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E-raamat: Computational Methods in Drug Discovery and Repurposing for Cancer Therapy

Edited by (Assistant Professor, Department of Bioinformatics, School of Life Sciences, Pondicherry University, India), Edited by (P), Edited by (Assistant Professor, School of Medicine, Division of Hematology and Oncology, University of Alabama, Birmingham, AL, USA)
  • Formaat: EPUB+DRM
  • Ilmumisaeg: 22-Mar-2023
  • Kirjastus: Academic Press Inc
  • Keel: eng
  • ISBN-13: 9780443152818
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  • Formaat: EPUB+DRM
  • Ilmumisaeg: 22-Mar-2023
  • Kirjastus: Academic Press Inc
  • Keel: eng
  • ISBN-13: 9780443152818

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Computational Methods in Drug Discovery and Repurposing for Cancer Therapy provides knowledge about ongoing research as well as computational approaches for drug discovery and repurposing for cancer therapy. The book also provides detailed descriptions about target molecules, pathways, and their inhibitors for easy understanding and applicability.

The book discusses tools and techniques such as integrated bioinformatics approaches, systems biology tools, molecular docking, computational chemistry, artificial intelligence, machine learning, structure-based virtual screening, biomarkers, and transcriptome; those are discussed in the context of different cancer types, such as colon, pancreatic, glioblastoma, endometrial, and retinoblastoma, among others.

This book is a valuable resource for researchers, students, and members of the biomedical and medical fields who want to learn more about the use of computational modeling to better tailor the treatment for cancer patients.

  • Discusses in silico remodeling of effective phytochemical compounds for discovering improved anticancer agents for substantial/significant cancer therapy
  • Covers potential tools of bioinformatics that are applied toward discovering new targets by drug repurposing and strategies to cure different types of cancers
  • Demonstrates the significance of computational and artificial intelligence approaches in anticancer drug discovery
  • Explores how these various advances can be integrated into a precision and personalized medicine approach that can eventually enhance patient care
Contributors xv
About the editors xxi
Preface xxiii
1 Computational approaches for anticancer drug design
1(10)
Tha Luong
Grace Persis Burri
Yuvasri Golivi
Ganji Purnachandra Nagaraju
Bassel F. El-Rayes
1 Introduction
2(1)
2 Current computational approaches for cancer drug designs
2(4)
3 Applications of computational approaches in cancer drug designing
6(2)
4 Challenges and future directions
8(1)
5 Conclusion
9(2)
References
9(2)
2 Molecular modeling approach for cancer drug therapy
11(8)
Bhavini Singh
Rishabh Rege
Ganji Purnachandra Nagaraju
1 Introduction
11(1)
2 Drug designing
12(1)
3 Molecular modeling
13(1)
4 Methods of molecular modeling
13(1)
5 Applications of molecular modeling
14(1)
6 Applications in multidrug-resistant proteins
15(2)
7 Conclusion
17(2)
References
17(2)
3 Discovery of anticancer therapeutics: Computational chemistry and Artificial Intelligence-assisted approach
19(24)
Subrata Das
Anupam Das Talukdar
Deepa Nath
Manabendra Dutta Choudhury
1 Introduction
20(1)
2 Drug repurposing
20(2)
3 Computational chemistry in drug designing
22(8)
4 Structure-based drug designing
30(1)
5 ADME/Tox screening and drug-likeness prediction
31(1)
6 Molecular docking
32(1)
7 Quantitative structure-activity relationship modeling
32(1)
8 Molecular dynamics simulation
33(1)
9 Artificial Intelligence in drug discovery
33(1)
10 Conclusion
34(9)
References
35(8)
4 Artificial intelligence in oncological therapies
43(16)
Shloka Adluru
1 Introduction
43(1)
2 Importance of early diagnosis
44(1)
3 How Al can improve accuracy and speed of cancer diagnoses
45(2)
4 How Al can assess patient background information to determine risk of cancer
47(1)
5 Diagnosis of cancer subtype and stage
47(2)
6 Al in cancer drug discovery and development
49(1)
7 De novo drug design
50(1)
8 Al in recommending drug combinations and repurposing drugs
51(1)
9 Al in identifying drug-target interactions
51(1)
10 Deep learning, black boxes, and hidden layers
52(2)
11 Future of Al in oncology
54(1)
12 Conclusion
55(4)
References
55(4)
5 Approach of artificial intelligence in colorectal cancer and in precision medicine
59(14)
Grace Persis Burri
Yuvasri Golivi
Tha Luong
Neha Merchant
Ganji Purnachandra Nagaraju
1 Introduction
59(2)
2 Applications of Al in CRC
61(5)
3 Robotic-assisted surgery
66(1)
4 Precision medicine in CRC
67(1)
5 Benefits
67(1)
6 Limitations
67(1)
7 Current challenges and prospects
67(1)
8 Conclusion
68(5)
Conflict of interest
68(1)
Funding
68(1)
References
68(5)
6 Artificial intelligence in breast cancer: An opportunity for early diagnosis
73(18)
Rama Rao Malla
Vedavathi Katneni
1 Machine learning
74(4)
2 Breast cancer
78(8)
3 Conclusion
86(5)
References
86(5)
7 Quantitative structure-activity relationship and its application to cancer therapy
91(10)
Bhavini Singh
Rishabh Rege
Ganji Purnachandra Nagaraju
1 Introduction
91(1)
2 Function
92(2)
3 Origin of QSAR
94(1)
4 Advanced techniques of QSAR
94(1)
5 Application in drug design
95(1)
6 Application in cancer therapy
96(1)
7 Concerns
97(1)
8 Conclusion
98(3)
References
98(3)
8 Structure-based virtual screening for the identification of novel Greatwall kinase inhibitors
101(16)
Anbumani Velmurugan Ilavarasi
Tulsi Saswati Sarita Mohanty
Umamahesh Katike
Ishwar Patidar
Amouda Venkatesan
Dinakara Rao Ampasala
1 Introduction
102(2)
2 Computational methods
104(2)
3 Results and discussion
106(7)
4 Conclusion
113(1)
Acknowledgements
114(1)
Conflict of interest
114(3)
References
114(3)
9 Strategies for drug repurposing
117(12)
Aparna Vema
Arunasree M. Kalle
1 Introduction
118(1)
2 Computational drug repurposing
118(6)
3 Experimental drug repurposing
124(1)
4 Conclusions and perspectives
125(1)
Author contributions
126(1)
Financial disclosures
126(1)
Conflict of interest
126(3)
References
126(3)
10 Principles of computational drug designing and drug repurposing--An algorithmic approach
129(18)
Angshuman Bagchi
1 Introduction
130(1)
2 Overview of basic thermodynamic principles involved in computational algorithms
131(1)
3 Fundamentals of computational algorithms
132(3)
4 Searching the conformational space
135(1)
5 Analysis of protein flexibility
136(2)
6 Drug repurposing
138(1)
7 Conclusion
138(9)
Acknowledgment
138(1)
References
139(8)
11 Drug discovery and repositioning for glioblastoma multiforme and low-grade astrocytic tumors
147(54)
Asmita Dasgupta
Sanjukta Ghosh
Kastro Kalidass
Shabnam Farisha
1 Introduction
148(3)
2 Approved therapeutics for astrocytic tumors
151(3)
3 Drug discovery approaches against astrocytic tumors
154(10)
4 Drug discovery for astrocytic tumors by virtual screening
164(10)
5 Drug repositioning in astrocytic tumor therapy
174(15)
6 Conclusion
189(12)
Acknowledgments
191(1)
Conflict of interest
191(1)
References
191(10)
12 Repurposing of phytocompounds-derived novel bioactive compounds possessing promising anticancer and cancer therapeutic efficacy through molecular docking, MD simulation, and drug-likeness/ADMET studies
201(22)
Rajalakshmi Manikkam
Vijayalakshmi Periyasamy
Indu Sabapathy
1 Drug repurposing
202(1)
2 Strategies in drug repurposing
203(1)
3 Pros and cons of drug repurposing
203(1)
4 Computational advancements in oncology research
204(1)
5 Structure-based and target-based virtual screening
205(1)
6 Systems biology integrated approach in drug repositioning
206(1)
7 In silico databases and web-based tools for drug repurposing
207(2)
8 Phytochemicals repurposed in cancer therapy
209(5)
9 Antidiabetic phytocompounds repurposed for cancer therapy
214(1)
10 Conclusion
214(9)
References
215(8)
13 Old drugs and new opportunities--Drug repurposing in colon cancer prevention
223(14)
Vemula Sarojamma
Manoj Kumar Gupta
Jeelan Basha Shaik
Ramakrishna Vadde
1 Introduction
224(1)
2 Principles and tools used in drug repurposing
225(2)
3 CategoTies of repurposed drugs against human cancers
227(1)
4 Drugs used in the treatment of colon cancer
227(2)
5 Drug repurposing in the prevention of colon cancer
229(1)
6 Drug repurposing pitfalls
230(1)
7 Computational approaches in drug repurposing for colorectal cancer
230(2)
8 Conclusions and perspectives
232(5)
Conflicts of interest
233(1)
References
233(4)
14 Repurposing cardiac glycosides as the hallmark of immunogenic modulators in cancer therapy
237(22)
Honey Pavithran
Angelina Job Kolady
Ranjith Kumavath
1 Introduction
238(1)
2 Repurposing cardiac glycosides in cancer treatment
239(7)
3 CGs hamper Na+/K+-ATPase signaling complex in cancer
246(1)
4 Role of the immune system in cancer
247(5)
5 Conclusions
252(7)
Acknowledgments
252(1)
Consent for publication
253(1)
Ethics approval and consent to participate
253(1)
Conflict of interest
253(1)
References
253(6)
15 Systems biology tools for the identification of potential drug targets and biological markers effective for cancer therapeutics
259(34)
Gayathri Ashok
P. Priyamvada
Sravan Kumar Miryala
Anand Anbarasu
Sudha Ramaiah
1 Introduction
260(1)
2 Current problems in cancer therapies
261(1)
3 Need for alternative approaches in cancer
261(1)
4 GIN: A systems biology approach
261(1)
5 Types of biological networks
262(3)
6 Cancer databases
265(5)
7 Databases for interaction data curation
270(2)
8 Network construction and visualization
272(3)
9 Network analysis
275(8)
10 How can the identified targets be used for cancer therapy?
283(1)
11 Conclusion
284(9)
Acknowledgments
285(1)
Conflict of interest
285(1)
Authors' contribution
285(1)
References
285(8)
16 Role of human body fluid biomarkers in liver cancer: A systematic review
293(18)
Dahru Paul
Vigneshwar Suriya Prakash Sinnarasan
Rajesh Das
Dinakara Rao Ampasala
Amouda Venkatesan
1 Introduction
294(1)
2 Methods
295(1)
3 Results
295(6)
4 Discussion
301(4)
5 Conclusions
305(1)
References
305(6)
17 Study on biomarkers in endometrial cancer using transcriptome data: A machine learning approach
311(18)
Vigneshwar Suriya Prakash Sinnarasan
Dahrii Paul
Rajesh Das
Dinakara Rao Ampasala
Amouda Venkatesan
1 Introduction
312(1)
2 Materials and methods
313(2)
3 Results
315(7)
4 Discussion
322(2)
5 Conclusion
324(5)
References
324(5)
18 Drug targeting PIWI like protein-piRNA complex, a novel paradigm in the therapeutic framework of retinoblastoma
329(58)
Rupa Roy
Muthuramalingam Karpagavalli
Athira Ramesh
Jayamuruga Pandian Arunachalam
Sudha Rani Sadras
Subbulakshmi Chidambaram
1 Introduction
330(2)
2 Biological functions of PIWI/piRNA in physiological conditions
332(8)
3 Emerging significance of PIWI/piRNA in various cancers
340(11)
4 Retina and its structure
351(8)
5 Potential role of PIWI and piRNA in RB
359(1)
6 PIWI/piRNA as future biomarkers in cancer
360(4)
7 Conclusion
364(23)
Acknowledgments
366(1)
Declaration of competing interest
366(1)
References
366(19)
Further reading
385(2)
19 Emerging role of biosimilars: Focus on Bevacizumab and hepatocellular carcinoma
387(16)
Anum Jalil
James Wert
Akriti Gupta Jain
Sarfraz Ahmad
1 Introduction
388(1)
2 Biologies and biosimilars
388(1)
3 FDA approved biosimilars to date
389(1)
4 Role of Bevacizumab and its biosimilar in hepatocellular carcinoma
389(5)
5 Clinical trials with Bevacizumab and its biosimilar in HCC
394(5)
6 Conclusions and future perspectives
399(4)
Funding
399(1)
Authors' contribution
399(1)
References
399(4)
20 Integrated computational approaches to aid precision medicine for cancer therapy: Present scenario and future prospects
403(22)
Hithesh Kumar
Sravan Kumar Miryala
Anand Anbarasu
Sudha Ramaiah
1 Introduction
404(2)
2 Precision cancer medicine: Prospects and hurdles
406(3)
3 Next generation sequencing and computational genomics in PCM
409(6)
4 Drug repositioning using translational bioinformatics
415(1)
5 Future perspectives
415(2)
6 Conclusion
417(8)
Acknowledgment
418(1)
Author contributions
418(1)
Declaration of interests
418(1)
References
418(7)
Index 425
Dr. Nagaraju obtained his MSc and his PhD, both in Biotechnology, from Sri Venkateswara University in Tirupati, Andhra Pradesh, India. He received his DSc from Berhampur University in Berhampur, Odisha, India. Dr. Nagarajus research focuses on translational projects related to gastrointestinal malignancies. He has published over 100 research papers in highly reputed international journals and has presented more than 50 abstracts at various national and international conferences. Dr. Nagaraju is author and editor of several published books in Elsevier and Springer Nature. He serves as editorial board member of several internationally recognized academic journals. Dr. Nagaraju has received several international awards including FAACC. He also holds memberships with the Association of Scientists of Indian Origin in America (ASIOA), the Society for Integrative and Comparative Biology (SICB), The Science Advisory Board, The RNA Society, The American Association for Clinical Chemistry (AACC) and the American Association of Cancer Research (AACR). Dr. V. Amouda is an Assistant Professor with a demonstrated history of working in higher education at the Department of Bioinformatics, Pondicherry University, Puducherry, India. She possesses a doctoral degree in Computer Science & Engineering from Pondicherry University. She has more than a decade of research and development experience in new computational data technologies focusing on Data analysis, Machine learning, Data mining, and Big Data analytics across biomedical areas. She has published more than 50 research articles in peer-reviewed international journals and presented many abstracts at national and international conferences. Dr. V. Amouda is a co-author of 4 book chapters published by International publishers and a reviewer of many international journals. She promotes science and progress by organizing 35 national and international conferences at various platforms in the Bioinformatics and Computer Science fields. She has a strong administrative professional experience with a track of contributing science to society by associating with various scientific bodies of Government & NGOs. She has experience in extension activities as she is a member of learned societies of national professional agencies. Dr. Ampasala earned his PhD degree in biochemistry from Sri Venkateswara University. He spent 12 years in research and teaching at Pondicherry University, Puducherry, India, and 10 years in postdoctoral studies in cancer research in United States and Canada. Dr. Ampasalas current research focuses are on functional genomics, molecular mechanisms of cancer, signal transduction, and computational neurobiology and has published nearly 70 peer-reviewed scholarly research articles and book chapters, which are extensively cited globally. He is a reviewer and editorial member for several biomedical/bioinformatics journals and has received several competitive research grants for his research accomplishments/contributions. He has been honored with fellow award from the Society of Plant Research (2019), and he has bagged other prestigious awards such as DST-Young Scientist (2008), DBT-Young Investigator (2015), Science Communicator-ISCA (2013, 2014), and the Best Teacher Award (2011, Pondicherry University). He received VA Merit Award from Wayne State University, Detroit, MI, United States (20052007) for his postdoctoral studies; research associate fellowship funded by Genomic Canada, Canada (2001-2005); and postdoctoral fellowship funded by DBT, Indian Institute of Science (19992001).