|
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) |
|
|
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) |
|
|
15 | (1) |
|
|
16 | (3) |
|
2.2.3 Qualitative and Quantitative Screens and Filters |
|
|
19 | (1) |
|
2.2.4 Structure-Activity Methods (SAR/QSAR) |
|
|
20 | (1) |
|
|
21 | (1) |
|
|
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) |
|
|
27 | (1) |
|
|
27 | (1) |
|
3.1.3 Molecular Mechanics |
|
|
27 | (1) |
|
|
28 | (1) |
|
3.1.5 Receptor Based QSAR Methods |
|
|
28 | (1) |
|
|
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) |
|
|
33 | (1) |
|
|
34 | (1) |
|
|
34 | (2) |
|
|
36 | (1) |
|
|
36 | (3) |
|
4 Integrative Systems Biology II---Molecular Biology: Phase 2 Lead Discovery and In Silico Screening |
|
|
39 | (12) |
|
|
40 | (2) |
|
|
40 | (1) |
|
|
41 | (1) |
|
|
42 | (1) |
|
|
42 | (1) |
|
|
43 | (1) |
|
4.4 Minimal Phenotype and Synthetic Biology |
|
|
43 | (1) |
|
|
44 | (1) |
|
4.5 Reconstructing Biological Networks |
|
|
44 | (2) |
|
|
46 | (1) |
|
|
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) |
|
|
58 | (1) |
|
|
59 | (1) |
|
5.7 Computational Systems Biology |
|
|
60 | (3) |
|
|
63 | (1) |
|
|
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) |
|
|
72 | (1) |
|
|
73 | (1) |
|
|
73 | (1) |
|
|
73 | (1) |
|
6.5 In Silico Pharmacology: Future |
|
|
74 | (1) |
|
|
75 | (1) |
|
|
76 | (1) |
|
7 Development: Pharmacokinetics---Systems Biology in Health and Disease III |
|
|
77 | (10) |
|
|
78 | (1) |
|
|
78 | (1) |
|
7.2 Adaptive Trial Design |
|
|
78 | (1) |
|
7.3 Equilibrium Versus Non-Equilibrium PK Models |
|
|
79 | (1) |
|
|
80 | (1) |
|
|
80 | (1) |
|
7.5 In Silico Toxicity Prediction |
|
|
81 | (1) |
|
7.6 Quantitative PKPD/Tox Modeling |
|
|
82 | (1) |
|
|
83 | (1) |
|
|
84 | (3) |
|
8 Development: Multiscale CSB---Simulation Tools |
|
|
87 | (16) |
|
|
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) |
|
|
99 | (1) |
|
|
99 | (4) |
|
9 Development: Drug Formulation and Delivery |
|
|
103 | (6) |
|
9.1 Targeting Concept and Mechanisms |
|
|
103 | (2) |
|
|
104 | (1) |
|
9.2 Nanoscale Drug Delivery Systems |
|
|
105 | (1) |
|
9.3 CSB at Formulation and Delivery |
|
|
105 | (1) |
|
|
106 | (1) |
|
|
106 | (3) |
|
10 Development: Preclinical Model Based Drug Development |
|
|
109 | (6) |
|
|
109 | (3) |
|
|
112 | (1) |
|
|
112 | (3) |
|
11 Systems Biology: Impact on Pharma and Biotech |
|
|
115 | |
|
|
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) |
|
|
123 | (4) |
|
|
127 | |