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E-raamat: Systems Biology in Biotech & Pharma: A Changing Paradigm

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The US is currently well ahead of the rest of the world in the development and application of SB and its principles especially as they pertain to basic medical research and development. This lead is largely due to its earlier start in the academic arena. However, there is evidence of rapid development in both the UK/EU and Japan, and the gap is narrowing, particularly in the UK. From an industrial point of view, the Pharmaceutical Industry based in the US and UK can capitalize on these opportunities and gain the benefits of this technology. Many educational institutions (particularly their medical divisions) at present are heavily business-oriented, realize that in this particular industrial environment, that every dollar counts.
1 Introduction: Discovery and Development---New Facet of Industry, New Tools and Lead Optimization
1(10)
1.1 Scope and Content of this Review
2(4)
1.2 Drug Discovery and Development
6(1)
1.3 Defining SB: Key Components
7(1)
1.4 A Brief History of Systems Biology (SB): In Terms of Key Advances
8(1)
1.5 Perspective and Potential Impact of Systems Biology on Academic Funding and Pharma R&D and Cost Savings
9(1)
References
10(1)
2 Discovery: Use of Systems Biology for Identifying Targets
11(14)
2.1 Identifying Targets and Druggability Space
12(3)
2.1.1 Bioinformatics Inputs (BI Inputs)
14(1)
2.2 Combinatorial Chemistry Tools
15(6)
2.2.1 BI Inputs
15(1)
2.2.2 Diversity Tools
16(3)
2.2.3 Qualitative and Quantitative Screens and Filters
19(1)
2.2.4 Structure-Activity Methods (SAR/QSAR)
20(1)
2.3 Summarizing
21(1)
References
22(3)
3 Integrative Systems Biology I---Biochemistry: Phase I Lead Discovery and Molecular Interactions
25(14)
3.1 Molecular Screens: Receptor--Ligand (R--L) Interaction and Molecular Modeling
26(3)
3.1.1 Molecular Modeling
27(1)
3.1.2 Quantum Chemistry
27(1)
3.1.3 Molecular Mechanics
27(1)
3.1.4 Molecular Dynamics
28(1)
3.1.5 Receptor Based QSAR Methods
28(1)
3.1.6 Biomimetics
28(1)
3.2 Collateral Efficacy and Permissive Antagonism
29(1)
3.3 Co-Drugging: Multiple Targets, Combination Therapy & Multistage Targeting
29(2)
3.3.1 Multicomponent Drugs
30(1)
3.3.2 Multi-Target Approach
30(1)
3.3.3 Multi-Stage Targeting
31(1)
3.4 Text Mining for Interactions
31(1)
3.5 Employment of Biochemical Networks
32(1)
3.6 Overview of Deterministic Models
32(2)
3.6.1 Emergence
33(1)
3.6.2 Reactome
34(1)
3.7 Bioinformatics
34(2)
3.8 Summarizing
36(1)
References
36(3)
4 Integrative Systems Biology II---Molecular Biology: Phase 2 Lead Discovery and In Silico Screening
39(12)
4.1 OMICs
40(2)
4.1.1 BI Inputs
40(1)
4.1.2 Metabolomics
41(1)
4.2 Chemogenomics
42(1)
4.2.1 BI Inputs
42(1)
4.3 Morphogenics
43(1)
4.4 Minimal Phenotype and Synthetic Biology
43(1)
4.4.1 SB and BI Inputs
44(1)
4.5 Reconstructing Biological Networks
44(2)
4.6 Summarizing
46(1)
References
47(4)
5 Discovery: Computational Systems Biology (CSB) in Health and Disease I
51(18)
5.1 Cellular Environment: Network Reconstruction and Inference from Experimental Data
52(2)
5.2 Reconstructing Gene Networks
54(1)
5.3 Data Mining and Heuristic Data Preprocessing Tools
54(1)
5.4 Analysis of Disease `Correlation Network™' and Concerted Metabolic Activation: Disease as a Systems Network Property
55(3)
5.5 Challenges for Stem Cells: Control
58(1)
5.5.1 SB and BI Inputs
58(1)
5.6 Emergent Properties
59(1)
5.7 Computational Systems Biology
60(3)
5.8 Summarizing
63(1)
References
64(5)
6 Development: In Vivo Pharmacology---Systems Biology in Health and Disease II
69(8)
6.1 Animal Disease Models
70(1)
6.1.1 Gene Knockout Animal Models
71(1)
6.2 Pheno- and Genotyping
71(1)
6.3 RNA Interference
72(1)
6.3.1 BI Inputs
73(1)
6.4 Pharmacogenomics
73(1)
6.4.1 SB and BI Inputs
73(1)
6.5 In Silico Pharmacology: Future
74(1)
6.6 Summarizing
75(1)
References
76(1)
7 Development: Pharmacokinetics---Systems Biology in Health and Disease III
77(10)
7.1 Microdosing in PK
78(1)
7.1.1 BI Inputs
78(1)
7.2 Adaptive Trial Design
78(1)
7.3 Equilibrium Versus Non-Equilibrium PK Models
79(1)
7.4 Toxicity Biomarkers
80(1)
7.4.1 SB and BI Inputs
80(1)
7.5 In Silico Toxicity Prediction
81(1)
7.6 Quantitative PKPD/Tox Modeling
82(1)
7.7 Summarizing
83(1)
References
84(3)
8 Development: Multiscale CSB---Simulation Tools
87(16)
8.1 Defining CSB
88(3)
8.2 Redefining (and Discovering) Emergent Properties at Higher-Level Hierarchies
91(1)
8.3 Virtual Organs, Disease Models, Virtual Patient
92(1)
8.4 Population Level Model: Towards Individualized Medicine
93(1)
8.5 Targeting Networks: Towards Organismic, Full-Scale Design
94(1)
8.6 Redefining the Traditional R&D Paradigm
95(4)
8.7 Summarizing
99(1)
References
99(4)
9 Development: Drug Formulation and Delivery
103(6)
9.1 Targeting Concept and Mechanisms
103(2)
9.1.1 SB and BI Inputs
104(1)
9.2 Nanoscale Drug Delivery Systems
105(1)
9.3 CSB at Formulation and Delivery
105(1)
9.4 Summarizing
106(1)
References
106(3)
10 Development: Preclinical Model Based Drug Development
109(6)
10.1 Defining MBDD
109(3)
10.2 Summarizing
112(1)
References
112(3)
11 Systems Biology: Impact on Pharma and Biotech
115
11.1 SB Impact
115(5)
11.2 Key Technologies and Tools Needed for Development of Systems Biology/CSB
120(1)
11.3 Steps in System Biology/CSB
120(3)
11.4 Benefits of Systems Biology and CSB
123(1)
11.5 Summary
123(4)
References
127