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Aleksandrova YI, Shurpik DN, Nazmutdinova VA, Zelenikhin PV, Subakaeva EV, Sokolova EA, Leonteva YO, Mironova AV, Kayumov AR, Petrovskii VS, Potemkin II, Stoikov II. Antibacterial Activity of Various Morphologies of Films Based on Guanidine Derivatives of Pillar[5]arene: Influence of the Nature of One Substitute on Self-assembly. ACS APPLIED MATERIALS & INTERFACES 2024; 16:17163-17181. [PMID: 38530408 DOI: 10.1021/acsami.3c18610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/28/2024]
Abstract
The progress of the pillar[5]arene chemistry allowed us to set out a new concept on application of the supramolecular assemblies to create antimicrobial films with variable surface morphologies and biological activities. Antibacterial films were derived from the substituted pillar[5]arenes containing nine pharmacophoric guanidine fragments and one thioalkyl substituent. Changing the only thioalkyl fragment in the macrocycle structure made it possible to control the biological activity of the resulting antibacterial coating. Pretreatment of the surface with aqueous solution of the amphiphilic pillar[5]arenes reduced the biofilm thickness by 56 ± 10% of Gram-positive Staphylococcus aureus in the case of the pillar[5]arene containing a thiooctyl fragment and by 52 ± 7% for the biofilm of Gram-negative Klebsiella pneumoniae in the case of pillar[5]arene containing a thiooctadecyl fragment. Meanwhile, the cytotoxicity of the synthesized macrocycles was examined at a concentration of 50 μg/mL, which was significantly lower than that of bis-guanidine-based antimicrobial preparations.
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Affiliation(s)
- Yulia I Aleksandrova
- A. M. Butlerov Chemistry Institute, Kazan Federal University, 420008 Kremlevskaya Street, 18, Kazan, Russian Federation
| | - Dmitriy N Shurpik
- A. M. Butlerov Chemistry Institute, Kazan Federal University, 420008 Kremlevskaya Street, 18, Kazan, Russian Federation
| | - Viktoriya A Nazmutdinova
- A. M. Butlerov Chemistry Institute, Kazan Federal University, 420008 Kremlevskaya Street, 18, Kazan, Russian Federation
| | - Pavel V Zelenikhin
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kremlevskaya, 18, Kazan, Russian Federation
| | - Evgeniya V Subakaeva
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kremlevskaya, 18, Kazan, Russian Federation
| | - Evgeniya A Sokolova
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kremlevskaya, 18, Kazan, Russian Federation
| | - Yulia O Leonteva
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kremlevskaya, 18, Kazan, Russian Federation
| | - Anna V Mironova
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kremlevskaya, 18, Kazan, Russian Federation
| | - Airat R Kayumov
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kremlevskaya, 18, Kazan, Russian Federation
| | - Vladislav S Petrovskii
- Physics Department, M. V. Lomonosov Moscow State University, Leninskie Gory 1-2, 119991 Moscow, Russian Federation
- N. N. Semenov Federal Research Center of Chemical Physics of Russian Academy of Sciences, Kosygina 4, 119991 Moscow, Russian Federation
| | - Igor I Potemkin
- Physics Department, M. V. Lomonosov Moscow State University, Leninskie Gory 1-2, 119991 Moscow, Russian Federation
| | - Ivan I Stoikov
- A. M. Butlerov Chemistry Institute, Kazan Federal University, 420008 Kremlevskaya Street, 18, Kazan, Russian Federation
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2
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Ma N, Liu Y, Ling G, Zhang P. Preparation of meloxicam-salicylic acid co-crystal and its application in the treatment of rheumatoid arthritis. J Drug Deliv Sci Technol 2022. [DOI: 10.1016/j.jddst.2022.103542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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3
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Masłowska K, Witkowska E, Tymecka D, Halik PK, Misicka A, Gniazdowska E. Synthesis, Physicochemical and Biological Study of Gallium-68- and Lutetium-177-Labeled VEGF-A 165/NRP-1 Complex Inhibitors Based on Peptide A7R and Branched Peptidomimetic. Pharmaceutics 2022; 14:pharmaceutics14010100. [PMID: 35056995 PMCID: PMC8779334 DOI: 10.3390/pharmaceutics14010100] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 12/22/2021] [Accepted: 12/28/2021] [Indexed: 02/01/2023] Open
Abstract
Neuropilin-1 (NRP-1) is a surface receptor found on many types of cancer cells. The overexpression of NRP-1 and its interaction with vascular endothelial growth factor-165 (VEGF165) are associated with tumor growth and metastasis. Therefore, compounds that block the VEGF165/NRP-1 interaction represent a promising strategy to image and treat NRP-1-related pathologies. The aim of the presented work was to design and synthesize radioconjugates of two known peptide-type inhibitors of the VEGF165/NRP-1 complex: A7R peptide and its shorter analog, the branched peptidomimetic Lys(hArg)-Dab-Pro-Arg. Both peptide-type inhibitors were coupled to a radionuclide chelator (DOTA) via a linker (Ahx) and so radiolabeled with Ga-68 and Lu-177 radionuclides, for diagnostic and therapeutic uses, respectively. The synthesized radioconjugates were tested for their possible use as theranostic-like radiopharmaceuticals for the imaging and therapy of cancers that overexpress NRP-1. The obtained results indicate good efficiency of the radiolabeling reaction and satisfactory stability, at least 3t1/2 for the 68Ga- and 1t1/2 for the 177Lu-radiocompounds, in solutions mimicking human body fluids. However, enzymatic degradation of both the studied inhibitors caused insufficient stability of the radiocompounds in human serum, indicating that further modifications are needed to sufficiently stabilize the peptidomimetics with inhibitory properties against VEGF165/NRP-1 complex formation.
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Affiliation(s)
- Katarzyna Masłowska
- Centre of Radiochemistry and Nuclear Chemistry, Institute of Nuclear Chemistry and Technology, Dorodna 16, 03-195 Warsaw, Poland; (P.K.H.); (E.G.)
- Correspondence: (K.M.); (A.M.)
| | - Ewa Witkowska
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland; (E.W.); (D.T.)
| | - Dagmara Tymecka
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland; (E.W.); (D.T.)
| | - Paweł Krzysztof Halik
- Centre of Radiochemistry and Nuclear Chemistry, Institute of Nuclear Chemistry and Technology, Dorodna 16, 03-195 Warsaw, Poland; (P.K.H.); (E.G.)
| | - Aleksandra Misicka
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland; (E.W.); (D.T.)
- Correspondence: (K.M.); (A.M.)
| | - Ewa Gniazdowska
- Centre of Radiochemistry and Nuclear Chemistry, Institute of Nuclear Chemistry and Technology, Dorodna 16, 03-195 Warsaw, Poland; (P.K.H.); (E.G.)
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Barratt MD, Castell JV, Chamberlain M, Combes RD, Dearden JC, Fentem JH, Gerner I, Giuliani A, Gray TJ, Livingstone DJ, Provan WM, Rutten FA, Verhaar HJ, Zbinden P. The Integrated Use of Alternative Approaches for Predicting Toxic Hazard. Altern Lab Anim 2020. [DOI: 10.1177/026119299502300315] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Affiliation(s)
- Martin D. Barratt
- Environmental Safety Laboratory, Unilever Research, Colworth House, Sharnbrook, Bedford MK44 1LQ, UK
| | - Jose V. Castell
- Unidad de Hepatologia Experimental, Hospital Universitario La Fe, Avda de Campanar 21, 46009 Valencia, Spain
| | - Mark Chamberlain
- Environmental Safety Laboratory, Unilever Research, Colworth House, Sharnbrook, Bedford MK44 1LQ, UK
| | - Robert D. Combes
- FRAME, Russell & Burch House, 96–98 North Sherwood Street, Nottingham NG1 4EE, UK
| | - John C. Dearden
- School of Pharmacy, Liverpool John Moores University, Byrom Street, Liverpool L3 3AF, UK
| | | | - Ingrid Gerner
- Bundesinstitut für gesundheitlichen Verbraucherschutz und Veterinärmedizin (BgVV), Thielallee 88–92, 14195 Berlin, Germany
| | - Alessandro Giuliani
- Istituto di Ricerca sulla Senescenza, Sigma-Tau, Via Pontina, km 30.400, 00040 Pomezia, Italy
| | - Tim J.B. Gray
- Sanofi Research Division, Alnwick Research Centre, Alnwick, Northumberland NE66 2 JH, UK
| | - David J. Livingstone
- ChemQuest, Cheyney House, 19–21 Cheyney Street, Steeple Morden, Herts. SG8 OLP, UK
| | - W. McLean Provan
- ZENECA Central Toxicology Laboratory, A Iderley Park, Macclesfield, Cheshire SK10 4TJ, UK
| | - Fons A.J.J.L. Rutten
- TNO Nutrition and Food Research Institute, Division of Toxicology, P.O. Box 360, 3700 AJ Zeist, The Netherlands
| | - Henk J.M. Verhaar
- Research Institute of Toxicology (RITOX), Utrecht University, P.O. Box 80.176, Yalelaan 2, 3508 TD Utrecht, The Netherlands
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The wide-spectrum antimicrobial effect of novel N-alkyl monoquaternary ammonium salts and their mixtures; the QSAR study against bacteria. Eur J Med Chem 2020; 206:112584. [PMID: 32853858 DOI: 10.1016/j.ejmech.2020.112584] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 05/05/2020] [Accepted: 06/14/2020] [Indexed: 11/23/2022]
Abstract
Quaternary ammonium salts (QASs) have been widely used for disinfection purposes because of their low price, high efficacy and low human toxicity for decades. However, precise mechanisms of action nor the powerful versatile agent against all antimicrobial species are known. In this study we have prepared 43 novel N-alkyl monoquaternary ammonium salts including 7 N,N-dialkyl monoquaternary ammonium salts differing bearing alkyl chain either of 12, 14 or 16 carbons. Together with 15 already published QASs we have studied the antimicrobial efficacy of all water-soluble compounds together with standard benzalkonium salts against Gram-positive (G+) and Gram-negative (G-) bacteria, anaerobic spore-forming Cl. difficile, yeasts, filamentous fungi and enveloped Varicella zoster virus (VZV). To address the mechanism of action, lipophilicity seems to be a key parameter which determines antimicrobial efficacy, however, exceptions are likely to occur and therefore QSAR analysis on the efficacy against G+ and G- bacteria was applied. We showed that antibacterial activity is higher when the molecule is larger, more lipophilic, less polar, and contains fewer oxygen atoms, fewer methyl groups bound to heteroatoms or fewer hydrogen atoms bound to polarized carbon atoms. In addition, from an application point of view, we have formulated mixtures, on the basis of obtained efficiency of individual compounds, in order to receive wide-spectrum agent. All formulated mixtures completely eradicated tested G+ and G- strains, including the multidrug-resistant P. aeruginosa as well as in case of yeasts. However, effect on A. fumigatus, Cl. difficile and VZV the exposition towards mixture resulted in significant reduction only. Finally, 3 out of 4 formulated mixtures were safer than reference commercial agent based on benzalkonium salts only in the skin irritation test using reconstructed human epidermidis.
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Synthesis of New Oxindoles and Determination of Their Antibacterial Properties. HETEROATOM CHEMISTRY 2020. [DOI: 10.1155/2020/8021920] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
A versatile method for the synthesis of new oxindoles was developed by the reaction between substituted isatins and 5-aminopyrazoles. The reaction was carried out at room temperature in ethanol using p-toluenesulfonic acid as the catalyst. The products were obtained with acceptable to excellent yields (44–96%). Structures of the new compounds were unambiguously established by spectroscopic and analytical techniques. The antibacterial activity was determined by microdilution assays. Compounds 3b, 3e, and 3g showed antistaphylococcal activity, particularly compound 3e displayed a potent activity against the vancomycin intermediate Staphylococcus aureus (VISA). Compounds 3i, 3j, and 3o inhibited Neisseria gonorrhoeae growth.
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Caroline, Foe K, Yesery Esar S, Soewandi A, Wihadmadyatami H, Widharna RM, Tamayanti WD, Kasih E, Tjahjono Y. Evaluation of analgesic and antiplatelet activity of 2-((3-(chloromethyl)benzoyl)oxy)benzoic acid. Prostaglandins Other Lipid Mediat 2019; 145:106364. [PMID: 31356853 DOI: 10.1016/j.prostaglandins.2019.106364] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 07/11/2019] [Accepted: 07/12/2019] [Indexed: 02/07/2023]
Abstract
Acetylsalicylic acid is used as a non-steroidal anti-inflammatory drugs (NSAID) and antiplatelet agents by inhibiting cyclooxygenases. However, therapy using acetylsalicylic acid could induce gastric bleeding and cause other gastrointestinal toxicity. The aim of this study was to demonstrate the synthesis of a new compound bearing salicylic acid residue namely 2-((3-(chloromethyl)benzoyl)oxy)benzoic acid, to analyze its potential as a ligand for human cyclooxygenase-2 (COX-2) receptor, to evaluate its toxicity level and its effectiveness for analgesic and antiplatelet agent compared with acetylsalicylic acid. Synthesis of 2-((3-(chloromethyl)benzoyl)oxy)benzoic acid was conducted by microwave irradiation. The purity of this compound was evaluated with TLC, IR, NMR, and EDS spectroscopy. The chemical characterization and docking studies against human COX-2 (PDB:5F1A) was performed in-silico. The acute oral toxicity assay was performed under OECD guidelines. The analgesic activity study was performed by plantar and writhing test on animal model. For anti-platelet activity study, we performed tail-bleeding assay and flow cytometry based platelet aggregation assay. We could successfully synthesize a pure white crystalline 2-((3-(chloromethyl)benzoyl)oxy)benzoic acid. In-Silico G-Score result of those compounds gives us preliminary hint of the potential affinity of this compound as a ligand for COX-2 receptor (PDB: 5F1A). Acute toxicity and microscopic gastrointestinal assessments indicated non-observable harmful toxicity parameters. The plantar response time of 2-((3-(chloromethyl)benzoyl)oxy)benzoic acid treated groups showed a significant increment (P < 0.01), and the nociceptive response in writhing test demonstrated a significant dose-dependent decrement. This indicated that its analgesic activity was better than acetylsalicylic acid. The platelet aggregation of 2-((3-(chloromethyl)benzoyl)oxy)benzoic acid was lower than its controls, indicating an aggregation inhibition pattern. The animals treated with 2-((3-(chloromethyl)benzoyl)oxy)benzoic acid gave a longer bleeding time. Overall, this study demonstrated a successful synthesis of pure 2-((3-(chloromethyl)benzoyl)oxy) benzoic acid. We postulated that this compound was better than acetylsalicylic acid, exhibiting excellent analgesic and antiplatelet activity with no toxicity impact.
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Affiliation(s)
- Caroline
- Faculty of Pharmacy, Widya Mandala Catholic University Surabaya, Jalan Kalisari Selatan 1, 60237 Surabaya, East Java, Indonesia
| | - Kuncoro Foe
- Faculty of Pharmacy, Widya Mandala Catholic University Surabaya, Jalan Kalisari Selatan 1, 60237 Surabaya, East Java, Indonesia
| | - Senny Yesery Esar
- Faculty of Pharmacy, Widya Mandala Catholic University Surabaya, Jalan Kalisari Selatan 1, 60237 Surabaya, East Java, Indonesia
| | - Ami Soewandi
- Faculty of Pharmacy, Widya Mandala Catholic University Surabaya, Jalan Kalisari Selatan 1, 60237 Surabaya, East Java, Indonesia
| | - Hevi Wihadmadyatami
- Faculty of Veterinary Science, Gadjah Mada University, Jalan Fauna 2, 55281 Sleman, Yogyakarta, Indonesia
| | - Ratna Megawati Widharna
- Faculty of Pharmacy, Widya Mandala Catholic University Surabaya, Jalan Kalisari Selatan 1, 60237 Surabaya, East Java, Indonesia
| | - Wahyu Dewi Tamayanti
- Faculty of Pharmacy, Widya Mandala Catholic University Surabaya, Jalan Kalisari Selatan 1, 60237 Surabaya, East Java, Indonesia
| | - Elisabeth Kasih
- Faculty of Pharmacy, Widya Mandala Catholic University Surabaya, Jalan Kalisari Selatan 1, 60237 Surabaya, East Java, Indonesia
| | - Yudy Tjahjono
- Faculty of Pharmacy, Widya Mandala Catholic University Surabaya, Jalan Kalisari Selatan 1, 60237 Surabaya, East Java, Indonesia.
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8
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Tsai MK, Lai CH, Chen LM, Jong GP. Calcium Channel Blocker-Related Chylous Ascites: A Systematic Review and Meta-Analysis. J Clin Med 2019; 8:jcm8040466. [PMID: 30959848 PMCID: PMC6518248 DOI: 10.3390/jcm8040466] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2019] [Revised: 03/27/2019] [Accepted: 04/03/2019] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Chylous ascites is an uncommon condition characterized by a white, milky-appearing peritoneal fluid, and is related to disruption of the lymphatic system from any cause. There have been very few previous reports of calcium channel blockers (CCBs) as potential causes of chylous ascites, and most of the patients were undergoing peritoneal dialysis. AIMS To review the pathogenesis, clinical manifestations, laboratory examinations, treatment options, and prognosis of patients with CCB-related chylous ascites. METHOD A retrospective analysis was conducted for patients with CCB-related chylous ascites from publications in PubMed, EMBASE, and LILACS between January 1993 and December 2018. RESULTS A total of 48 cases were included. The average age at disease onset was 50.2 ± 10.9 years, with a male:female ratio of 1.5:1.0. The symptoms of abdominal distension/pain and chylous ascites were observed within 48⁻72 h of drug initiation and disappeared within 24 h of drug withdrawal. Rechallenge was performed in 10 patients, and all (100%) of them showed chylous effluents that disappeared within 24 h after stopping drug treatment. CONCLUSIONS To summarize, CCB-related chylous ascites is formed of white, milky ascites/effluents that appear after administration of CCBs. Physicians must be aware of the possibility of chylous ascites when administering CCBs, particularly in patients with renal function impairment or patients with end-stage renal disease who are undergoing peritoneal dialysis.
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Affiliation(s)
- Meng-Ko Tsai
- Department of Internal Medicine, Taichung Armed Forces General Hospital, Taichung 41168, Taiwan.
- National Defense Medical Center, Taipei 11490, Taiwan.
| | - Chao-Hung Lai
- Department of Internal Medicine, Taichung Armed Forces General Hospital, Taichung 41168, Taiwan.
| | - Li-Mien Chen
- Department of Internal Medicine, Taichung Armed Forces General Hospital, Taichung 41168, Taiwan.
| | - Gwo-Ping Jong
- Department of Internal Medicine, Chung Shan Medical University Hospital and Chung Shan Medical University, Taichung 40201, Taiwan.
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Amidon GE, Anderson BD, Balthasar JP, Bergstrom CAS, Huang SM, Kasting G, Kesisoglou F, Khinast JG, Mager DE, Roberts CJ, Yu L. Fifty-Eight Years and Counting: High-Impact Publishing in Computational Pharmaceutical Sciences and Mechanism-Based Modeling. J Pharm Sci 2018; 108:2-7. [PMID: 30423338 DOI: 10.1016/j.xphs.2018.11.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 11/02/2018] [Indexed: 11/19/2022]
Abstract
With this issue of the Journal of Pharmaceutical Sciences, we celebrate the nearly 6 decades of contributions to mechanistic-based modeling and computational pharmaceutical sciences. Along with its predecessor, The Journal of the American Pharmaceutical Association: Scientific Edition first published in 1911, JPharmSci has been a leader in the advancement of pharmaceutical sciences beginning with its inaugural edition in 1961. As one of the first scientific journals focusing on pharmaceutical sciences, JPharmSci has established a reputation for publishing high-quality research articles using computational methods and mechanism-based modeling. The journal's publication record is remarkable. With over 15,000 articles, 3000 notes, and more than 650 reviews from industry, academia, and regulatory agencies around the world, JPharmSci has truly been the leader in advancing pharmaceutical sciences.
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Affiliation(s)
| | | | - Joseph P Balthasar
- University at Buffalo, State University of New York, Buffalo, New York 14260
| | | | - Shiew-Mei Huang
- Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland 20993
| | | | | | - Johannes G Khinast
- Institute for Process and Particle Engineering, Graz University of Technology, Graz, Austria
| | - Donald E Mager
- University at Buffalo, State University of New York, Buffalo, New York 14260
| | | | - Lian Yu
- University of Wisconsin, Madison, Wisconsin 53706
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Bak A, Kozik V, Malik I, Jampilek J, Smolinski A. Probability-driven 3D pharmacophore mapping of antimycobacterial potential of hybrid molecules combining phenylcarbamoyloxy and N-arylpiperazine fragments. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2018; 29:801-821. [PMID: 30230355 DOI: 10.1080/1062936x.2018.1517278] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2018] [Accepted: 08/25/2018] [Indexed: 06/08/2023]
Abstract
The current study examines in silico characterization of the structure-inhibitory potency for a set of phenylcarbamic acid derivatives containing an N-arylpiperazine scaffold, considering the electronic, steric and lipophilic properties. The main objective of the ligand-based modelling was the systematic study of classical comparative molecular field analysis (CoMFA)/comparative molecular surface analysis (CoMSA) performance for the modelling of in vitro efficiency observed for these phenylcarbamates, revealing their inhibitory activities against a virulent Mycobacterium tuberculosis H37Rv strain. We compared the findings of efficiency modelling produced by a standard 3D methodology (CoMFA) and its neural counterparts (CoMSA) regarding multiple training/test subsets and variables used. Moreover, systematic space inspection, splitting values into the analysed training/test subsets, was performed to monitor statistical estimator performance while mapping the probability-driven pharmacophore pattern. Consequently, a 'pseudo-consensus' 3D-quantitative structure-activity relationship (3D-QSAR) approach was applied to retrieve an 'average' pharmacophore hypothesis by the investigation of the most densely populated training/test subpopulations to specify the potentially important factors contributing to the inhibitory activity of phenylcarbamic acid analogues. In addition, examination of descriptor-based similarity with a principal component analysis (PCA) procedure was employed to visualize noticeable variations in the performance of these molecules with respect to their structure and activity profiles.
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Affiliation(s)
- A Bak
- a Department of Synthesis Chemistry , Institute of Chemistry, University of Silesia , Katowice , Poland
| | - V Kozik
- a Department of Synthesis Chemistry , Institute of Chemistry, University of Silesia , Katowice , Poland
| | - I Malik
- b Department of Pharmaceutical Chemistry, Faculty of Pharmacy , Comenius University , Bratislava , Slovakia
| | - J Jampilek
- b Department of Pharmaceutical Chemistry, Faculty of Pharmacy , Comenius University , Bratislava , Slovakia
| | - A Smolinski
- c Department of Energy Saving and Air Protection , Central Mining Institute , Katowice , Poland
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Malík I, Csöllei J, Solovič I, Pospíšilová Š, Michnová H, Jampílek J, Čížek A, Kapustíková I, Čurillová J, Pecháčová M, Stolaříková J, Pecher D, Oravec M. Dibasic Derivatives of Phenylcarbamic Acid against Mycobacterial Strains: Old Drugs and New Tricks? Molecules 2018; 23:E2493. [PMID: 30274224 PMCID: PMC6222509 DOI: 10.3390/molecules23102493] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 09/21/2018] [Accepted: 09/24/2018] [Indexed: 12/11/2022] Open
Abstract
In order to provide a more detailed view on the structure⁻antimycobacterial activity relationship (SAR) of phenylcarbamic acid derivatives containing two centers of protonation, 1-[2-[({[2-/3-(alkoxy)phenyl]amino}carbonyl)oxy]-3-(dipropylammonio)propyl]pyrrolidinium oxalates (1a⁻d)/dichlorides (1e⁻h) as well as 1-[2-[({[2-/3-(alkoxy)phenyl]amino}carbonyl)oxy]-3-(di-propylammonio)propyl]azepanium oxalates (1i⁻l)/dichlorides (1m⁻p; alkoxy = butoxy to heptyloxy) were physicochemically characterized by estimation of their surface tension (γ; Traube's stalagmometric method), electronic features (log ε; UV/Vis spectrophotometry) and lipophilic properties (log kw; isocratic RP-HPLC) as well. The experimental log kw dataset was studied together with computational logarithms of partition coefficients (log P) generated by various methods based mainly on atomic or combined atomic and fragmental principles. Similarities and differences between the experimental and in silico lipophilicity descriptors were analyzed by unscaled principal component analysis (PCA). The in vitro activity of compounds 1a⁻p was inspected against Mycobacterium tuberculosis CNCTC My 331/88 (identical with H37Rv and ATCC 2794, respectively), M. tuberculosis H37Ra ATCC 25177, M. kansasii CNCTC My 235/80 (identical with ATCC 12478), the M. kansasii 6509/96 clinical isolate, M. kansasii DSM 44162, M. avium CNCTC My 330/80 (identical with ATCC 25291), M. smegmatis ATCC 700084 and M. marinum CAMP 5644, respectively. In vitro susceptibility of the mycobacteria to reference drugs isoniazid, ethambutol, ofloxacin or ciprofloxacin was tested as well. A very unique aspect of the research was that many compounds from the set 1a⁻p were highly efficient almost against all tested mycobacteria. The most promising derivatives showed MIC values varied from 1.9 μM to 8 μM, which were lower compared to those of used standards, especially if concerning ability to fight M. tuberculosis H37Ra ATCC 25177, M. kansasii DSM 44162 or M. avium CNCTC My 330/80. Current in vitro biological assays and systematic SAR studies based on PCA approach as well as fitting procedures, which were supported by relevant statistical descriptors, proved that the compounds 1a⁻p represented a very promising molecular framework for development of 'non-traditional' but effective antimycobacterial agents.
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Affiliation(s)
- Ivan Malík
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Comenius University in Bratislava, Odbojárov 10, SK-832 32 Bratislava, Slovakia.
| | - Jozef Csöllei
- Department of Chemical Drugs, Faculty of Pharmacy, University of Veterinary and Pharmaceutical Sciences in Brno, Palackého 1946/1, CZ-612 42 Brno, Czech Republic.
| | - Ivan Solovič
- Clinic for Tuberculosis and Lung Diseases, National Institute for Tuberculosis, Lung Diseases and Thoracic Surgery, Vyšné Hágy, SK-059 84 Vysoké Tatry, Slovakia.
- Department of Public Health, Faculty of Health, Catholic University in Ružomberok, Hrabovská cesta 1A, SK-034 01 Ružomberok, Slovakia.
| | - Šárka Pospíšilová
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Comenius University in Bratislava, Odbojárov 10, SK-832 32 Bratislava, Slovakia.
| | - Hana Michnová
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Comenius University in Bratislava, Odbojárov 10, SK-832 32 Bratislava, Slovakia.
| | - Josef Jampílek
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Comenius University in Bratislava, Odbojárov 10, SK-832 32 Bratislava, Slovakia.
| | - Alois Čížek
- Clinic for Department of Infectious Diseases and Microbiology, Faculty of Veterinary Medicine, University of Veterinary and Pharmaceutical Sciences, Palackého 1946/1, CZ-612 42 Brno, Czech Republic.
| | - Iva Kapustíková
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Comenius University in Bratislava, Odbojárov 10, SK-832 32 Bratislava, Slovakia.
| | - Jana Čurillová
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Comenius University in Bratislava, Odbojárov 10, SK-832 32 Bratislava, Slovakia.
| | - Mária Pecháčová
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Comenius University in Bratislava, Odbojárov 10, SK-832 32 Bratislava, Slovakia.
| | - Jiřina Stolaříková
- Laboratory for Mycobacterial Diagnostics and Tuberculosis, Regional Institute of Public Health, Partyzánské náměstí 7, CZ-702 00 Ostrava, Czech Republic.
| | - Daniel Pecher
- Department of Pharmaceutical Analysis and Nuclear Pharmacy, Faculty of Pharmacy, Comenius University in Bratislava, Odbojárov 10, SK-832 32 Bratislava, Slovakia.
- Toxicological and Antidoping Center, Faculty of Pharmacy, Comenius University in Bratislava, Odbojárov 10, SK-832 32 Bratislava, Slovakia.
| | - Michal Oravec
- Global Change Research Institute CAS, Belidla 986/4a, CZ-603 00 Brno, Czech Republic.
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12
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Martin YC. How medicinal chemists learned about log P. J Comput Aided Mol Des 2018; 32:809-819. [PMID: 30019206 DOI: 10.1007/s10822-018-0127-9] [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: 03/21/2018] [Accepted: 06/14/2018] [Indexed: 11/24/2022]
Abstract
Although log P is now recognized to be a key factor that determines the bioactivity of a molecule, the focus of medicinal chemists on hydrophobicity and log P started with the quantitative structure-activity relationships (QSAR) publications of Hansch and Fujita. Their original publication represents a dramatic change of focus to incorporate consideration of log P after a decade of work unsuccessfully attempting to use the Hammett equation to explain the structure-activity relationships of plant growth regulators. QSAR allows one to explore the quantitative relationship between log P and biological activity even when other factors also influence potency. In particular, Hansch's publications of thousands of QSAR equations demonstrate that a relationship of biological activity with log P is indeed a general phenomenon. Hansch's group also provided data and tools that enable others to explore the relationship between log P and the biological activity of compounds of interest.
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Lambrinidis G, Tsantili-Kakoulidou A. Challenges with multi-objective QSAR in drug discovery. Expert Opin Drug Discov 2018; 13:851-859. [DOI: 10.1080/17460441.2018.1496079] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- George Lambrinidis
- Division of Pharmaceutical Chemistry, Department of Pharmacy, National and Kapodistrian University of Athens, Zografou, Athens, Greece
| | - Anna Tsantili-Kakoulidou
- Division of Pharmaceutical Chemistry, Department of Pharmacy, National and Kapodistrian University of Athens, Zografou, Athens, Greece
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Synthesis and In Vitro Antimycobacterial Activity of Novel N-Arylpiperazines Containing an Ethane-1,2-diyl Connecting Chain. Molecules 2017; 22:molecules22122100. [PMID: 29189762 PMCID: PMC6149664 DOI: 10.3390/molecules22122100] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 11/20/2017] [Accepted: 11/27/2017] [Indexed: 11/17/2022] Open
Abstract
Novel 1-(2-{3-/4-[(alkoxycarbonyl)amino]phenyl}-2-hydroxyethyl)-4-(2-fluorophenyl)-piperazin-1-ium chlorides (alkoxy = methoxy to butoxy; 8a-h) have been designed and synthesized through multistep reactions as a part of on-going research programme focused on finding new antimycobacterials. Lipophilic properties of these compounds were estimated by RP-HPLC using methanol/water mobile phases with a various volume fraction of the organic modifier. The log kw values, which were extrapolated from intercepts of a linear relationship between the logarithm of a retention factor k (log k) and volume fraction of a mobile phase modifier (ϕM), varied from 2.113 (compound 8e) to 2.930 (compound 8h) and indicated relatively high lipophilicity of these salts. Electronic properties of the molecules 8a-h were investigated by evaluation of their UV/Vis spectra. In a next phase of the research, the compounds 8a-h were in vitro screened against M. tuberculosis CNCTC My 331/88 (identical with H37Rv and ATCC 2794), M. kansasii CNCTC My 235/80 (identical with ATCC 12478), a M. kansasii 6 509/96 clinical isolate, M. avium CNCTC My 330/80 (identical with ATCC 25291) and M. avium intracellulare ATCC 13950, respectively, as well as against M. kansasii CIT11/06, M. avium subsp. paratuberculosis CIT03 and M. avium hominissuis CIT10/08 clinical isolates using isoniazid, ethambutol, ofloxacin, ciprofloxacin or pyrazinamide as reference drugs. The tested compounds 8a-h were found to be the most promising against M. tuberculosis; a MIC = 8 μM was observed for the most effective 1-(2-{4-[(butoxycarbonyl)amino]phen-ylphenyl}-2-hydroxyethyl)-4-(2-fluorophenyl)piperazin-1-ium chloride (8h). In addition, all of them showed low (insignificant) in vitro toxicity against a human monocytic leukemia THP-1 cell line, as observed LD50 values > 30 μM indicated. The structure-antimycobacterial activity relationships of the analyzed 8a-h series are also discussed.
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Pilipović A, Ajduković J, Đurendić E, Sakač M, Poša M. Importance of reversed-phase chromatographic parameters in predicting biopharmaceutical and pharmacokinetic descriptors on the group of androgen derivatives. Eur J Pharm Sci 2017; 106:166-176. [DOI: 10.1016/j.ejps.2017.05.058] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 05/08/2017] [Accepted: 05/25/2017] [Indexed: 01/01/2023]
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Yellapu NK, Kilaru RB, Chamarthi N, PVGK S, Matcha B. Structure based design, synthesis and biological evaluation of amino phosphonate derivatives as human glucokinase activators. Comput Biol Chem 2017; 68:118-130. [DOI: 10.1016/j.compbiolchem.2017.02.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 02/03/2017] [Indexed: 11/29/2022]
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Abstract
It is widely accepted that modern QSAR began in the early 1960s. However, as long ago as 1816 scientists were making predictions about physical and chemical properties. The first investigations into the correlation of biological activities with physicochemical properties such as molecular weight and aqueous solubility began in 1841, almost 60 years before the important work of Overton and Meyer linking aquatic toxicity to lipid-water partitioning. Throughout the 20th century QSAR progressed, though there were many lean years. In 1962 came the seminal work of Corwin Hansch and co-workers, which stimulated a huge interest in the prediction of biological activities. Initially that interest lay largely within medicinal chemistry and drug design, but in the 1970s and 1980s, with increasing ecotoxicological concerns, QSAR modelling of environmental toxicities began to grow, especially once regulatory authorities became involved. Since then QSAR has continued to expand, with over 1400 publications annually from 2011 onwards.
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Pan S, Gupta AK, Subramanian V, Chattaraj PK. Quantitative Structure-Activity/Property/Toxicity Relationships through Conceptual Density Functional Theory-Based Reactivity Descriptors. PHARMACEUTICAL SCIENCES 2017. [DOI: 10.4018/978-1-5225-1762-7.ch058] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Developing effective structure-activity/property/toxicity relationships (QSAR/QSPR/QSTR) is very helpful in predicting biological activity, property, and toxicity of a given set of molecules. Regular change in these properties with the structural alteration is the main reason to obtain QSAR/QSPR/QSTR models. The advancement in making different QSAR/QSPR/QSTR models to describe activity, property, and toxicity of various groups of molecules is reviewed in this chapter. The successful implementation of Conceptual Density Functional Theory (CDFT)-based global as well as local reactivity descriptors in modeling effective QSAR/QSPR/QSTR is highlighted.
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Affiliation(s)
- Sudip Pan
- Indian Institute of Technology Kharagpur, India
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Matysiak J, Niewiadomy A. QSAR models of antiproliferative activity of imidazo[2,1-b][1,3,4]thiadiazoles in various cancer cell lines. Mol Divers 2016; 21:211-218. [PMID: 27722985 DOI: 10.1007/s11030-016-9705-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 09/26/2016] [Indexed: 11/26/2022]
Abstract
Imidazo[2,1-b][1,3,4]thiadiazoles have been recognized to possess antiproliferative potency towards a wide spectrum of cancer cell lines. QSAR investigations on a set of 42 di(tri)substituted imidazo[2,1-b][1,3,4]thiadiazoles were carried out to find the descriptors determining their biological potency. Three-variable equations were obtained by combinatorial protocols in multiple linear regression (CP MLR) for all three studied cancer cell lines. They showed that lipophilicity, electronic, and steric factors are decisive for the antiproliferative potency of compounds and indicate the important role of nitrogen atoms of imidazothiadiazole ring in the interactions with the molecular target. The best models gave high r squared values in the range from 0.887 to 0.924. They also have good predictive accuracy confirmed by the high value LOO cross-validation coefficient [Formula: see text] (from 0.842 to 0.904) and by the external validation quantities.
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Affiliation(s)
- Joanna Matysiak
- Department of Chemistry, University of Life Sciences in Lublin, Akademicka 15, 20-950, Lublin, Poland.
| | - Andrzej Niewiadomy
- Department of Chemistry, University of Life Sciences in Lublin, Akademicka 15, 20-950, Lublin, Poland
- Institute of Industrial Organic Chemistry, Annopol 6, 03-236, Warsaw, Poland
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20
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Quintana DS, Guastella AJ, Westlye LT, Andreassen OA. The promise and pitfalls of intranasally administering psychopharmacological agents for the treatment of psychiatric disorders. Mol Psychiatry 2016; 21:29-38. [PMID: 26552590 DOI: 10.1038/mp.2015.166] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Revised: 08/27/2015] [Accepted: 09/29/2015] [Indexed: 01/29/2023]
Abstract
Accumulating research demonstrates the potential of intranasal delivery of psychopharmacological agents to treat a range of psychiatric disorders and symptoms. It is believed that intranasal administration offers both direct and indirect pathways to deliver psychopharmacological agents to the central nervous system. This administration route provides a unique opportunity to repurpose both old drugs for new uses and improve currently approved drugs that are indicated for other administration routes. Despite this promise, however, the physiology of intranasal delivery and related assumptions behind the bypassing of the blood brain barrier is seldom considered in detail in clinical trials and translational research. In this review, we describe the current state of the art in intranasal psychopharmacological agent delivery research and current challenges using this administration route, and discuss important aspects of nose-to-brain delivery that may improve the efficacy of these new therapies in future research. We also highlight current gaps in the literature and suggest how research can directly examine the assumptions of nose-to-brain delivery of psychopharmacological agents in humans.
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Affiliation(s)
- D S Quintana
- NORMENT, KG Jebsen Centre for Psychosis Research, Division of Mental Health and Addiction, University of Oslo, and Oslo University Hospital, Oslo, Norway
| | - A J Guastella
- Brain and Mind Center, Central Clinical School, University of Sydney, Sydney, NSW, Australia
| | - L T Westlye
- NORMENT, KG Jebsen Centre for Psychosis Research, Division of Mental Health and Addiction, University of Oslo, and Oslo University Hospital, Oslo, Norway.,Department of Psychology, University of Oslo, Oslo, Norway
| | - O A Andreassen
- NORMENT, KG Jebsen Centre for Psychosis Research, Division of Mental Health and Addiction, University of Oslo, and Oslo University Hospital, Oslo, Norway
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21
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Dearden JC, Rowe PH. Use of artificial neural networks in the QSAR prediction of physicochemical properties and toxicities for REACH legislation. Methods Mol Biol 2015; 1260:65-88. [PMID: 25502376 DOI: 10.1007/978-1-4939-2239-0_5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
With the introduction of the REACH legislation in the European Union, there is a requirement for property and toxicity data on chemicals produced in or imported into the EU at levels of 1 tonne/year or more. This has meant an increase in the in silico prediction of such data. One of the chief predictive approaches is QSAR (quantitative structure-activity relationships), which is widely used in many fields. A QSAR approach that is increasingly being used is that of artificial neural networks (ANNs), and this chapter discusses its application to the range of physicochemical properties and toxicities required by REACH. ANNs generally outperform the main QSAR approach of multiple linear regression (MLR), although other approaches such as support vector machines sometimes outperform ANNs. Most ANN QSARs reported to date comply with only two of the five OECD Guidelines for the Validation of (Q)SARs.
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Affiliation(s)
- John C Dearden
- School of Pharmacy & Biomolecular Sciences, Liverpool John Moores University, Byrom Street, Liverpool, L3 3AF, UK,
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Filipe HAL, Salvador A, Silvestre JM, Vaz WLC, Moreno MJ. Beyond Overton’s Rule: Quantitative Modeling of Passive Permeation through Tight Cell Monolayers. Mol Pharm 2014; 11:3696-706. [DOI: 10.1021/mp500437e] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- H. A. L. Filipe
- Centro de Química de Coimbra, Largo D. Dinis, Rua Larga, 3004-535 Coimbra, Portugal
- Centro
de Neurociências e Biologia Celular, Universidade de Coimbra, 3000-214 Coimbra, Portugal
| | - A. Salvador
- Centro
de Neurociências e Biologia Celular, Universidade de Coimbra, 3000-214 Coimbra, Portugal
- Chemistry
Department, FCTUC, Largo D. Dinis, Rua Larga, 3004-535 Coimbra, Portugal
| | - J. M. Silvestre
- Centro
de Neurociências e Biologia Celular, Universidade de Coimbra, 3000-214 Coimbra, Portugal
| | - W. L. C. Vaz
- Centro de Química de Coimbra, Largo D. Dinis, Rua Larga, 3004-535 Coimbra, Portugal
- Chemistry
Department, FCTUC, Largo D. Dinis, Rua Larga, 3004-535 Coimbra, Portugal
| | - M. J. Moreno
- Centro de Química de Coimbra, Largo D. Dinis, Rua Larga, 3004-535 Coimbra, Portugal
- Centro
de Neurociências e Biologia Celular, Universidade de Coimbra, 3000-214 Coimbra, Portugal
- Chemistry
Department, FCTUC, Largo D. Dinis, Rua Larga, 3004-535 Coimbra, Portugal
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Yilancioglu K, Weinstein ZB, Meydan C, Akhmetov A, Toprak I, Durmaz A, Iossifov I, Kazan H, Roth FP, Cokol M. Target-independent prediction of drug synergies using only drug lipophilicity. J Chem Inf Model 2014; 54:2286-93. [PMID: 25026390 PMCID: PMC4144720 DOI: 10.1021/ci500276x] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
![]()
Physicochemical
properties of compounds have been instrumental
in selecting lead compounds with increased drug-likeness. However,
the relationship between physicochemical properties of constituent
drugs and the tendency to exhibit drug interaction has not been systematically
studied. We assembled physicochemical descriptors for a set of antifungal
compounds (“drugs”) previously examined for interaction.
Analyzing the relationship between molecular weight, lipophilicity,
H-bond donor, and H-bond acceptor values for drugs and their propensity
to show pairwise antifungal drug synergy, we found that combinations
of two lipophilic drugs had a greater tendency to show drug synergy.
We developed a more refined decision tree model that successfully
predicted drug synergy in stringent cross-validation tests based on
only lipophilicity of drugs. Our predictions achieved a precision
of 63% and allowed successful prediction for 58% of synergistic drug
pairs, suggesting that this phenomenon can extend our understanding
for a substantial fraction of synergistic drug interactions. We also
generated and analyzed a large-scale synergistic human toxicity network,
in which we observed that combinations of lipophilic compounds show
a tendency for increased toxicity. Thus, lipophilicity, a simple and
easily determined molecular descriptor, is a powerful predictor of
drug synergy. It is well established that lipophilic compounds (i)
are promiscuous, having many targets in the cell, and (ii) often penetrate
into the cell via the cellular membrane by passive diffusion. We discuss
the positive relationship between drug lipophilicity and drug synergy
in the context of potential drug synergy mechanisms.
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Affiliation(s)
- Kaan Yilancioglu
- Faculty of Engineering and Natural Sciences, Biological Sciences and Bioengineering Program, ⊥Faculty of Engineering and Natural Sciences, Computer Science and Engineering Program, and ▽Nanotechnology Research and Application Center, Sabanci University , Istanbul 34956, Turkey
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Cruz I, Cheetham JJ, Arnason JT, Yack JE, Smith ML. Alkamides from Echinacea disrupt the fungal cell wall-membrane complex. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2014; 21:435-442. [PMID: 24252333 DOI: 10.1016/j.phymed.2013.10.025] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Revised: 08/15/2013] [Accepted: 10/17/2013] [Indexed: 06/02/2023]
Abstract
We tested the hypothesis that alkamides from Echinacea exert antifungal activity by disrupting the fungal cell wall/membrane complex. Saccharomyces cerevisiae cells were treated separately with each of seven synthetic alkamides found in Echinacea extracts. The resulting cell wall damage and cell viability were assessed by fluorescence microscopy after mild sonication. Membrane disrupting properties of test compounds were studied using liposomes encapsulating carboxyfluorescein. Negative controls included hygromycin and nourseothricin (aminoglycosides that inhibit protein synthesis), and the positive control used was caspofungin (an echinocandin that disrupts fungal cell walls). The results show that yeast cells exposed to sub-inhibitory concentrations of each of the seven alkamides and Echinacea extract exhibit increased frequencies of cell wall damage and death that were comparable to caspofungin and significantly greater than negative controls. Consistent with effects of cell wall damaging agents, the growth inhibition by three representative alkamides tested and caspofungin, but not hygromycin B, were partially reversed in sorbitol protection assays. Membrane disruption assays showed that the Echinacea extract and alkamides have pronounced membrane disruption activity, in contrast to caspofungin and other controls that all had little effect on membrane stability. A Quantitative Structure-Activity Relationship (QSAR) analysis was performed to study the effect of structural substituents on the antifungal activity of the alkamides. Among the set studied, diynoic alkamides showed the greatest antifungal and cell wall disruption activities while an opposite trend was observed in the membrane disruption assay where the dienoic group was more effective. We propose that alkamides found in Echinacea act synergistically to disrupt the fungal cell wall/membrane complex, an excellent target for specific inhibition of fungal pathogens. Structure-function relationships provide opportunities for synthesis of alkamide analogs with improved antifungal activities.
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Affiliation(s)
- I Cruz
- Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario K1S 5B6, Canada
| | - J J Cheetham
- Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario K1S 5B6, Canada
| | - J T Arnason
- Department of Biology, University of Ottawa, 30 Marie Curie, Ottawa, Ontario K1N 6N5, Canada
| | - J E Yack
- Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario K1S 5B6, Canada
| | - M L Smith
- Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario K1S 5B6, Canada.
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Riahi S, Pourbasheer E, Ganjali MR, Norouzi P, Moghaddam AZ. QSPR Study of the Distribution Coefficient Property for Hydantoin and 5-Arylidene Derivatives. A Genetic Algorithm Application for the Variable Selection in the MLR and PLS Methods. J CHIN CHEM SOC-TAIP 2013. [DOI: 10.1002/jccs.200800159] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Prediction of enhancement effect of nitroimidazoles on irradiation by gene expression programming. Chem Res Chin Univ 2013. [DOI: 10.1007/s40242-013-2422-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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27
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Yellapu NK, Atluri N, Kandlapalli K, Kilaru RB, Vangavaragu JR, Osuru H, Chamarthi N, Sarma PVGK, Matcha B. Design, synthesis, in silico, and in vitro evaluation of novel pyrimidine phosphonates with cytotoxicity against breast cancer cells. Med Chem Res 2013. [DOI: 10.1007/s00044-013-0628-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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28
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Siwek A, Bielawska A, Maciorkowska E, Lepiarczyk M, Bielawski K, Trotsko N, Wujec M. Cytotoxicity and topoisomerase I/II inhibition activity of novel 4-aryl/alkyl-1-(piperidin-4-yl)-carbonylthiosemicarbazides and 4-benzoylthiosemicarbazides. J Enzyme Inhib Med Chem 2013; 29:243-8. [DOI: 10.3109/14756366.2013.768987] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Agata Siwek
- Department of Organic Chemistry, Medical University
LublinPoland
| | | | | | | | - Krzysztof Bielawski
- Department of Synthesis and Technology of Drugs, Medical University
BialystokPoland
| | - Nazar Trotsko
- Department of Organic Chemistry, Medical University
LublinPoland
| | - Monika Wujec
- Department of Organic Chemistry, Medical University
LublinPoland
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Yerramsetty KM, Neely BJ, Gasem KAM. A NON-LINEAR STRUCTURE-PROPERTY MODEL FOR OCTANOL-WATER PARTITION COEFFICIENT. FLUID PHASE EQUILIBRIA 2012; 332:85-93. [PMID: 23185102 PMCID: PMC3505089 DOI: 10.1016/j.fluid.2012.07.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Octanol-water partition coefficient (K(ow)) is an important thermodynamic property used to characterize the partitioning of solutes between an aqueous and organic phase and has importance in such areas as pharmacology, pharmacokinetics, pharmacodynamics, chemical production and environmental toxicology. We present a non-linear quantitative structure-property relationship model for determining K(ow) values of new molecules in silico. A total of 823 descriptors were generated for 11,308 molecules whose K(ow) values are reported in the PhysProp dataset by Syracuse Research. Optimum network architecture and its associated inputs were identified using a wrapper-based feature selection algorithm that combines differential evolution and artificial neural networks. A network architecture of 50-33-35-1 resulted in the least root-mean squared error (RMSE) in the training set. Further, to improve on single-network predictions, a neural network ensemble was developed by combining five networks that have the same architecture and inputs but differ in layer weights. The ensemble predicted the K(ow) values with RMSE of 0.28 and 0.38 for the training set and internal validation set, respectively. The ensemble performed reasonably well on an external dataset when compared with other popular K(ow) models in the literature.
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Affiliation(s)
| | - Brian J. Neely
- School of Chemical Engineering, 423 Engineering North, Oklahoma State University, Stillwater, OK 74078, Phone (405) 744-5280, Fax: (405) 744-6338,
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31
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Stepwise MLR and PCR QSAR study of the pharmaceutical activities of antimalarial 3-hydroxypyridinone agents using B3LYP/6-311++G** descriptors. Med Chem Res 2012. [DOI: 10.1007/s00044-012-0152-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Zhang C, Li J, Xu L, Shi ZG. Fast immobilized liposome chromatography based on penetrable silica microspheres for screening and analysis of permeable compounds. J Chromatogr A 2012; 1233:78-84. [DOI: 10.1016/j.chroma.2012.02.013] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2011] [Revised: 02/04/2012] [Accepted: 02/07/2012] [Indexed: 11/26/2022]
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Prokai-Tatrai K, Prokai L. Prodrug design for brain delivery of small- and medium-sized neuropeptides. Methods Mol Biol 2012; 789:313-36. [PMID: 21922418 DOI: 10.1007/978-1-61779-310-3_21] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The blood-brain barrier (BBB) represents multiple barriers for drug delivery from the circulation. Peptides potentially useful to treat maladies of the brain are especially limited in their ability to cross the BBB due to several shortcomings. Specific delivery strategies have been conceived to outwit the BBB to target neuropeptides into the brain. It should be noted, however, that no unified method is possible for true brain-targeting of these fascinating biomolecules due to their structural features, properties, and intricate interplays among factors governing their entrance into and retention within the brain. In most brain-targeting prodrug approaches, a lipophilic and bioreversible moiety(ies) is covalently attached to the peptide that results in the complete loss of the innate biological activity of the parent peptide (prodrugs are inactive per definition) but significantly improves brain uptake and metabolic stability in the plasma and the interstitial fluid. Once the peptide prodrug has crossed the BBB, specific enzymes liberate the parent agent from its prodrug in the brain. To illustrate the applicability of the prodrug strategy for brain delivery of small neuropeptides, pGlu-Glu-Pro-NH(2), [Glu(2)TRH], a thyrotropin-releasing hormone (TRH) analogue with a vast array of central activities, was chosen as an example. An ester prodrug provided significantly improved brain delivery compared to the unmodified parent peptide. The synthesis, in vitro and in vivo evaluations of this prodrug as specific examples are given for typical exploratory prodrug validation.
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Affiliation(s)
- Katalin Prokai-Tatrai
- Department of Pharmacology and Neuroscience, University of North Texas Health Science Center, Fort Worth, TX, USA
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Bayat Z, Reyhani Yassavoli AR. The structure—bioresponse relationships studies of nucleoside derivatives conjugated with the 1-adamantane moiety. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2012. [DOI: 10.1134/s0036024412020069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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35
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Siwek A, Stączek P, Stefańska J. Synthesis and structure-activity relationship studies of 4-arylthiosemicarbazides as topoisomerase IV inhibitors with Gram-positive antibacterial activity. Search for molecular basis of antibacterial activity of thiosemicarbazides. Eur J Med Chem 2011; 46:5717-26. [PMID: 21978836 DOI: 10.1016/j.ejmech.2011.09.034] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2011] [Revised: 09/16/2011] [Accepted: 09/20/2011] [Indexed: 11/25/2022]
Abstract
1-(indol-2-carbonyl)-4-(4-nitrophenyl)-thiosemicarbazide was synthesized and antibacterial and type IIA topoisomerases (DNA gyrase and topoisomerase IV) activity was evaluated. It was found that it shows activity against Gram-positive bacteria with MICs of 50 μg/mL and inhibitory action against topoisomerase IV with an IC(50) of 14 μM. Although modification of its structure resulted in molecules with a lower biological profile, our observations strongly implicate that thiosemicarbazide derivatives participate in at least two different mechanisms of antibacterial activity; one is connected with the inhibition of topoisomerase IV, while the nature of the other cannot be elucidated from the limited data collected thus far. The differences in bioactivity further investigated by the molecular modeling approach and docking studies suggest that inhibitory activity of 4-arylthiosemicarbazides is connected with electronic structure rather than the geometry of the molecule.
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Affiliation(s)
- Agata Siwek
- Department of Organic Chemistry, Faculty of Pharmacy, Medical University, Chodźki 4a, 20-093 Lublin, Poland.
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36
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Ma Z, Moulton B. Recent advances of discrete coordination complexes and coordination polymers in drug delivery. Coord Chem Rev 2011. [DOI: 10.1016/j.ccr.2011.01.031] [Citation(s) in RCA: 245] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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37
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Maximum transepidermal flux for similar size phenolic compounds is enhanced by solvent uptake into the skin. J Control Release 2011; 154:50-7. [DOI: 10.1016/j.jconrel.2011.04.018] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2010] [Revised: 03/22/2011] [Accepted: 04/17/2011] [Indexed: 11/19/2022]
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38
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Ghafourian T, Samaras EG, Brooks JD, Riviere JE. Modelling the effect of mixture components on permeation through skin. Int J Pharm 2010; 398:28-32. [PMID: 20643197 DOI: 10.1016/j.ijpharm.2010.07.014] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2010] [Revised: 07/08/2010] [Accepted: 07/09/2010] [Indexed: 10/19/2022]
Abstract
A vehicle influences the concentration of penetrant within the membrane, affecting its diffusivity in the skin and rate of transport. Despite the huge amount of effort made for the understanding and modelling of the skin absorption of chemicals, a reliable estimation of the skin penetration potential from formulations remains a challenging objective. In this investigation, quantitative structure-activity relationship (QSAR) was employed to relate the skin permeation of compounds to the chemical properties of the mixture ingredients and the molecular structures of the penetrants. The skin permeability dataset consisted of permeability coefficients of 12 different penetrants each blended in 24 different solvent mixtures measured from finite-dose diffusion cell studies using porcine skin. Stepwise regression analysis resulted in a QSAR employing two penetrant descriptors and one solvent property. The penetrant descriptors were octanol/water partition coefficient, logP and the ninth order path molecular connectivity index, and the solvent property was the difference between boiling and melting points. The negative relationship between skin permeability coefficient and logP was attributed to the fact that most of the drugs in this particular dataset are extremely lipophilic in comparison with the compounds in the common skin permeability datasets used in QSAR. The findings show that compounds formulated in vehicles with small boiling and melting point gaps will be expected to have higher permeation through skin. The QSAR was validated internally, using a leave-many-out procedure, giving a mean absolute error of 0.396. The chemical space of the dataset was compared with that of the known skin permeability datasets and gaps were identified for future skin permeability measurements.
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Affiliation(s)
- T Ghafourian
- Medway School of Pharmacy, Universities of Kent and Greenwich, Chatham, Kent ME4 4TB, UK.
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Abstract
Garlic has been used medicinally since antiquity because of its antimicrobial activity, anticancer activity, antioxidant activity, ability to reduce cardiovascular diseases, improving immune functions, and antidiabetic activities and also in reducing cardiovascular diseases and improving immune functions. Recent studies identify that the wide variety of medicinal functions are attributed to the sulfur compounds present in garlic. Epidemiological observations and laboratory studies in animal models have also showed anticarcinogenic potential of organosulfur compounds of garlic. In this study, in silico analysis of organosulfur compounds is reported using the methods of theoretical chemistry to elucidate the molecular properties of garlic as it is more time and cost efficient, reduces the number of wet experiments, and offers the possibility of replacing some animal tests with suitable in silico models. The analysis of molecular descriptors defined by Lipinski has been done. The solubility of drug in water has been determined as it is of useful importance in the process of drug discovery from molecular design to pharmaceutical formulation and biopharmacy. All toxicities associated with candidate drug have been calculated. P-Glycoprotein expressed in normal tissues as a cause of drug pharmacokinetics and pharmacodynamics has been examined. Drug-plasma protein binding and volume of distribution have also been calculated. To avoid rejection of drugs, it is becoming more important to determine pK(a), absorption, polar surface area, and other physiochemical properties associated with a drug, before synthetic work is undertaken. The present in silico study is aimed at examining these compounds of garlic to evaluate its possible efficacy and toxicity under conditions of actual use in humans.
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Affiliation(s)
- Yogendra P Singh
- Department of Physics, Government Women's Polytechnic College, Sagar, Madhya Pradesh, India.
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Shin BS, Youn YS, Jeong SH, Park ES, Lee MH, Yoo SD. Current Methodologies for Membrane Permeability Assessment. JOURNAL OF PHARMACEUTICAL INVESTIGATION 2010. [DOI: 10.4333/kps.2010.40.s.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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41
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Youn YS, Lee JH, Jeong SH, Shin BS, Park ES. Pharmaceutical Usefulness of Biopharmaceutics Classification System: Overview and New Trend. JOURNAL OF PHARMACEUTICAL INVESTIGATION 2010. [DOI: 10.4333/kps.2010.40.s.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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42
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Predicting the cross-reactivities of polycyclic aromatic hydrocarbons in ELISA by regression analysis and CoMFA methods. Anal Bioanal Chem 2010; 397:2551-7. [DOI: 10.1007/s00216-010-3785-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2010] [Revised: 04/15/2010] [Accepted: 04/24/2010] [Indexed: 10/19/2022]
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43
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Synthesis and antimicrobial activity of a series of optically active quaternary ammonium salts derived from phenylalanine. OPEN CHEM 2010. [DOI: 10.2478/s11532-009-0126-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
AbstractWe synthesized nine quaternary ammonium compounds (QUATs) starting from phenylalanine, N-alkyl-N,N-dimethyl-(1-hydroxy-3-phenylpropyl)-2-ammonium bromides, which were prepared as optically pure substances. Five compounds were prepared as S-enantiomers and four compounds as R-enantiomers. These compounds were evaluated by their activities against bacteria and fungi. Three microbial strains were used in the study: the gram-negative bacteria Escherichia coli, the gram-positive bacteria Staphylococcus aureus and the fungi Candida albicans. The activities were expressed as minimum bactericidal or fungicidal concentrations (MBC). The most active compounds were (2S)-N-tetradecyl-N,N-dimethyl-(1-hydroxy-3-phenylpropyl)-2-ammonium bromide and (2R)-N-tetradecyl-N,N-dimethyl-(1-hydroxy-3-phenylpropyl)-2-ammonium bromide, with MBC values exceeding those of commercial benzalkoniumbromide (BAB) used as standard. The relationships between structure and biological activity of the tested QUATs were quantified by the bilinear model (QSAR) and are discussed.
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44
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Long W, Liu P. Quantitative structure activity relationship modeling for predicting radiosensitization effectiveness of nitroimidazole compounds. JOURNAL OF RADIATION RESEARCH 2010; 51:563-572. [PMID: 20921823 DOI: 10.1269/jrr.10053] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
This paper provides quantitative structure activity relationship (QSAR) models for predicting the radiosensitization effectiveness of nitroimidazole compounds. A new method, combining a heuristic method and projection pursuit regression, was used to build an advanced QSAR model. Compared to the conventional multi-linear regression model, this model showed better predictive ability and reliability, with the values of regression coefficient (R(2)) and root mean square error (RMSE) 0.92 and 0.18 for the training set and 0.90 and 0.17 for the test set, respectively. The provided models were useful tools to predict the radiosensitization effectiveness of nitroimidazole compounds. Also, the new finding descriptors derived from this study will help us to facilitate the design of new radiation sensitizers with better activities.
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Affiliation(s)
- Wei Long
- Tianjin Key Laboratory of Molecular Nuclear Medicine, Institute of Radiation Medicine, Peking Union Medical College, Chinese Academic of Medical Sciences, Tianjin, China
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Nishimoto M, Morimitsu T, Tamai N, Kaneshina S, Nagamune H, Matsuki H. Inhibition of anti-fluorescent probe monoclonal antibody by long-chain amphiphiles. Colloids Surf B Biointerfaces 2010; 75:80-7. [DOI: 10.1016/j.colsurfb.2009.08.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2009] [Revised: 08/07/2009] [Accepted: 08/08/2009] [Indexed: 11/24/2022]
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46
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Skin Solubility Determines Maximum Transepidermal Flux for Similar Size Molecules. Pharm Res 2009; 26:1974-85. [DOI: 10.1007/s11095-009-9912-4] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2009] [Accepted: 05/11/2009] [Indexed: 10/20/2022]
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47
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Affiliation(s)
- Stefan Balaz
- Department of Pharmaceutical Sciences, College of Pharmacy, North Dakota State University, Fargo, North Dakota 58105, USA.
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48
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Chapter 24 Discovery of Novel Positron Emission Tomography Tracers. ANNUAL REPORTS IN MEDICINAL CHEMISTRY 2009. [DOI: 10.1016/s0065-7743(09)04424-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register]
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49
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Yous S, Lebegue N, Poupaert JH, Chavatte P, Berthelot P. Lipid-lowering properties of 6-benzoyl-2(3H)-benzothiazolone and structurally related compounds. J Enzyme Inhib Med Chem 2008; 20:525-32. [PMID: 16408788 DOI: 10.1080/03067310500212037] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
Fifteen compounds derived from the 2(3H)-benzothiazolone template with an acyl side-chain in position-6 were evaluated for their lipid-lowering action in mice. Among these compounds, 6-benzoyl-2(3H)-benzothiazolone was found to be the most potent one both in mice models receiving a hypercholesterolemic diet (for 15 days) or a standard diet (for 21 days). 6-Benzoyl-2(3H)-benzothiazolone compares favorably with fenofibrate, the standard drug, both in terms of HDL-C/Chol (High Density Lipoprotein-Cholesterol/Total Cholesterol) ratio and absence of liver hepatomegaly.
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Affiliation(s)
- Saïd Yous
- Laboratoire de Chimie Thérapeutique, EA 1043, Faculté des Sciences Pharmaceutiques et Biologiques de Lille, 3 rue du Professeur Laguesse, B. P. 83 59006, Lille Cedex, France
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50
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Yamaotsu N, Oda A, Hirono S. Determination of ligand-binding sites on proteins using long-range hydrophobic potential. Biol Pharm Bull 2008; 31:1552-8. [PMID: 18670088 DOI: 10.1248/bpb.31.1552] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Here we developed a new program, HydrophoBicity On a Protein (HBOP), to find the ligand-binding site of a protein using the long-range hydrophobic-potential function estimated from the experimental data of Israelachvili and Pashley. We calculated the hydrophobic-potential energies at each grid point of a lattice around a protein using the potential function. The hydrophobic potential was evaluated using the carbon atoms of the hydrophobic residues, with the exception of those of the amide groups. We tested HBOP on 26 types of protein (72 protein-ligand complexes), the three-dimensional structures of which were determined experimentally. Although only one hydrophobic function was used, HBOP could successfully identify the binding sites in all of the proteins tested. Moreover, in 24 of the proteins, the binding sites were located in the most hydrophobic region. Surprisingly, the binding sites on sugar binding proteins were the most hydrophobic sites. It implies that the hydrophobic interaction plays an important role in the formation of protein-ligand complexes.
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Affiliation(s)
- Noriyuki Yamaotsu
- Laboratory of Physical Chemistry for Drug Design, School of Pharmaceutical Sciences, Kitasato University, Tokyo, Japan.
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