Summary Targeting cellular processes
to treat disease
Book chapter 8: Bioenergetics and Oxidative Metabolism---------------------------------------- 3
Oxidation as a source of energy--------------------------------------------------------------------------3
Free energy---------------------------------------------------------------------------------------------------- 3
Conservation of energy by coupling of reactions to hydrolysis of ATP------------------------- 3
Mitochondrial synthesis of adenosine triphosphate from reduced coenzymes--------------- 4
The mitochondrial electron transport system----------------------------------------------------------5
Transfer of electrons from NADH into mitochondria------------------------------------------------- 7
Synthesis of adenosine triphosphate: the chemiosmotic hypothesis----------------------------7
Inhibitors of oxidative metabolism------------------------------------------------------------------------9
Regulation of oxidative phosphorylation-------------------------------------------------------------- 10
Book chapter 9: Glycolysis and the Pentose Phosphate Pathway---------------------------- 11
Introduction--------------------------------------------------------------------------------------------------- 11
The erythrocyte---------------------------------------------------------------------------------------------- 11
Glycolysis----------------------------------------------------------------------------------------------------- 11
The pentose phosphate pathway----------------------------------------------------------------------- 14
LE Mitochondrial diseases: Pre-clinical drug discovery in academia----------------------- 14
Mitochondrial function and disease-------------------------------------------------------------------- 14
Take home message--------------------------------------------------------------------------------------- 18
Isolated human complex I (CI) deficiency------------------------------------------------------------ 18
Cellular consequences CI deficiency------------------------------------------------------------------ 19
Does mitochondrial shape play a role in CI deficiency?------------------------------------------ 20
Paper - Mitochondrial disorders in children: Toward development of small molecule
treatment strategies-------------------------------------------------------------------------------------------21
Paper - Monogenic mitochondrial disorders--------------------------------------------------------- 22
iRAT 1-------------------------------------------------------------------------------------------------------------- 23
Assignments 1 - Mitochondria-----------------------------------------------------------------------------27
LE Mitochondrial disease: Small molecule drug development at Khondrion------------- 31
General drug development principles----------------------------------------------------------------- 31
Specific challenges development for drugs for mitochondrial diseases---------------------- 32
Summary primary mitochondrial diseases-------------------------------------------------------33
A general view on the mitochondrial therapy development-------------------------------------- 33
Khondrion development of sonlicromanol------------------------------------------------------------ 33
iRAT 2-------------------------------------------------------------------------------------------------------------- 35
Assignment 2 - Drug development-----------------------------------------------------------------------37
Integrins are transmembrane heterodimers----------------------------------------------------------40
Integrins must interact with the cytoskeleton to bind cells to the ECM------------------------41
Cells can regulate the activity of their integrins----------------------------------------------------- 42
Integrins activate intracellular signaling pathways------------------------------------------------- 42
Paper - Exploring the role of RGD-recognizing integrins in cancer-------------------------- 45
Paper - Beta1 integrin targeting in cancer-------------------------------------------------------------49
,Paper - AlphaIIbbeta3 targeting in cardiovascular medicine (Beta3)-------------------------49
Paper - Alpha4beta7 targeting in IBD (Beta7)-------------------------------------------------------- 50
LE Integrin adhesion & signaling-------------------------------------------------------------------------51
Integrin classes-----------------------------------------------------------------------------------------52
LE Targeting integrin function in cell migration----------------------------------------------------- 57
Extracellular matrix----------------------------------------------------------------------------------------- 57
Integrins in focal contact formation---------------------------------------------------------------------57
Integrins in (cancer) cell migration--------------------------------------------------------------------- 58
Impact of integrin expression on migration efficiency and mode------------------------------- 63
Principles of experimental integrin targeting--------------------------------------------------------- 63
Experimental integrin targeting in vivo - a combination therapy with irradiation------------ 63
Computer practical-------------------------------------------------------------------------------------------- 64
Exam questions------------------------------------------------------------------------------------------------ 65
SSA 7 - Small molecules vs biologics------------------------------------------------------------------ 66
Assignment 3 - Biologic development in context of integrins/cell migration------------- 68
SSA 8 - Stem cells--------------------------------------------------------------------------------------------- 71
LE - Cell based therapeutics------------------------------------------------------------------------------- 75
Regenerative medicine------------------------------------------------------------------------------------ 77
Regulatory issues-------------------------------------------------------------------------------------------79
,Book chapter 8: Bioenergetics and Oxidative
Metabolism
Oxidation as a source of energy
The BMR (basal metabolic rate) is a measure of the toal daily energy expenditure by the
body at rest. Heat production by mitochondria accounts for the largest portion of the BMR.
The RMR (resting metabolic rate) is the same as BMR but measured under less restrictive
conditions.
Stages of fuel oxidation (overall image summarizing the processes in the body):
Free energy
The direction of a reaction depends on the difference between the free energy of reactants
and products. When reactant A reacts to form product B, the free energy change in this
reaction, ΔG, can be determined. All reactions in biological systems are considered to be
reversible reactions.
The free energy of metabolic reactions is related to their equilibrium constants by the Gibb’s
equation. When ΔG is negative, the reaction ‘creates’ energy and when it is positive energy
is used. A negative ΔG means that the reaction is favorable.
Conservation of energy by coupling of reactions to hydrolysis of
ATP
ATP is a product of catabolic reactions and a driver of biosynthetic reactions. Living systems
must transfer energy from one molecule to another without losing all of it as heat. Some of
the energy must be conserved in a chemical form to drive nonspontaneous biosynthetic
reactions. Nearly half of the energy obtained from the oxidation of metabolic fuels is
channeled into the synthesis of ATP.
Within the ATP molecule, the two phosphoanhydride linkages are said to be high energy
bonds because their hydrolysis yields a large negative change in free energy. When these
are broken ATP is converted to ADP or AMP.
, Nearly all biosynthetic pathways are thermodynamically unfavorable, but they are made
favorable by coupling various reactions with hydrolysis of high energy compounds.
The coupling of an unfavorable reaction to a favorable reaction is done by kinase enzymes.
Metabolic function of ATP requires magnesium. ATP forms a complex with magnesium,
which is required in all reactions in which ATP participates. A magnesium deficiency impairs
virtually all of metabolism because ATP can neither be made nor utilized in adequate
amounts.
Mitochondrial synthesis of adenosine triphosphate from
reduced coenzymes
Oxidative phosphorylation is the mechanism by which energy derived from fuel oxidation is
conserved in the form of ATP.
Glycolytic pathway begins in the cytoplasm. Energy production from fatty acids occurs in
the mitochondrion.
Mitochondria:
Outer mitochondrial membrane (OMM)
- Contains enzyme and transport proteins.
- Via the pore-forming protein porin (P) it is permeable to virtually all ions, small
molecules and proteins less than 10.000 Da.
- Large proteins must be transported via the TOM (translocase in the outer
mitochondrial membrane) and TIM (translocale in the inner mitochondrial membrane)
- A vital process because the majority of mitochondrial proteins are nuclear
encoded and must be transported into the mitochondrion.
Mitochondrial genome (mtDNA)
- Encodes 13 vital subunits of the proton pumps and ATP synthase.
Inner mitochondrial membrane (IMM)
- Pleated with cristae
- Impermeable to most ions and small molecules, such as nucleotides (also ATP),
coenzymes, phosphate and protons.
- Transporter proteins are required to selectively facilitate translocation of specific
molecules across the inner membrane.
- Contains components of oxidative phosphorylation.
to treat disease
Book chapter 8: Bioenergetics and Oxidative Metabolism---------------------------------------- 3
Oxidation as a source of energy--------------------------------------------------------------------------3
Free energy---------------------------------------------------------------------------------------------------- 3
Conservation of energy by coupling of reactions to hydrolysis of ATP------------------------- 3
Mitochondrial synthesis of adenosine triphosphate from reduced coenzymes--------------- 4
The mitochondrial electron transport system----------------------------------------------------------5
Transfer of electrons from NADH into mitochondria------------------------------------------------- 7
Synthesis of adenosine triphosphate: the chemiosmotic hypothesis----------------------------7
Inhibitors of oxidative metabolism------------------------------------------------------------------------9
Regulation of oxidative phosphorylation-------------------------------------------------------------- 10
Book chapter 9: Glycolysis and the Pentose Phosphate Pathway---------------------------- 11
Introduction--------------------------------------------------------------------------------------------------- 11
The erythrocyte---------------------------------------------------------------------------------------------- 11
Glycolysis----------------------------------------------------------------------------------------------------- 11
The pentose phosphate pathway----------------------------------------------------------------------- 14
LE Mitochondrial diseases: Pre-clinical drug discovery in academia----------------------- 14
Mitochondrial function and disease-------------------------------------------------------------------- 14
Take home message--------------------------------------------------------------------------------------- 18
Isolated human complex I (CI) deficiency------------------------------------------------------------ 18
Cellular consequences CI deficiency------------------------------------------------------------------ 19
Does mitochondrial shape play a role in CI deficiency?------------------------------------------ 20
Paper - Mitochondrial disorders in children: Toward development of small molecule
treatment strategies-------------------------------------------------------------------------------------------21
Paper - Monogenic mitochondrial disorders--------------------------------------------------------- 22
iRAT 1-------------------------------------------------------------------------------------------------------------- 23
Assignments 1 - Mitochondria-----------------------------------------------------------------------------27
LE Mitochondrial disease: Small molecule drug development at Khondrion------------- 31
General drug development principles----------------------------------------------------------------- 31
Specific challenges development for drugs for mitochondrial diseases---------------------- 32
Summary primary mitochondrial diseases-------------------------------------------------------33
A general view on the mitochondrial therapy development-------------------------------------- 33
Khondrion development of sonlicromanol------------------------------------------------------------ 33
iRAT 2-------------------------------------------------------------------------------------------------------------- 35
Assignment 2 - Drug development-----------------------------------------------------------------------37
Integrins are transmembrane heterodimers----------------------------------------------------------40
Integrins must interact with the cytoskeleton to bind cells to the ECM------------------------41
Cells can regulate the activity of their integrins----------------------------------------------------- 42
Integrins activate intracellular signaling pathways------------------------------------------------- 42
Paper - Exploring the role of RGD-recognizing integrins in cancer-------------------------- 45
Paper - Beta1 integrin targeting in cancer-------------------------------------------------------------49
,Paper - AlphaIIbbeta3 targeting in cardiovascular medicine (Beta3)-------------------------49
Paper - Alpha4beta7 targeting in IBD (Beta7)-------------------------------------------------------- 50
LE Integrin adhesion & signaling-------------------------------------------------------------------------51
Integrin classes-----------------------------------------------------------------------------------------52
LE Targeting integrin function in cell migration----------------------------------------------------- 57
Extracellular matrix----------------------------------------------------------------------------------------- 57
Integrins in focal contact formation---------------------------------------------------------------------57
Integrins in (cancer) cell migration--------------------------------------------------------------------- 58
Impact of integrin expression on migration efficiency and mode------------------------------- 63
Principles of experimental integrin targeting--------------------------------------------------------- 63
Experimental integrin targeting in vivo - a combination therapy with irradiation------------ 63
Computer practical-------------------------------------------------------------------------------------------- 64
Exam questions------------------------------------------------------------------------------------------------ 65
SSA 7 - Small molecules vs biologics------------------------------------------------------------------ 66
Assignment 3 - Biologic development in context of integrins/cell migration------------- 68
SSA 8 - Stem cells--------------------------------------------------------------------------------------------- 71
LE - Cell based therapeutics------------------------------------------------------------------------------- 75
Regenerative medicine------------------------------------------------------------------------------------ 77
Regulatory issues-------------------------------------------------------------------------------------------79
,Book chapter 8: Bioenergetics and Oxidative
Metabolism
Oxidation as a source of energy
The BMR (basal metabolic rate) is a measure of the toal daily energy expenditure by the
body at rest. Heat production by mitochondria accounts for the largest portion of the BMR.
The RMR (resting metabolic rate) is the same as BMR but measured under less restrictive
conditions.
Stages of fuel oxidation (overall image summarizing the processes in the body):
Free energy
The direction of a reaction depends on the difference between the free energy of reactants
and products. When reactant A reacts to form product B, the free energy change in this
reaction, ΔG, can be determined. All reactions in biological systems are considered to be
reversible reactions.
The free energy of metabolic reactions is related to their equilibrium constants by the Gibb’s
equation. When ΔG is negative, the reaction ‘creates’ energy and when it is positive energy
is used. A negative ΔG means that the reaction is favorable.
Conservation of energy by coupling of reactions to hydrolysis of
ATP
ATP is a product of catabolic reactions and a driver of biosynthetic reactions. Living systems
must transfer energy from one molecule to another without losing all of it as heat. Some of
the energy must be conserved in a chemical form to drive nonspontaneous biosynthetic
reactions. Nearly half of the energy obtained from the oxidation of metabolic fuels is
channeled into the synthesis of ATP.
Within the ATP molecule, the two phosphoanhydride linkages are said to be high energy
bonds because their hydrolysis yields a large negative change in free energy. When these
are broken ATP is converted to ADP or AMP.
, Nearly all biosynthetic pathways are thermodynamically unfavorable, but they are made
favorable by coupling various reactions with hydrolysis of high energy compounds.
The coupling of an unfavorable reaction to a favorable reaction is done by kinase enzymes.
Metabolic function of ATP requires magnesium. ATP forms a complex with magnesium,
which is required in all reactions in which ATP participates. A magnesium deficiency impairs
virtually all of metabolism because ATP can neither be made nor utilized in adequate
amounts.
Mitochondrial synthesis of adenosine triphosphate from
reduced coenzymes
Oxidative phosphorylation is the mechanism by which energy derived from fuel oxidation is
conserved in the form of ATP.
Glycolytic pathway begins in the cytoplasm. Energy production from fatty acids occurs in
the mitochondrion.
Mitochondria:
Outer mitochondrial membrane (OMM)
- Contains enzyme and transport proteins.
- Via the pore-forming protein porin (P) it is permeable to virtually all ions, small
molecules and proteins less than 10.000 Da.
- Large proteins must be transported via the TOM (translocase in the outer
mitochondrial membrane) and TIM (translocale in the inner mitochondrial membrane)
- A vital process because the majority of mitochondrial proteins are nuclear
encoded and must be transported into the mitochondrion.
Mitochondrial genome (mtDNA)
- Encodes 13 vital subunits of the proton pumps and ATP synthase.
Inner mitochondrial membrane (IMM)
- Pleated with cristae
- Impermeable to most ions and small molecules, such as nucleotides (also ATP),
coenzymes, phosphate and protons.
- Transporter proteins are required to selectively facilitate translocation of specific
molecules across the inner membrane.
- Contains components of oxidative phosphorylation.
