2024-2025
THERAPEUTIC MODALITIES
TYPES OF THERAPEUTICS
Conven4onal therapeu4cs: all types of interven4on aimed at allevia4ng the effects of disease.
⇨ improve disease symptoms and/or prognosis, disease preven4on, permanent cure
Non-conven4onal health products: not really therapeu4cs, but use “eu4cals” to give it a therapeu4c flavor.
⇨ Nutraceu4cals (dietary prepara4ons) or cosmoceu4cals (cosme4c with ac4ve (?) substances)
CURRENT THERAPEUTICS
CONVENTIONAL THERAPEUTIC DRUGS
Small molecule synthe4c compounds (most of the current drugs)
+ broad ‘chemical space’ - decreasing flow of ‘new’ molecules
+ accepted by profession and community - lower lever of selec4vity (e.g., Toxicity)
+ various routes of administra4on - pharmacokine4c limita4ons
+ longterm pharmaceu4cal experience - frequent poor oral absorp4on
Natural products (an4bio4cs, an4cancer, opiates, sta4ns…) or semi-synthe4cally derived
BIOPHARMACEUTICALS
Biopharmaceu4cals: Therapeu4c protein or nucleic acid prepara4ons made by techniques involving DNA technology
§ Pep4de/protein mediators
§ Blood clo\ng factors
§ Enzymes
§ An4bodies
§ Vaccines
§ Cells/4ssues
+ open new therapeu4c op4ons - expensive produc4on methods
+ more straigh_orward discovery - lack or oral ac4vity and short half-life
+ unexpected toxicity is less common - longer and more expensive development
+ higher product quality - species-specific ac4on (no animal models
Gene therapy
Gene therapy: correc4ng gene4c defects by altering gene4c material of cells by recombinant DNA technology
§ Introduce new genes to replace missing or dysfunc4onal ones
§ Aim at single-gene disorders and cancer
§ Restricted to soma4c cell treatments (not on germ cells)
An4sense-DNA: oligonucleo4de sequence complementary to part of a known mRNA sequence ⇨ selec4ve blocking of
expression (but degrades quickly in plasma and needs liposomal packing to enter cells)
Ribozymes: specific RNA-sequences that inac4vate genes by catalyzing DNA cleavage
Cell-based therapy
Cell-based therapy: cell replacement therapies in various kinds of degenera4ve diseases
Established clinical use: stem cells of own 4ssue
§ Autologous cell grabs: leukemia, bone-marrow malignancies
§ Autologous chondrocytes: car4lage repair
§ Autologous kera4nocytes: trea4ng burns
Experimental explora4on: stem cells of embryonic 4ssues (ethical concerns!)
§ Neuronal cells in brain: Parkinson, ALS, Hun4ngton
§ Insulin-secre4ng cells: diabetes
§ Cardiac muscle cells: restora4on aber myocardial infarc4on
Organ- and 3ssue transplanta3on
Bionic devices
1
,2024-2025
GENERAL PRINCIPLES OF DRUG DISCOVERY
PHASES IN DRUG DISCOVERY AND DEVELOPMENT
Main phases: drug discovery (research) – drug development – commercializa4on (marke4ng)
Not just sequen4al process ⇨ different clinical packages needed before each clinical phase
Drug discovery phase:
1. Choose a disease area and define the therapeu4c need
2. Select the target (biochemical, cellular or pathophysiological mechanism)
3. Validate the target
4. Iden4fica4on of a lead compound
5. design, tes4ng and op4miza4on of the drug molecule ⇨ candidate drug
STAGES OF DRUG DISCOVERY
1. Compound sources + filtering: pick the molecules that will likely s4ck to your target + are available and can be
synthesized
2. Screening libraries: In silico screening for target affinity, Lipinski rules, stability, toxicology…
3. Ac4ves and valida4on: eliminate artefacts + test for selec4vity + evaluate structure-ac4vity rela4onships (SAR)
4. Hits: iden4fica4on of drug metabolism, pharmacokine4cs, toxicity to get to lead iden4fica4on
5. Leads: solve pharmacokine4c issues, evaluate potency, selec4vity and pharmacokine4cs to establish a detailed
SAR ⇨ lead op4miza4on
6. Drug candidates ⇨ preclinical development
7. Development of the compounds
SELECTION CRITERIA FOR DRUG DISCOVERY
Typical selec4on criteria for oral drug candidates in the early discovery phase:
Chemical Pharmacological Pharmacokine0c Toxicological
- Patentable structure - Defined potency on target - Cell-permeable in vitro - In vitro genotoxicity tests
- Water-soluble - Selec0vity for specific - Adequate oral nega0ve
- Chemically stable target rela0ve to other bioavailability - Preliminary in vivo
- Large-scale synthesis related targets - CNS: penetrates BBB toxicology tests showing
feasible - Pharmacodynamic ac0vity - Appropriate plasma half- adequate margin between
- Non-chiral in vitro and in vivo life expected ‘therapeu0c’
- No known toxophoric - No adverse effects in - Defined metabolism by dose and maximum No
groups standard safety human liver microsomes Adverse Effect Dose
pharmacology tests - No inhibi0on or induc0on
- Ac0ve in disease models of cytochrome P450
2
,2024-2025
Criteria when making the decision of whether or not to start a new drug discovery project:
A) Strategic issues ⇨ desirability of the project (Should we do it?)
§ Unmet medical need ⇨ disease severity versus prevalence
§ Market considera4ons ⇨ will you make profit?
§ Company strategy and franchise
B) Scien4fic and technical issues ⇨ feasibility of the project (Could be do it?)
§ Scien4fic and technological basis: hypothesis, targets, assays…
§ State of compe44on and patent situa4on
§ Development and regulatory hurdles: Short or indefinite administra4on? Status of exis4ng therapies? Type of
product? Route of administra4on?
C) Opera4onal issues (Can we do it?)
IDENTIFICATION AND VALIDATION
DRUG TARGETS
Drug target: The molecular recogni4on site to which a drug will bind.
§ Lipids: cell membrane lipids
§ Proteins: receptors, enzymes, carrier proteins, structural proteins
§ Nucleic acids: DNA, RNA
§ Carbohydrates: cell surface carbohydrates, an4gens and recogni4on molecules
DRUG TARGET: CHARACTERISTICS
§ Drug targets are macromolecules
§ Drugs are generally much smaller than their targets (not the case when talking about biologicals)
§ Drugs interact with their targets by binding to binding sites
§ Binding sites are typically hydrophobic pockets on the surface of macromolecules
§ Binding interac4ons typically involve intermolecular bonds
§ Most drugs are in equilibrium between being bound and unbound to their target
§ Func4onal groups on the drug that are involved in binding interac4ons are binding groups
§ Specific regions within the binding site that are involved in binding interac4ons are called binding regions
DRUG-TARGET INTERACTION
Drug-target interac4ons are obtained from 3D structures of protein-ligand complexes and binding affini4es.
Characteris4cs are:
§ High level of steric complementarity between protein and ligand: lock-and-key paradigm
§ High complementarity of surface proper4es between protein and ligand
§ Ligand binds in an energe4cally favorable conforma4on
DRUG TARGET IDENTIFICATION: STRATEGIES
CONVENTIONAL STRATEGIES
Forward approach: analysis of pathophysiology ⇨ you know the disease and its target
§ Inflammatory disease: Target is COX-2, drug developed is Celecoxib.
§ Depression: Target is MAO-A, drug developed is Moclobemide
Backward approach: analysis of mechanism of ac4on of exis4ng therapeu4cs
§ Benzodiazepines: Disease is anxiety, sleep disorders and Target is BDZ binding site on GABAA receptor
NEW STRATEGIES
A drug can intervene at expression level, regulatory factors or by ac4va4ng compensatory mechanisms.
Nearly all drug targets are proteins so can be found in the proteome. Its genes can be found in the genome.
General: one gene ⇨ one protein ⇨ one drug target BUT take into account:
§ Splice variants may result in different proteins from the same gene
§ Mul4meric/heteromeric receptors: non-iden4cal subunits encoded by different genes
§ Associa4on between protein and non-protein receptors (RAMPs ⇨ are no conven4onal receptors itself but can
modify other receptors when interac4ng)
Genome studies
Disease genes: muta4ons associated with par4cular disease
§ Single gene: gene products are not drug-targetable
§ Mul4ple genes: gene products may be drug-targetable
3
, 2024-2025
Disease modifying genes: muta4ons in regulatory genes ⇨ over- or underexpression of normal non-mutated genes
§ Gene expression profiling: microarrays, serial analysis of gene expression
§ Gene knock-out screening: transgenic mice, C. elegans
Druggable genes: gene product with drug-recogni4on binding site
Gene expression profiling = transcriptomics and proteomics
Transcriptome: popula4on of mRNAs present in the cell/4ssue
Profiling of transcriptome ⇨ DNA microarrays and heatmapping (not sensi4ve enough)
DRUG TARGET VALIDATION
PHARMACOLOGICAL VALIDATION
Combined with ‘lead’ discovery in HTS se\ngs
§ Use of ‘prototype’ inhibitors of the puta4ve target
§ Use of specific Ab to puta4ve target protein
GENETIC VALIDATION
= selec4ve suppression of expression of specific genes
Specific mechanisms do not need to be known.
1. An4sense oligonucleo4des
§ Synthe4c oligonucleo4des, complementary to the gene of interest.
§ Will bind to the cellular mRNA and prevent transla4on so you don’t get transla4on of disease proteins.
§ Careful because depending on modifica4on it can be toxic
2. RNA interference (RNAi)
§ Inac4va4on by cleavage of specific mRNAs or whole gene families
3. Transgenic animals
§ Exogenous gene is introduced so that the animal will have a new muta4on and can transfer to offspring
FUNCTIONAL GENOMICS
Is this a good approach for target iden4fica4on and valida4on? No model is completely representa4ve for the human
model so you must be cri4cal to what you see. Target valida4on with knock-out models is a valid approach.
Func4onal genomics: Assign all genes of an organism in a func4onal framework according to the ac4vity of the encoded
proteins in the biology of the organism.
1. Iden4fica4on and valida4on of possible drug targets
⇨ control of gene expression at cellular level
§ Transfec4on of cells: overexpression, dele4on…
§ An4sense nucleo4des, RNAi…
§ Transgenic animals: Tet-on/Tet-off and Cre/Lox system
2. Animal models
⇨ control of gene expression at 4ssue /whole organism level
§ Natural or induced muta4ons
§ Strain-specifici4es following in-breeding
§ Possibility for ‘humaniza4on’
§ Specific techniques (BACs, YACs)
MEDICINAL CHEMISTRY AND DRUG ACTION
Medicinal chemistry is very important in drug discovery:
1. Inven4on, discovery, iden4fica4on and prepara4on of biologically ac4ve compounds
2. Pharmaceu4cal phase: upscaling and pre-formula4on
3. Pharmacokine4c phase: assessment of absorp4on, distribu4on, metabolism, excre4on (ADME)
4. Pharmacodynamic phase: interpret the mode-of-ac4on at molecular level & structure-ac4vity rela4onship (SAR)
4
THERAPEUTIC MODALITIES
TYPES OF THERAPEUTICS
Conven4onal therapeu4cs: all types of interven4on aimed at allevia4ng the effects of disease.
⇨ improve disease symptoms and/or prognosis, disease preven4on, permanent cure
Non-conven4onal health products: not really therapeu4cs, but use “eu4cals” to give it a therapeu4c flavor.
⇨ Nutraceu4cals (dietary prepara4ons) or cosmoceu4cals (cosme4c with ac4ve (?) substances)
CURRENT THERAPEUTICS
CONVENTIONAL THERAPEUTIC DRUGS
Small molecule synthe4c compounds (most of the current drugs)
+ broad ‘chemical space’ - decreasing flow of ‘new’ molecules
+ accepted by profession and community - lower lever of selec4vity (e.g., Toxicity)
+ various routes of administra4on - pharmacokine4c limita4ons
+ longterm pharmaceu4cal experience - frequent poor oral absorp4on
Natural products (an4bio4cs, an4cancer, opiates, sta4ns…) or semi-synthe4cally derived
BIOPHARMACEUTICALS
Biopharmaceu4cals: Therapeu4c protein or nucleic acid prepara4ons made by techniques involving DNA technology
§ Pep4de/protein mediators
§ Blood clo\ng factors
§ Enzymes
§ An4bodies
§ Vaccines
§ Cells/4ssues
+ open new therapeu4c op4ons - expensive produc4on methods
+ more straigh_orward discovery - lack or oral ac4vity and short half-life
+ unexpected toxicity is less common - longer and more expensive development
+ higher product quality - species-specific ac4on (no animal models
Gene therapy
Gene therapy: correc4ng gene4c defects by altering gene4c material of cells by recombinant DNA technology
§ Introduce new genes to replace missing or dysfunc4onal ones
§ Aim at single-gene disorders and cancer
§ Restricted to soma4c cell treatments (not on germ cells)
An4sense-DNA: oligonucleo4de sequence complementary to part of a known mRNA sequence ⇨ selec4ve blocking of
expression (but degrades quickly in plasma and needs liposomal packing to enter cells)
Ribozymes: specific RNA-sequences that inac4vate genes by catalyzing DNA cleavage
Cell-based therapy
Cell-based therapy: cell replacement therapies in various kinds of degenera4ve diseases
Established clinical use: stem cells of own 4ssue
§ Autologous cell grabs: leukemia, bone-marrow malignancies
§ Autologous chondrocytes: car4lage repair
§ Autologous kera4nocytes: trea4ng burns
Experimental explora4on: stem cells of embryonic 4ssues (ethical concerns!)
§ Neuronal cells in brain: Parkinson, ALS, Hun4ngton
§ Insulin-secre4ng cells: diabetes
§ Cardiac muscle cells: restora4on aber myocardial infarc4on
Organ- and 3ssue transplanta3on
Bionic devices
1
,2024-2025
GENERAL PRINCIPLES OF DRUG DISCOVERY
PHASES IN DRUG DISCOVERY AND DEVELOPMENT
Main phases: drug discovery (research) – drug development – commercializa4on (marke4ng)
Not just sequen4al process ⇨ different clinical packages needed before each clinical phase
Drug discovery phase:
1. Choose a disease area and define the therapeu4c need
2. Select the target (biochemical, cellular or pathophysiological mechanism)
3. Validate the target
4. Iden4fica4on of a lead compound
5. design, tes4ng and op4miza4on of the drug molecule ⇨ candidate drug
STAGES OF DRUG DISCOVERY
1. Compound sources + filtering: pick the molecules that will likely s4ck to your target + are available and can be
synthesized
2. Screening libraries: In silico screening for target affinity, Lipinski rules, stability, toxicology…
3. Ac4ves and valida4on: eliminate artefacts + test for selec4vity + evaluate structure-ac4vity rela4onships (SAR)
4. Hits: iden4fica4on of drug metabolism, pharmacokine4cs, toxicity to get to lead iden4fica4on
5. Leads: solve pharmacokine4c issues, evaluate potency, selec4vity and pharmacokine4cs to establish a detailed
SAR ⇨ lead op4miza4on
6. Drug candidates ⇨ preclinical development
7. Development of the compounds
SELECTION CRITERIA FOR DRUG DISCOVERY
Typical selec4on criteria for oral drug candidates in the early discovery phase:
Chemical Pharmacological Pharmacokine0c Toxicological
- Patentable structure - Defined potency on target - Cell-permeable in vitro - In vitro genotoxicity tests
- Water-soluble - Selec0vity for specific - Adequate oral nega0ve
- Chemically stable target rela0ve to other bioavailability - Preliminary in vivo
- Large-scale synthesis related targets - CNS: penetrates BBB toxicology tests showing
feasible - Pharmacodynamic ac0vity - Appropriate plasma half- adequate margin between
- Non-chiral in vitro and in vivo life expected ‘therapeu0c’
- No known toxophoric - No adverse effects in - Defined metabolism by dose and maximum No
groups standard safety human liver microsomes Adverse Effect Dose
pharmacology tests - No inhibi0on or induc0on
- Ac0ve in disease models of cytochrome P450
2
,2024-2025
Criteria when making the decision of whether or not to start a new drug discovery project:
A) Strategic issues ⇨ desirability of the project (Should we do it?)
§ Unmet medical need ⇨ disease severity versus prevalence
§ Market considera4ons ⇨ will you make profit?
§ Company strategy and franchise
B) Scien4fic and technical issues ⇨ feasibility of the project (Could be do it?)
§ Scien4fic and technological basis: hypothesis, targets, assays…
§ State of compe44on and patent situa4on
§ Development and regulatory hurdles: Short or indefinite administra4on? Status of exis4ng therapies? Type of
product? Route of administra4on?
C) Opera4onal issues (Can we do it?)
IDENTIFICATION AND VALIDATION
DRUG TARGETS
Drug target: The molecular recogni4on site to which a drug will bind.
§ Lipids: cell membrane lipids
§ Proteins: receptors, enzymes, carrier proteins, structural proteins
§ Nucleic acids: DNA, RNA
§ Carbohydrates: cell surface carbohydrates, an4gens and recogni4on molecules
DRUG TARGET: CHARACTERISTICS
§ Drug targets are macromolecules
§ Drugs are generally much smaller than their targets (not the case when talking about biologicals)
§ Drugs interact with their targets by binding to binding sites
§ Binding sites are typically hydrophobic pockets on the surface of macromolecules
§ Binding interac4ons typically involve intermolecular bonds
§ Most drugs are in equilibrium between being bound and unbound to their target
§ Func4onal groups on the drug that are involved in binding interac4ons are binding groups
§ Specific regions within the binding site that are involved in binding interac4ons are called binding regions
DRUG-TARGET INTERACTION
Drug-target interac4ons are obtained from 3D structures of protein-ligand complexes and binding affini4es.
Characteris4cs are:
§ High level of steric complementarity between protein and ligand: lock-and-key paradigm
§ High complementarity of surface proper4es between protein and ligand
§ Ligand binds in an energe4cally favorable conforma4on
DRUG TARGET IDENTIFICATION: STRATEGIES
CONVENTIONAL STRATEGIES
Forward approach: analysis of pathophysiology ⇨ you know the disease and its target
§ Inflammatory disease: Target is COX-2, drug developed is Celecoxib.
§ Depression: Target is MAO-A, drug developed is Moclobemide
Backward approach: analysis of mechanism of ac4on of exis4ng therapeu4cs
§ Benzodiazepines: Disease is anxiety, sleep disorders and Target is BDZ binding site on GABAA receptor
NEW STRATEGIES
A drug can intervene at expression level, regulatory factors or by ac4va4ng compensatory mechanisms.
Nearly all drug targets are proteins so can be found in the proteome. Its genes can be found in the genome.
General: one gene ⇨ one protein ⇨ one drug target BUT take into account:
§ Splice variants may result in different proteins from the same gene
§ Mul4meric/heteromeric receptors: non-iden4cal subunits encoded by different genes
§ Associa4on between protein and non-protein receptors (RAMPs ⇨ are no conven4onal receptors itself but can
modify other receptors when interac4ng)
Genome studies
Disease genes: muta4ons associated with par4cular disease
§ Single gene: gene products are not drug-targetable
§ Mul4ple genes: gene products may be drug-targetable
3
, 2024-2025
Disease modifying genes: muta4ons in regulatory genes ⇨ over- or underexpression of normal non-mutated genes
§ Gene expression profiling: microarrays, serial analysis of gene expression
§ Gene knock-out screening: transgenic mice, C. elegans
Druggable genes: gene product with drug-recogni4on binding site
Gene expression profiling = transcriptomics and proteomics
Transcriptome: popula4on of mRNAs present in the cell/4ssue
Profiling of transcriptome ⇨ DNA microarrays and heatmapping (not sensi4ve enough)
DRUG TARGET VALIDATION
PHARMACOLOGICAL VALIDATION
Combined with ‘lead’ discovery in HTS se\ngs
§ Use of ‘prototype’ inhibitors of the puta4ve target
§ Use of specific Ab to puta4ve target protein
GENETIC VALIDATION
= selec4ve suppression of expression of specific genes
Specific mechanisms do not need to be known.
1. An4sense oligonucleo4des
§ Synthe4c oligonucleo4des, complementary to the gene of interest.
§ Will bind to the cellular mRNA and prevent transla4on so you don’t get transla4on of disease proteins.
§ Careful because depending on modifica4on it can be toxic
2. RNA interference (RNAi)
§ Inac4va4on by cleavage of specific mRNAs or whole gene families
3. Transgenic animals
§ Exogenous gene is introduced so that the animal will have a new muta4on and can transfer to offspring
FUNCTIONAL GENOMICS
Is this a good approach for target iden4fica4on and valida4on? No model is completely representa4ve for the human
model so you must be cri4cal to what you see. Target valida4on with knock-out models is a valid approach.
Func4onal genomics: Assign all genes of an organism in a func4onal framework according to the ac4vity of the encoded
proteins in the biology of the organism.
1. Iden4fica4on and valida4on of possible drug targets
⇨ control of gene expression at cellular level
§ Transfec4on of cells: overexpression, dele4on…
§ An4sense nucleo4des, RNAi…
§ Transgenic animals: Tet-on/Tet-off and Cre/Lox system
2. Animal models
⇨ control of gene expression at 4ssue /whole organism level
§ Natural or induced muta4ons
§ Strain-specifici4es following in-breeding
§ Possibility for ‘humaniza4on’
§ Specific techniques (BACs, YACs)
MEDICINAL CHEMISTRY AND DRUG ACTION
Medicinal chemistry is very important in drug discovery:
1. Inven4on, discovery, iden4fica4on and prepara4on of biologically ac4ve compounds
2. Pharmaceu4cal phase: upscaling and pre-formula4on
3. Pharmacokine4c phase: assessment of absorp4on, distribu4on, metabolism, excre4on (ADME)
4. Pharmacodynamic phase: interpret the mode-of-ac4on at molecular level & structure-ac4vity rela4onship (SAR)
4
