Molecular Evolutionary Models in Drug Discovery

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MOLECULAR
EVOLUTIONARY
MODELS IN DRUG
DISCOVERY
Copyright
Dedication
Preface
1
Molecular evolution: The origins of interaction
	Introduction
	Aperiodic crystals and biological molecules
	Cell-to-cell communication
	Biofilm as an evolutionary niche
	The rise of macroscopic symbiotic holobionts
	Secondary metabolism: Innovations for survival
	Complex biological systems, cooperation, and solidarity
	Biotechnology of molecular evolution: Interaction in the application
	Conclusions
	Acknowledgments
	References
2
Thermodynamics of secondary metabolism: The triumph of living systems
	Introduction
	Life in the second law of thermodynamics
	Thermodynamics of intercellular communication
	Thermodynamic epigenetics of secondary metabolism
	Symbiotic holobiont thermodynamics
	Entropic interactomes and their influence in the hologenome
	Biosynthetic gene clusters: Communication and entropy
	Thermodynamics in complex biological systems: Implications in health and disease
	Biotechnological applications of hologenomics: The power of holobiontic adaptation
	Conclusions
	References
3
Natural products and molecular networks
	Introduction
	Life and secondary metabolism: Interactions in evolution
	Natural products as molecular communicators
	Natural products: Networks in the RNA world
	Epigenetics of secondary metabolism
	The symbiotic holobiont as a molecular network
	Chemical signaling and the hologenome
	Holobiont health communication and symbiosis
	Conclusions
	References
	Further reading
4
Chemical evolution: Life as the lab of the universe
	Introduction
	Chemical evolution and communication in the RNA world
	Chemical evolution and proteins: The first model
	Multifunctional enzymes and the secondary metabolites explosion
	Cytochromes as enhancers of specialized metabolites
	The interaction between the environment and multifunctional enzymes: Adaptation in chemical diversity
	Symbiosis: The role of the holobiont as a source of chemical evolution
	Conclusions
	References
5
Autopoietic symbiogenesis in secondary metabolism
	Introduction
	Secondary metabolism in interactions and mutualism
	Ribosomes, secondary metabolism, and molecular evolution
	Metabolomics in the holobiontic unit
	Metagenomics in the symbiopoiesis of holobionts
	Hologenome metabolomics: Adaptation in chemical diversity
	Symbiopoiesis and cognition: Life has commitment, concentration, and will
	Conclusions
	References
6
Metabolomics of epigenetics: A history of the integrome
	Introduction
	Metabolic flux analysis of epigenetics: The route toward chemical diversity
	Epigenetics in the RNA world: The rise of fitness
	Multifunctional enzymes and epigenetic regulation: The source of promiscuity
	Fluxomics, adaptomics, and epigenomics in the holobiontic unit
	Inheritable symbiosis in adaptation
	Epigenetics, epitranscriptomics, and the integrome: Adaptation in biotechnological innovation
	Conclusions
	References
7
Systems biology, drug development, and clinical outcomes
	Introduction
	Systems biology in the exposome
	Evolutoma and interactomes: Toward a protocol of personalized medicine
	Phenomics of personalized medicine
	Systems biology and symbiosis in homeostasis
	Metagenomics in personalized medicine and drug development: The microbiome makes the holobiont
	Symbiotic approaches in the development of new drugs, balance, pliability, adaptation, and healing
	Conclusions
	References
8
Toxical autopoiesis
	Introduction
	Evolutionary hormesis
	ROS in the RNA world
	Mitohormesis as an adaptative response
	Microbiomes and the proteasome, endoplasmic reticulum, and mitochondria (PERM) hypothesis
	Hormesis, autopoiesis, and drug discovery
	Conclusions
	References
	Further reading
9
Autocatakinesis systems in drug discovery
	Introduction
	Metabolic autocatakinesis
	The RNA world, proteostasis, and thermodynamic equilibrium
	Heat shock proteins, adaptative response, and thermodynamic evolution
	Autocatakinesis, symbiosis, interactions, and balance in mutualism
	Autocatakinesis systems in drug discovery
	Conclusions
	References
10
Biophysics applications in drug discovery: Working toward a new integrative model
	Introduction
	Systems biology in an evolutionary model in drug discovery
	Biophysical methods and thermodynamic drug discovery
	The metabolomics of homeostasis
	Metagenomics, metabolomics, and symbiotic drugs
	Biophysical methods in biotechnology
	Conclusions
	References
Index
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