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Wang Z, Dong J, Wu L, Dai C, Wang J, Wen Y, Zhang Y, Yang X, He S, Bo X. DEML: Drug Synergy and Interaction Prediction Using Ensemble-Based Multi-Task Learning. MOLECULES (BASEL, SWITZERLAND) 2023; 28:molecules28020844. [PMID: 36677903 PMCID: PMC9861702 DOI: 10.3390/molecules28020844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 01/11/2023] [Accepted: 01/12/2023] [Indexed: 01/18/2023]
Abstract
Synergistic drug combinations have demonstrated effective therapeutic effects in cancer treatment. Deep learning methods accelerate identification of novel drug combinations by reducing the search space. However, potential adverse drug-drug interactions (DDIs), which may increase the risks for combination therapy, cannot be detected by existing computational synergy prediction methods. We propose DEML, an ensemble-based multi-task neural network, for the simultaneous optimization of five synergy regression prediction tasks, synergy classification, and DDI classification tasks. DEML uses chemical and transcriptomics information as inputs. DEML adapts the novel hybrid ensemble layer structure to construct higher order representation using different perspectives. The task-specific fusion layer of DEML joins representations for each task using a gating mechanism. For the Loewe synergy prediction task, DEML overperforms the state-of-the-art synergy prediction method with an improvement of 7.8% and 13.2% for the root mean squared error and the R2 correlation coefficient. Owing to soft parameter sharing and ensemble learning, DEML alleviates the multi-task learning 'seesaw effect' problem and shows no performance loss on other tasks. DEML has a superior ability to predict drug pairs with high confidence and less adverse DDIs. DEML provides a promising way to guideline novel combination therapy strategies for cancer treatment.
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Affiliation(s)
- Zhongming Wang
- Academy of Medical Engineering and Translational Medicine, Tianjin University, Tianjin 300072, China
- Department of Bioinformatics, Institute of Health Service and Transfusion Medicine, Beijing 100850, China
| | - Jiahui Dong
- Department of Pharmaceutical Sciences, Institute of Radiation Medicine, Beijing 100850, China
| | - Lianlian Wu
- Academy of Medical Engineering and Translational Medicine, Tianjin University, Tianjin 300072, China
- Department of Bioinformatics, Institute of Health Service and Transfusion Medicine, Beijing 100850, China
| | - Chong Dai
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Jing Wang
- School of Medicine, Tsinghua University, Beijing 100084, China
| | - Yuqi Wen
- Department of Bioinformatics, Institute of Health Service and Transfusion Medicine, Beijing 100850, China
| | - Yixin Zhang
- Department of Bioinformatics, Institute of Health Service and Transfusion Medicine, Beijing 100850, China
| | - Xiaoxi Yang
- Department of Bioinformatics, Institute of Health Service and Transfusion Medicine, Beijing 100850, China
| | - Song He
- Department of Bioinformatics, Institute of Health Service and Transfusion Medicine, Beijing 100850, China
- Correspondence: (S.H.); (X.B.)
| | - Xiaochen Bo
- Department of Bioinformatics, Institute of Health Service and Transfusion Medicine, Beijing 100850, China
- Correspondence: (S.H.); (X.B.)
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Uney K, Terzi E, Durna Corum D, Ozdemir RC, Bilen S, Corum O. Pharmacokinetics and Pharmacokinetic/Pharmacodynamic Integration of Enrofloxacin Following Single Oral Administration of Different Doses in Brown Trout ( Salmo trutta). Animals (Basel) 2021; 11:ani11113086. [PMID: 34827818 PMCID: PMC8614407 DOI: 10.3390/ani11113086] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 10/25/2021] [Accepted: 10/26/2021] [Indexed: 11/23/2022] Open
Abstract
Simple Summary The pharmacokinetic/pharmacodynamic studies report the use of enrofloxacin at higher doses than 10 mg/kg in fish. Pharmacokinetic data for increasing doses of enrofloxacin can facilitate suggestions regarding the dose for the treatment of infections in brown trout. This study aims to determine single oral pharmacokinetics of enrofloxacin at 10, 20, and 40 mg/kg doses in brown trout and pharmacodynamics against Aeromonas hydrophila and A. sobria. Enrofloxacin exhibited non-linear and dose-disproportional pharmacokinetics. The long action of enrofloxacin following the single oral administration at 10 and 20 mg/kg doses may provide the unique dosage regimen to minimize handling, thereby reducing the cost of administration and stress in brown trout. Abstract The pharmacokinetic of enrofloxacin was investigated in brown trout (Salmo trutta) following oral administration of 10, 20, and 40 mg/kg doses at 11 ± 1.5 °C. Furthermore, MICs of enrofloxacin against Aeromonas hydrophila and A. sobria were determined. The plasma concentrations of enrofloxacin and ciprofloxacin were determined using HPLC–UV and analyzed by non-compartmental method. Following oral administration at dose of 10 mg/kg, total clearance (CL/F), area under the concentration–time curve (AUC0−∞) and peak plasma concentrations (Cmax) were 41.32 mL/h/kg, 242.02 h*μg/mL and 4.63 μg/mL, respectively. When compared to 10 mg/kg dose, the dose-normalized AUC0–∞ and Cmax were increased by 56.30% and 30.08%, respectively, while CL/F decreased by 38.4% at 40 mg/kg dose, suggesting the non-linearity. Ciprofloxacin was not detected in the all of plasma samples. The MIC values of enrofloxacin were ranged 0.0625–4 μg/mL for A. hydrophila and 0.0625–2 μg/mL for A. sobria. The oral administration of enrofloxacin at 10 (for 192 h) and 20 (for 240 h) mg/kg doses provided the AUC of enrofloxacin equal to 1.23 and 1.96-fold MICs, respectively, for A. hydrophila and A. sobria with the MIC90 values of 1 µg/mL. However, further researches are needed on the PK/PD study of enrofloxacin for the successful treatment of infections caused by A. hydrophila and A. sobria in brown trout.
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Affiliation(s)
- Kamil Uney
- Department of Pharmacology and Toxicology, Faculty of Veterinary Medicine, University of Selcuk, Konya 42031, Turkey;
| | - Ertugrul Terzi
- Faculty of Fisheries, University of Kastamonu, Kastamonu 37200, Turkey; (E.T.); (R.C.O.); (S.B.)
| | - Duygu Durna Corum
- Department of Pharmacology and Toxicology, Faculty of Veterinary Medicine, University of Kastamonu, Kastamonu 37200, Turkey;
| | - Rahmi Can Ozdemir
- Faculty of Fisheries, University of Kastamonu, Kastamonu 37200, Turkey; (E.T.); (R.C.O.); (S.B.)
| | - Soner Bilen
- Faculty of Fisheries, University of Kastamonu, Kastamonu 37200, Turkey; (E.T.); (R.C.O.); (S.B.)
| | - Orhan Corum
- Department of Pharmacology and Toxicology, Faculty of Veterinary Medicine, University of Kastamonu, Kastamonu 37200, Turkey;
- Correspondence: ; Tel.: +90-3662805112
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Durna Corum D, Uney K. Gender Differences in the Effect of Calcitriol on the Body Disposition and Excretion of Doxorubicin in Mice. Eur J Drug Metab Pharmacokinet 2021; 45:653-664. [PMID: 32613470 DOI: 10.1007/s13318-020-00632-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
BACKGROUND AND OBJECTIVE The antitumor activity and toxicity of doxorubicin are potentiated and attenuated by calcitriol, respectively. Potentially, calcitriol can be combined with doxorubicin for clinical benefit in chemotherapy. To gain insight into the interaction between doxorubicin and calcitriol, proposed for combined use in cancer treatment, we studied calcitriol's effect on the plasma pharmacokinetics, tissue distribution and excretion of doxorubicin in female and male mice. METHODS The control and calcitriol-treated groups, including an equal number of both sexes, received corn oil and calcitriol (2.5 μg/kg), respectively, intraperitoneally every other day for 8 days. At day 9, doxorubicin was administered intraperitoneally at a 6 mg/kg dose to each group. Doxorubicin concentrations in biologic specimens were determined by a high-performance liquid chromatographic-ultraviolet detector and analyzed using a non-compartmental model. RESULTS The plasma pharmacokinetics of doxorubicin were similar in the control and calcitriol-treated groups. While calcitriol did not alter the area under the plasma concentration-time curves (AUCs) and peak concentrations (Cmax) of doxorubicin in the small intestine and testis, it significantly reduced the AUCs and Cmax of doxorubicin in the lung, kidney, spleen, liver, stomach and ovaries. However, calcitriol increased the AUCs and Cmax of doxorubicin in the heart of females, brain of males and duodenum content and vitreous humor of female and male mice. The percent cumulative urine and fecal amounts of doxorubicin in calcitriol-treated mice were higher at 89.23% and 29.37% for female mice and 118.57% and 41.65% for male mice than those in the control mice, respectively. CONCLUSIONS The tissue concentrations and excretion of doxorubicin in both female and male mice are influenced by calcitriol without changes in the plasma pharmacokinetics. The results from this study can provide insights to help obtain the optimal drug combination effects of doxorubicin with calcitriol in cancer treatment.
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Affiliation(s)
- Duygu Durna Corum
- Department of Pharmacology and Toxicology, Faculty of Veterinary Medicine, University of Kastamonu, 37200, Kastamonu, Turkey.
| | - Kamil Uney
- Department of Pharmacology and Toxicology, Faculty of Veterinary Medicine, University of Selcuk, 42031, Konya, Turkey
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Makihara K, Shimeda Y, Matsumura T. Influence of Concomitant Polypharmacy on Docetaxel-induced Febrile Neutropenia. CANCER DIAGNOSIS & PROGNOSIS 2021; 1:135-141. [PMID: 35399310 DOI: 10.21873/cdp.10018] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 07/31/2021] [Indexed: 01/18/2023]
Abstract
Background/Aim Docetaxel (DTX) is metabolized by liver cytochromes P450 (CYP) 3A4 (CYP3A4) and 3A5 (CYP3A5) CYP3A4 activity is considered the main factor affecting the effectiveness in DTX clearance. We, therefore, explored the association between DTX-induced febrile neutropenia (FN) and concomitant polypharmacy involving CYP3A4 inhibitors in cancer patients. Patients and Methods Among patients who received docetaxel, we compared the number of concomitant medications between patients with and without FN, and risk factors associated with FN were identified. Results The total number of concomitant CYP3A4 inhibitors and substrates used was significantly higher in patients with FN [mean: 2.1 (95% confidence interval (CI)=1.5-2.9)] than in those without FN [mean: 1.4 (95% CI=1.0-1.8)] (p=0.01). The only risk factor for FN was the use of ≥2 concomitant CYP3A4 inhibitors and substrates in total (OR=4.82, 95% CI=1.77-14.1; p=0.002). Conclusion Polypharmacy involving CYP3A4 inhibitors and substrates increases the risk of DTX-induced FN.
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Affiliation(s)
- Katsuya Makihara
- Department of Pharmacy, Yodogawa Christian Hospital, Osaka, Japan
| | - Yuka Shimeda
- Department of Pharmacy, Yodogawa Christian Hospital, Osaka, Japan
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Turk E, Tekeli IO, Corum O, Durna Corum D, Kirgiz FC, Cetin G, Arslan Atessahin D, Uney K. Pharmacokinetics of meloxicam, carprofen, and tolfenamic acid after intramuscular and oral administration in Japanese quails (Coturnix coturnix japonica). J Vet Pharmacol Ther 2021; 44:388-396. [PMID: 33846990 DOI: 10.1111/jvp.12972] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Revised: 03/22/2021] [Accepted: 03/24/2021] [Indexed: 12/18/2022]
Abstract
The aim of this study was to determine the pharmacokinetics of meloxicam (MLX), carprofen (CRP), and tolfenamic acid (TA) in Japanese quails (Coturnix coturnix japonica) following intramuscular (IM) and oral administration at doses of 1, 10, and 2 mg/kg, respectively. A total of 72 quails were randomly divided into 3 equal groups as MLX, CRP, and TA. Each group was separated into two sub-groups that received IM and oral administration of each drug. Plasma concentrations of MLX, CRP, and TA were determined using HPLC-UV and analyzed by non-compartmental method. The t1/2ʎz and MRT of MLX, CRP, and TA after oral administration were similar to those after IM administration. The Vdarea /F of MLX, CRP, and TA after IM administration was 0.28, 2.05, and 0.20 L/kg. The Cl/F of MLX, CRP, and TA after IM administration was 0.12, 0.19, and 0.09 L/h/kg. MLX, CRP, and TA after oral administration showed significantly lower Cmax and longer Tmax compared with IM administration. The relative bioavailability of MLX, CRP, and TA following oral administration in quails was 76.13%, 61.46%, and 57.32%, respectively. The IM and oral route of MLX, CRP, and TA can be used for the treatment of various conditions in quails. However, further research is necessary to determine the pharmacodynamics and safety of MLX, CRP, and TA before use in quails.
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Affiliation(s)
- Erdinc Turk
- Department of Pharmacology and Toxicology, Faculty of Veterinary Medicine, University of Hatay Mustafa Kemal, Hatay, Turkey
| | - Ibrahim Ozan Tekeli
- Department of Pharmacology and Toxicology, Faculty of Veterinary Medicine, University of Hatay Mustafa Kemal, Hatay, Turkey
| | - Orhan Corum
- Department of Pharmacology and Toxicology, Faculty of Veterinary Medicine, University of Kastamonu, Kastamonu, Turkey
| | - Duygu Durna Corum
- Department of Pharmacology and Toxicology, Faculty of Veterinary Medicine, University of Kastamonu, Kastamonu, Turkey
| | - Fatma Ceren Kirgiz
- Department of Pharmacology and Toxicology, Faculty of Veterinary Medicine, University of Hatay Mustafa Kemal, Hatay, Turkey
| | - Gul Cetin
- Department of Pharmacology, Faculty of Pharmacy, University of Erzincan Binali Yıldırım, Erzincan, Turkey
| | - Dilek Arslan Atessahin
- Department of Biology, Faculty of Science, University of Cankiri Karatekin, Cankiri, Turkey
| | - Kamil Uney
- Department of Pharmacology and Toxicology, Faculty of Veterinary Medicine, University of Selcuk, Konya, Turkey
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Corum O, Durna Corum D, Er A, Terzi E, Uney K. Plasma and tissue disposition of danofloxacin in brown trout (Salmo trutta fario) after intravenous and intramuscular administrations. Food Addit Contam Part A Chem Anal Control Expo Risk Assess 2018; 35:2340-2347. [PMID: 30352010 DOI: 10.1080/19440049.2018.1530458] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Plasma and muscle pharmacokinetics of danofloxacin were investigated after 10 mg/kg intravenous (IV, caudal vein) and intramuscular (IM, right epaxial muscles) administrations in 168 healthy brown trout (Salmo trutta fario) at 10°C-13°C. High-performance liquid chromatography was used to determine its plasma and muscle concentrations. Pharmacokinetic parameters were analysed with a non-compartmental model. After IV administration, elimination half-life (t1/2ʎz), area under the concentration-time curve (AUC0-∞), mean residence time (MRT0-∞), volume of distribution at steady state, total body clearance in plasma and AUCMuscle/AUCPlasma ratio were 22.22 h, 140.66 h*µg/mL, 23.15 h, 2.28 L/kg, 0.07 L/h/kg and 3.79, respectively. After IM administration, t1/2ʎz, AUC0-∞, MRT0-∞, peak concentration (Cmax), time to reach Cmax, bioavailability in plasma and AUCMuscle/AUCPlasma ratio were 28.28 h, 84.39 h*µg/mL, 37.31 h, 4.79 µg/mL, 1 h, 59.99% and 8.46, respectively. Danofloxacin exhibited long t1/2ʎz and good bioavailability after IM administration. Therefore, 10 mg/kg IM administration of danofloxacin in brown trout can provide AUC0-24/MIC of > 125 and Cmax/MIC of > 10 to treat diseases caused by susceptible bacteria with ≤ 0.336 µg/mL MIC.
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Affiliation(s)
- Orhan Corum
- a Department of Pharmacology and Toxicology, Faculty of Veterinary Medicine , University of Kastamonu , Kastamonu , Turkey
| | - Duygu Durna Corum
- a Department of Pharmacology and Toxicology, Faculty of Veterinary Medicine , University of Kastamonu , Kastamonu , Turkey
| | - Ayse Er
- b Department of Pharmacology and Toxicology, Faculty of Veterinary Medicine , University of Selcuk , Konya , Turkey
| | - Ertugrul Terzi
- c Faculty of Fisheries , University of Kastamonu , Kastamonu , Turkey
| | - Kamil Uney
- b Department of Pharmacology and Toxicology, Faculty of Veterinary Medicine , University of Selcuk , Konya , Turkey
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Qin X, Lu J, Wang P, Xu P, Liu M, Wang X. Cytochrome P450 3A selectively affects the pharmacokinetic interaction between erlotinib and docetaxel in rats. Biochem Pharmacol 2017; 143:129-139. [PMID: 28716728 DOI: 10.1016/j.bcp.2017.07.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 07/12/2017] [Indexed: 10/19/2022]
Abstract
Erlotinib as a first-line drug is used in non-small cell lung cancer (NSCLC) patients with sensitive EGFR mutations, while resistance to this drug will occur after several years of treatment. Therefore, the microtubule disturber docetaxel is introduced as combined regimen in clinical trials. This report investigated the potentials and mechanisms of drug-drug interaction (DDI) between erlotinib and docetaxel using wild type (WT) and Cyp3a1/2 knockout (KO) rats. The erlotinib O-demethylation and docetaxel hydroxylation reactions in the absence or the presence of another drug were analyzed in vitro via the assay of rat liver microsomes. In whole animal studies, erlotinib and docetaxel were given to WT and KO rats individually or jointly, and the pharmacokinetic profiles of these two drugs were analyzed and compared among different groups. The results showed that docetaxel not only inhibited the CYP3A-mediated biotransformation of erlotinib in vitro, but also significantly increased the maximum concentration and systemic exposure of erlotinib in vivo in WT rats. In contrast, the DDI was significantly attenuated in KO rats. On the other hand, erlotinib did not influence docetaxel either in vitro biotransformation or in vivo pharmacokinetic behaviors. These results exhibited the potentials of erlotinib-docetaxel interaction and indicated that the CYP3A played the perpetrating role of docetaxel on erlotinib in rats. A better understanding of this DDI with CYP3A may help the regulation of the use of these two drugs, avoid potential problems, and adjust dose carefully and early in clinic.
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Affiliation(s)
- Xuan Qin
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Jian Lu
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Peili Wang
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Peipei Xu
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Mingyao Liu
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China; Center for Cancer and Stem Cell Biology, Institute of Biosciences and Technology, Texas A&M University Health Science Center, Houston, TX, USA
| | - Xin Wang
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China.
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Greene LM, Butini S, Campiani G, Williams DC, Zisterer DM. Pre-clinical evaluation of a novel class of anti-cancer agents, the Pyrrolo-1, 5-benzoxazepines. J Cancer 2016; 7:2367-2377. [PMID: 27994676 PMCID: PMC5166549 DOI: 10.7150/jca.16616] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 09/28/2016] [Indexed: 02/05/2023] Open
Abstract
Microtubules are currently ranked one of the most validated targets for chemotherapy; with clinical use of microtubule targeting agents (MTAs) extending beyond half a century. Recent research has focused on the development of novel MTAs to combat drug resistance and drug associated toxicities. Of particular interest are compounds structurally different to those currently used within the clinic. The pyrrolo-1, 5-benzoxazepines (PBOXs) are a structurally distinct novel group of anti-cancer agents, some of which target tubulin. Herein, we review the chemistry, mechanism of action, preclinical development of the PBOXs and comparisons with clinically relevant chemotherapeutics. The PBOXs induce a range of cellular responses including; cell cycle arrest, apoptosis, autophagy, anti-vascular and anti-angiogenic effects. The apoptotic potential of the PBOXs extends across a wide spectrum of cancer-derived cell lines, by targeting tubulin and multiple molecular pathways frequently deregulated in human cancers. Extensive experimental data suggest that combining the PBOXs with established chemotherapeutics or radiation is therapeutically advantageous. Pre-clinical highlights of the PBOXs include; cancer specificity and improved therapeutic efficacy as compared to some current first line therapeutics.
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Affiliation(s)
- L M Greene
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2, Ireland
| | - S Butini
- European Research Centre for Drug Discovery and Development, Department of Biotechnology, Chemistry and Pharmacy, and Istituto Toscano Tumori, University of Siena, via Aldo Moro 2, I-53100 Siena, Italy
| | - G Campiani
- European Research Centre for Drug Discovery and Development, Department of Biotechnology, Chemistry and Pharmacy, and Istituto Toscano Tumori, University of Siena, via Aldo Moro 2, I-53100 Siena, Italy
| | - D C Williams
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2, Ireland
| | - D M Zisterer
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2, Ireland
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