St., New York, New York 10036, United States
| | - Art D Bochevarov
- Schrödinger, Inc. , 120 West 45th St., New York, New York 10036, United States
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13
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Dearden JC. The History and Development of Quantitative Structure-Activity Relationships (QSARs). ACTA ACUST UNITED AC 2017. [DOI: 10.4018/ijqspr.2017070104] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Following the publication of the history and development of QSAR, it became apparent that a number of matters had not been covered. This addendum is an attempt to rectify that. A very early approach (ca. 60 B.C.) by Lucretius shows that he understood how molecular size and complexity affect liquid viscosity. Comments by Kant (1724-1804) emphasized the necessity of mathematics in science. A claim that the work of von Bibra and Harless in 1847 pre-dated that of Overton and H.H. Meyer is shown not to be correct. K.H. Meyer and Gottlieb-Billroth published in 1920 what is probably the first QSAR equation. Brown, who with his co-author Fraser is credited with the first definitive recognition in 1868-9 that biological activity is a function of molecular structure, is often cited as Crum Brown; in fact, Crum was his second given name. The QSAR work of the Soviet chemist N.V. Lazarev in the 1940s was far ahead of his time, showing numerous correlations of biological activities and physicochemical properties with molecular descriptors. The subject of inverse QSAR is discussed.
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Affiliation(s)
- John C. Dearden
- School of Pharmacy & Biomolecular Sciences, Liverpool John Moores University, Liverpool, UK
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14
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Borges NM, Kenny PW, Montanari CA, Prokopczyk IM, Ribeiro JFR, Rocha JR, Sartori GR. The influence of hydrogen bonding on partition coefficients. J Comput Aided Mol Des 2017; 31:163-181. [PMID: 28054187 DOI: 10.1007/s10822-016-0002-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 12/16/2016] [Indexed: 11/28/2022]
Abstract
This Perspective explores how consideration of hydrogen bonding can be used to both predict and better understand partition coefficients. It is shown how polarity of both compounds and substructures can be estimated from measured alkane/water partition coefficients. When polarity is defined in this manner, hydrogen bond donors are typically less polar than hydrogen bond acceptors. Analysis of alkane/water partition coefficients in conjunction with molecular electrostatic potential calculations suggests that aromatic chloro substituents may be less lipophilic than is generally believed and that some of the effect of chloro-substitution stems from making the aromatic π-cloud less available to hydrogen bond donors. Relationships between polarity and calculated hydrogen bond basicity are derived for aromatic nitrogen and carbonyl oxygen. Aligned hydrogen bond acceptors appear to present special challenges for prediction of alkane/water partition coefficients and this may reflect 'frustration' of solvation resulting from overlapping hydration spheres. It is also shown how calculated hydrogen bond basicity can be used to model the effect of aromatic aza-substitution on octanol/water partition coefficients.
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Affiliation(s)
- Nádia Melo Borges
- Grupo de Estudos em Química Medicinal - NEQUIMED, Instituto de Química de São Carlos - Universidade de São Paulo, Av. Trabalhador Sancarlense, 400, São Carlos, SP, 13566-590, Brazil
| | - Peter W Kenny
- Grupo de Estudos em Química Medicinal - NEQUIMED, Instituto de Química de São Carlos - Universidade de São Paulo, Av. Trabalhador Sancarlense, 400, São Carlos, SP, 13566-590, Brazil.
| | - Carlos A Montanari
- Grupo de Estudos em Química Medicinal - NEQUIMED, Instituto de Química de São Carlos - Universidade de São Paulo, Av. Trabalhador Sancarlense, 400, São Carlos, SP, 13566-590, Brazil
| | - Igor M Prokopczyk
- Grupo de Estudos em Química Medicinal - NEQUIMED, Instituto de Química de São Carlos - Universidade de São Paulo, Av. Trabalhador Sancarlense, 400, São Carlos, SP, 13566-590, Brazil
| | - Jean F R Ribeiro
- Grupo de Estudos em Química Medicinal - NEQUIMED, Instituto de Química de São Carlos - Universidade de São Paulo, Av. Trabalhador Sancarlense, 400, São Carlos, SP, 13566-590, Brazil
| | - Josmar R Rocha
- Grupo de Estudos em Química Medicinal - NEQUIMED, Instituto de Química de São Carlos - Universidade de São Paulo, Av. Trabalhador Sancarlense, 400, São Carlos, SP, 13566-590, Brazil
| | - Geraldo Rodrigues Sartori
- Grupo de Estudos em Química Medicinal - NEQUIMED, Instituto de Química de São Carlos - Universidade de São Paulo, Av. Trabalhador Sancarlense, 400, São Carlos, SP, 13566-590, Brazil
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15
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Extended solvent-contact model approach to blind SAMPL5 prediction challenge for the distribution coefficients of drug-like molecules. J Comput Aided Mol Des 2016; 30:1019-1033. [PMID: 27448686 DOI: 10.1007/s10822-016-9928-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 07/20/2016] [Indexed: 01/28/2023]
Abstract
The performance of the extended solvent-contact model has been addressed in the SAMPL5 blind prediction challenge for distribution coefficient (LogD) of drug-like molecules with respect to the cyclohexane/water partitioning system. All the atomic parameters defined for 41 atom types in the solvation free energy function were optimized by operating a standard genetic algorithm with respect to water and cyclohexane solvents. In the parameterizations for cyclohexane, the experimental solvation free energy (ΔG sol ) data of 15 molecules for 1-octanol were combined with those of 77 molecules for cyclohexane to construct a training set because ΔG sol values of the former were unavailable for cyclohexane in publicly accessible databases. Using this hybrid training set, we established the LogD prediction model with the correlation coefficient (R), average error (AE), and root mean square error (RMSE) of 0.55, 1.53, and 3.03, respectively, for the comparison of experimental and computational results for 53 SAMPL5 molecules. The modest accuracy in LogD prediction could be attributed to the incomplete optimization of atomic solvation parameters for cyclohexane. With respect to 31 SAMPL5 molecules containing the atom types for which experimental reference data for ΔG sol were available for both water and cyclohexane, the accuracy in LogD prediction increased remarkably with the R, AE, and RMSE values of 0.82, 0.89, and 1.60, respectively. This significant enhancement in performance stemmed from the better optimization of atomic solvation parameters by limiting the element of training set to the molecules with experimental ΔG sol data for cyclohexane. Due to the simplicity in model building and to low computational cost for parameterizations, the extended solvent-contact model is anticipated to serve as a valuable computational tool for LogD prediction upon the enrichment of experimental ΔG sol data for organic solvents.
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16
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Santoro AL, Carrilho E, Lanças FM, Montanari CA. Quantitative structure–retention relationships of flavonoids unraveled by immobilized artificial membrane chromatography. Eur J Pharm Sci 2016; 88:147-57. [DOI: 10.1016/j.ejps.2015.12.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Revised: 11/09/2015] [Accepted: 12/06/2015] [Indexed: 01/27/2023]
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17
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Chen D, Oezguen N, Urvil P, Ferguson C, Dann SM, Savidge TC. Regulation of protein-ligand binding affinity by hydrogen bond pairing. SCIENCE ADVANCES 2016; 2:e1501240. [PMID: 27051863 PMCID: PMC4820369 DOI: 10.1126/sciadv.1501240] [Citation(s) in RCA: 349] [Impact Index Per Article: 43.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 02/05/2016] [Indexed: 05/20/2023]
Abstract
Hydrogen (H)-bonds potentiate diverse cellular functions by facilitating molecular interactions. The mechanism and the extent to which H-bonds regulate molecular interactions are a largely unresolved problem in biology because the H-bonding process continuously competes with bulk water. This interference may significantly alter our understanding of molecular function, for example, in the elucidation of the origin of enzymatic catalytic power. We advance this concept by showing that H-bonds regulate molecular interactions via a hitherto unappreciated donor-acceptor pairing mechanism that minimizes competition with water. On the basis of theoretical and experimental correlations between H-bond pairings and their effects on ligand binding affinity, we demonstrate that H-bonds enhance receptor-ligand interactions when both the donor and acceptor have either significantly stronger or significantly weaker H-bonding capabilities than the hydrogen and oxygen atoms in water. By contrast, mixed strong-weak H-bond pairings decrease ligand binding affinity due to interference with bulk water, offering mechanistic insight into why indiscriminate strengthening of receptor-ligand H-bonds correlates poorly with experimental binding affinity. Further support for the H-bond pairing principle is provided by the discovery and optimization of lead compounds targeting dietary melamine and Clostridium difficile toxins, which are not realized by traditional drug design methods. Synergistic H-bond pairings have therefore evolved in the natural design of high-affinity binding and provide a new conceptual framework to evaluate the H-bonding process in biological systems. Our findings may also guide wider applications of competing H-bond pairings in lead compound design and in determining the origin of enzymatic catalytic power.
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Affiliation(s)
- Deliang Chen
- Key Laboratory of Organo-Pharmaceutical Chemistry of Jiangxi Province, Chemistry and Chemical Engineering College, Gannan Normal University, Ganzhou, Jiangxi 341000, P. R. China
| | - Numan Oezguen
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX 77030, USA
- Texas Children’s Microbiome Center, Texas Children’s Hospital, Houston, TX 77030, USA
| | - Petri Urvil
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX 77030, USA
- Texas Children’s Microbiome Center, Texas Children’s Hospital, Houston, TX 77030, USA
| | | | - Sara M. Dann
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Tor C. Savidge
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX 77030, USA
- Texas Children’s Microbiome Center, Texas Children’s Hospital, Houston, TX 77030, USA
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18
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Jensen DA, Gary RK. Estimation of alkane–water logP for neutral, acidic, and basic compounds using an alkylated polystyrene-divinylbenzene high-performance liquid chromatography column. J Chromatogr A 2015; 1417:21-9. [DOI: 10.1016/j.chroma.2015.09.020] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2015] [Revised: 09/05/2015] [Accepted: 09/07/2015] [Indexed: 12/30/2022]
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19
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Magenau AJD, Richards JA, Pasquinelli MA, Savin DA, Mathers RT. Systematic Insights from Medicinal Chemistry To Discern the Nature of Polymer Hydrophobicity. Macromolecules 2015. [DOI: 10.1021/acs.macromol.5b01758] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Andrew J. D. Magenau
- Materials
Science and Engineering, Drexel University, Philadelphia, Pennsylvania 19104, United States
| | - Jeffrey A. Richards
- Department
of Chemistry, Pennsylvania State University, New Kensington, Pennsylvania 15068, United States
| | - Melissa A. Pasquinelli
- Fiber
and Polymer Science Program, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Daniel A. Savin
- Department
of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Robert T. Mathers
- Department
of Chemistry, Pennsylvania State University, New Kensington, Pennsylvania 15068, United States
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20
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Kim T, Park H. Computational prediction of octanol–water partition coefficient based on the extended solvent-contact model. J Mol Graph Model 2015; 60:108-17. [DOI: 10.1016/j.jmgm.2015.06.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Revised: 06/09/2015] [Accepted: 06/10/2015] [Indexed: 01/10/2023]
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21
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Mead B, Morgan H, Mann-Knowlton A, Tedeschi L, Sloan C, Lang S, Hines C, Gragg M, Stofer J, Riemann K, Derr T, Heller E, Collins D, Landis P, Linna N, Jones D. Reveromycin A-Induced Apoptosis in Osteoclasts Is Not Accompanied by Necrosis. J Cell Biochem 2015; 116:1646-57. [DOI: 10.1002/jcb.25125] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Accepted: 02/02/2015] [Indexed: 12/23/2022]
Affiliation(s)
- Brittany Mead
- Division of Natural Sciences; Department of Biology; Indiana Wesleyan University; South Washington Street Marion Indiana
| | - Heather Morgan
- Division of Natural Sciences; Department of Biology; Indiana Wesleyan University; South Washington Street Marion Indiana
| | - Alyssa Mann-Knowlton
- Division of Natural Sciences; Department of Biology; Indiana Wesleyan University; South Washington Street Marion Indiana
| | - Laura Tedeschi
- Division of Natural Sciences; Department of Biology; Indiana Wesleyan University; South Washington Street Marion Indiana
| | - Chris Sloan
- Division of Natural Sciences; Department of Biology; Indiana Wesleyan University; South Washington Street Marion Indiana
| | - Spenser Lang
- Division of Natural Sciences; Department of Biology; Indiana Wesleyan University; South Washington Street Marion Indiana
| | - Cory Hines
- Division of Natural Sciences; Department of Biology; Indiana Wesleyan University; South Washington Street Marion Indiana
| | - Megan Gragg
- Division of Natural Sciences; Department of Biology; Indiana Wesleyan University; South Washington Street Marion Indiana
| | - Jonathan Stofer
- Division of Natural Sciences; Department of Biology; Indiana Wesleyan University; South Washington Street Marion Indiana
| | - Kaitlin Riemann
- Division of Natural Sciences; Department of Biology; Indiana Wesleyan University; South Washington Street Marion Indiana
| | - Tyler Derr
- Division of Natural Sciences; Department of Biology; Indiana Wesleyan University; South Washington Street Marion Indiana
| | - Emily Heller
- Division of Natural Sciences; Department of Biology; Indiana Wesleyan University; South Washington Street Marion Indiana
| | - David Collins
- Division of Natural Sciences; Department of Biology; Indiana Wesleyan University; South Washington Street Marion Indiana
| | - Paul Landis
- Division of Natural Sciences; Department of Biology; Indiana Wesleyan University; South Washington Street Marion Indiana
| | - Nathan Linna
- Division of Natural Sciences; Department of Biology; Indiana Wesleyan University; South Washington Street Marion Indiana
| | - Daniel Jones
- Division of Natural Sciences; Department of Biology; Indiana Wesleyan University; South Washington Street Marion Indiana
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22
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Ligand efficiency metrics considered harmful. J Comput Aided Mol Des 2014; 28:699-710. [DOI: 10.1007/s10822-014-9757-8] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Accepted: 05/26/2014] [Indexed: 10/25/2022]
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23
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The Block Relevance (BR) analysis supports the dominating effect of solutes hydrogen bond acidity on ΔlogPoct–tol. Eur J Pharm Sci 2014; 53:50-4. [DOI: 10.1016/j.ejps.2013.12.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Revised: 11/15/2013] [Accepted: 12/09/2013] [Indexed: 01/24/2023]
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24
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Feng H, Ding Y, Wang M, Zhou G, Zheng X, He H, Zhang X, Shen D, Shentu J. Where are signal molecules likely to be located in anaerobic granular sludge? WATER RESEARCH 2014; 50:1-9. [PMID: 24355329 DOI: 10.1016/j.watres.2013.11.021] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2013] [Revised: 09/30/2013] [Accepted: 11/18/2013] [Indexed: 06/03/2023]
Abstract
Quorum sensing is a concentration-sensing mechanism that plays a vital role in sludge granulation. In this study, the regularities of distribution of different signal molecules, including intra- and interspecific signal molecules (diffusible signal factor, DSF), interspecific signal molecules (autoinducter-2, AI-2) and intraspecific signal molecules (acyl-homoserine lactones, AHLs), from three types of anaerobic granular sludge were investigated. The results showed that 70-90% of DSF was distributed in sludge, while AI-2 in the Water phase accounted for over 80% of the total content. Interestingly, there was a positive correlation between DSF and AI-2, which played opposite roles in granulation. Moreover, more than 55% of short and medium acyl chain AHLs tended to spread in aqueous water, while the long acyl chain AHLs were closer to granular sludge than the short and medium acyl chain AHLs. With the exception of one type of sludge, the percentage of long acyl chain AHLs in the sludge phase was greater than 70%. The different distributions of signal molecules were primarily determined based on their physicochemical properties, including molecular weight and solubility in water or organic solutions. In addition, the basic properties of sludge, such as the granular level or the production of EPS, were closely related to the diversity, distribution and concentration of signal molecules. As a medium in granulation, extracellular polymeric substances production was regulated by different signal molecules from different parts of anaerobic granular sludge. This study provides a foundation for investigation of quorum sensing in the system of anaerobic granular sludge.
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Affiliation(s)
- Huajun Feng
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310012, China; Zhejiang Provincial Key Laboratory of Solid Waste Treatment and Recycling, Hangzhou 310012, China
| | - Yangcheng Ding
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310012, China; Zhejiang Provincial Key Laboratory of Solid Waste Treatment and Recycling, Hangzhou 310012, China
| | - Meizhen Wang
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310012, China; Zhejiang Provincial Key Laboratory of Solid Waste Treatment and Recycling, Hangzhou 310012, China
| | - Guanglan Zhou
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310012, China
| | - Xin Zheng
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310012, China; Zhejiang Provincial Key Laboratory of Solid Waste Treatment and Recycling, Hangzhou 310012, China
| | - Hongzhen He
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310012, China; Zhejiang Provincial Key Laboratory of Solid Waste Treatment and Recycling, Hangzhou 310012, China
| | - Xueqin Zhang
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310012, China; Zhejiang Provincial Key Laboratory of Solid Waste Treatment and Recycling, Hangzhou 310012, China
| | - Dongsheng Shen
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310012, China; Zhejiang Provincial Key Laboratory of Solid Waste Treatment and Recycling, Hangzhou 310012, China
| | - Jiali Shentu
- School of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310012, China; Zhejiang Provincial Key Laboratory of Solid Waste Treatment and Recycling, Hangzhou 310012, China.
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