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Béla Török
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ISBN: 978-0-12-822248-5
1. Introduction 1
2. The zebrafish model system 2
3. Use of the zebrafish model system in drug discovery 3
4. Significance of pharmaceutical pollution 6
5. Use of the zebrafish model system to assess pharmaceutical
pollutant toxicity 7
6. Methods and approaches to assess pharmaceutical pollutant
toxicity using the zebrafish model system 13
6.1 Acute developmental toxicity assessments with the
developing zebrafish 13
6.2 High-throughput screenings (HTS) for developmental toxicity
assessments 14
6.3 Zebrafish developmental and adult behavioral assays to assess
pharmaceutical pollutant toxicity 16
6.4 Cellular and molecular assays to identify mechanisms of
pharmaceutical pollutant toxicity 18
7. Future directions for the use of zebrafish in defining
pharmaceutical pollutant toxicity 20
8. Conclusions 21
Acknowledgments and Funding sources 21
References 21
v
vi Contents
1. Introduction 47
2. How antibiotics are reaching the aquatic environment? 49
2.1 From human use 49
2.2 From hospital waste 53
2.3 From animal use 56
2.4 From agricultural use 58
2.5 From pharmaceutical industry waste 59
3. Fate of antibiotics in aquatic environment 60
4. Conclusion 61
References 62
1. Introduction 89
2. Structure-based drug design (SBDD) 91
2.1 Protein structure prediction 92
3. Molecular docking 96
3.1 Search algorithms 96
3.2 Scoring functions 97
3.3 Target flexibility 101
3.4 De novo drug design 101
3.5 Binding energy estimation 103
3.6 Machine/deep learning methods in SBVS 104
4. Ligand-based drug discovery (LBDD) 107
4.1 Similarity searching 108
4.2 Ligand-based pharmacophore mapping 113
4.3 Quantitative structure-activity relationship (QSAR)
modeling 115
5. Summary and perspectives 117
References 119
1. Introduction 201
2. Catalysis 203
2.1 Homogeneous catalysis 204
2.2 Heterogeneous catalysis 217
3. Nontraditional activation methods and energy efficiency of
chemical processes 238
3.1 Microwave-assisted organic synthesis 238
3.2 Ultrasonic activation 242
3.3 Photochemical activation 248
3.4 Electrochemical activation 256
4. Conclusions 260
References 261
Contents ix
1. Introduction 457
2. The green impact of multitarget drug discovery 460
2.1 Green syntheses in multitarget drug development (MTDD) 462
2.2 Combining in silico and experimental methods:
inherently green improvement to design and
testing efficiency 464
3. Multitarget lead generationdscreening-versus
knowledge-based approaches 465
3.1 Knowledge-based rational design 466
3.2 Screening-based multitarget lead generation 468
3.3 Natural product-inspired scaffolds for designing MTDs 472
4. Selected case studies with multitarget focus 476
4.1 Neurodegenerative diseasesdAlzheimer’s disease 476
4.2 Infectious diseases 477
4.3 Cancer 478
4.4 Epigenetic polypharmacology 479
5. Challenges and limitations in multitarget drug design and
development 480
6. Conclusions 481
List of abbreviations 482
References 483
xii Contents
Index 535
List of contributors
xiii
xiv List of contributors
Gyorgy Szekely, Advanced Membranes and Porous Materials Center, Physical Science
and Engineering Division (PSE), King Abdullah University of Science and Tech-
nology (KAUST), Thuwal, Saudi Arabia
Ryszard Szyszka, The John Paul II Catholic University of Lublin, Lublin, Poland
Béla Török, Department of Chemistry, University of Massachusetts Boston, Boston,
MA, United States
Marianna Török, Department of Chemistry, University of Massachusetts Boston,
Boston, MA, United States
Sunil K. Tripathi, University of Michigan, Ann Arbor, MI, United States
Rita Bernadett Vlocskó, Department of Chemistry, University of Massachusetts
Boston, Boston, MA, United States
Justine C. Williams, Department of Chemistry, University of Waterloo, Waterloo, ON,
Canada
Guoshu Xie, Department of Chemistry, University of Massachusetts Boston, Boston,
MA, United States
Chapter 1
1. Introduction
With all eyes shifting toward the impacts of global climate change and
pollution on human and ecological health, sustainability and environmental
safety are eminent topics that need to be addressed. Specifically, there is much
focus toward how pharmaceutical waste and buildup in the environment may
affect the general health and wellness of exposed organisms.1 Pharmaceutical
pollution, which refers to the presence of synthetic drugs and their metabolites
in the environment, is largely unregulated and has the potential to be detri-
mental to human and ecological health. In the past, environmental toxicology
studies, including those assessing pharmaceutical pollution, have relied pri-
marily on rodent or other mammalian models to perform toxicity assessments.
Limitations and high economic costs of large-scale mammalian models for
assessing environmental toxicity have led to an expansion of other vertebrate
model systems being applied in this research area. As selecting the optimal
animal model is vital to understanding environmental toxicology, researchers
have enthusiastically turned to the zebrafish model to study the effects of
environmental pollutants including pharmaceutical pollution as an animal
model complementary to the traditional mammalian assays. In this chapter, we
discuss the advantages, strengths, and limitations for utilizing the zebrafish
model system in toxicological studies and in particular, those studies assessing
the adverse effects of pharmaceutical pollution. In addition, we detail common
zebrafish assays employed to assess developmental toxicity, morphology,
behavior, and molecular perturbations induced by pharmaceutical pollution
exposure.
FIGURE 1.1 Zebrafish fli1 [(Tg(fli1:eGFP)y1] transgenic larva. This transgenic line involves a
transgenic insertion of enhanced green fluorescent protein (eGFP) in the vasculature under control
of the fli1 promoter. This transgenic line is used to easily visualize vascular defects in zebrafish
following chemical exposures.
genome and the zebrafish genome, it was discovered that around 80% of genes
and expressed sequence tags are conserved.9 In a latter more extensive study,
results showed 82% of human disease genes have at least one zebrafish
ortholog.5 Moreover, gene mutations in zebrafish have been shown to produce
less embryonic lethality than the same gene mutations in mammalian models,
largely due to a genome duplication event.10 As such, researchers are better
able to study the affected gene function and the associated signaling pathways
in pathogenesis. In toxicological studies, this fact is vital as we are able to
study developmental changes and the molecular mechanisms of the xenobiotic
exposures.
biomarkers can address several major problems associated with drug devel-
opment. Biomarkers enhance determination of whether drug candidates are
promising early in development as well as reduce the costs of drug develop-
ment. Use of biomarkers can also identify applicable drugs with enhanced
safety and find treatments for those patients who need the best balance of risk
and benefit. Moreover, translational biomarkers between fish and mammalian
models can be established to further improve the accuracy and our under-
standing of preclinical toxicity during drug development. As done with the
DILI studies, biomarkers show to be a useful tool that may have great value in
drug discovery.14,16 Biomarkers can provide a bridge between fish, rodents,
and humans. Thus, it is important to expand upon the use of biomarkers in the
process of drug discovery when working with animal models. This expansion
can help detect future drug toxicity issues in humans, which can make the
process more efficient and lower the costs toward a more successful outcome
in the future. Overall, these applications support the use of the zebrafish in
future studies progressing toward promising drugs during the early develop-
mental phase of drug discovery. Furthermore, these studies provide confidence
for application of the zebrafish to address the environmental toxicity questions
surrounding pharmaceutical pollution, providing a connection between the
overall toxicity of these pharmaceuticals whether in the early stages of drug
discovery or at the latter stages evaluating the toxicity of pharmaceutical
pollution.
n Caffeine Larval exposure for 96 h (72 n decreased expression of cyp1a in all single No additive toxicity was 28
n Ibuprofen e168 hpf) pharmaceutical treatments, but increased observed, but differences
n Carbamazepine Exposures included single expression in high mixture treatment seen in between the
n Tamoxifen pharmaceuticals (Caffeine, n expression of vtg decreased in Tamoxifen individual and mixture
ibuprofen, or treatments treatments signifying need to
Carbamazepine at 0.05 or n EROD activity decreased in lower ibuprofen include mixture toxicity
5 mM; Tamoxifen at 0.003 or treatment and increased in the high mixture assessments.
0.3 mM) or a low or high treatment
mixture treatment with
negative (embryo media),
solvent (0.001% ethanol),
and positive (17a-
9
ethinylestradiol or
phenanthrene) controls
Continued
10 Contemporary Chemical Approaches for Green and Sustainable Drugs
TABLE 1.1 Summary of example studies defining pharmaceutical pollutant toxicity using the zebrafish model.dcont’d
Pharmaceuticals Exposure parameters Results Implications References
n Bezafibrate Embryonic exposure (2e50 n no visible acute toxicity for any single or Delayed behavioral 29
n Caffeine hpf) mixture treatments alterations were observed
n Carbamazepine Single pharmaceutical n delayed hatch at 72 hpf for Triclosan (1 ppb) for several pharmaceuticals
n Clarithromycin exposure at 0.01, 0.1, 1, 10, and ibuprofen (100 ppb) and the high mixture
n Diclofenac or 100 ppb n decreased swimming speed at 100 ppb of treatment.
n Ibuprofen Low (1X), medium (10X), or Triclosan, Clarithromycin, and the high
n Sulfamethoxazole high (100X) mixture of all 8 mixture treatment at 118 hpf
n Triclosan pharmaceuticals n increased swimming speed at 100 ppb of
Carbamazepine at 118 hpf
n paracetamol Developmental exposure n nondose response morphological alterations Environmentally relevant 30
(acetaminophen) (<3e96 hpf) at 48, 72, and 96 hpf for paracetamol concentrations of these
n Ciprofloxacin Paracetamol at 5, 25, 125, n hyper- and/or hypoactivity observed at 144 pharmaceuticals resulted in
625, or 3125 ppb hpf for paracetamol and Ciprofloxacin behavioral and biomarker
Ciprofloxacin at 0.005, dependent on phase and concentration alterations, while
0.013, 0.031, 0.078, 0.195, n paracetamol caused increase in AChE, total morphological and DNA
or 0.488 ppb GPx, and GST activity; alterations in GSH methylation changes were
Treatment water refreshed at metabolism; and increased lipid observed only for
48 hpf peroxidation paracetamol.
n Ciprofloxacin resulted in increased AChE
activity and a decrease in catalase activity
and lipid peroxidation
n increased DNA methylation following
paracetamol exposure
AChE: acetylcholinesterase; cyp1a: cytochrome P450 1a; cyp19a2: cytochrome P450 19a2; er-a: estrogen receptor-alpha; EROD: ethoxyresorufin-O-deethylase; gnrh3:
gonadotropin releasing hormone; GPx: glutathione peroxidase; GST: glutathione transferase; hpf: hours postfertilization; ppb: parts per billion (mg/L); vtg: vitellogenin.
Using the zebrafish model system to identify Chapter | 1 11
FIGURE 1.3 Phenotypic screening in multiwell plates permits high-content imaging in devel-
oping zebrafish. Embryos are attained from adult breeding pairs and arrayed in multiwell plates
immersed in solutions containing pharmaceutical pollutants of interest. Imaging software detects
and measures specific phenotypic outcomes to define developmental toxicity. Scoring systems can
be used to rank toxicity.
FOOTNOTES:
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