PHS602 DRUG DISCOVERY AND DEVELOPMENT

PHS602

DRUG DISCOVERY AND DEVELOPMENT

Fall - 2021

Drug Discovery: Targets and Receptors

Ligands

Sub-Classification by the effect of ligand interaction with a biomolecule

• Agonist- super – above target natural

activity level - full – 100% of natural activity- partial – below natural activity

• Antagonist• Inverse Agonist- partial – below basal level- full – complete deactivation

Log10[Ligand]

Activity, %

100

basal

0

Lecture 4 / Slide 1


Ligands

Sub-Classification by the effect of ligand interaction with a biomolecule

• Competitive Agonist• Non-Competitive Agonist• Irreversible (Full) Agonist

✘ Super Antagonist✘ Inverse Antagonist✘ Partial AntagonistLog10[Ligand]

Activity, %

100

basal

0

Lecture 4 / Slide 2


Ligands

Example of super-agonist drug: Goserelin/Zoladex ®- activates G-protein-coupled Gonadotropin-releasing hormone receptor- stimulates the continuous production of testosterone and estrogen above

normal physiological levels- higher than normal levels of testosterone and estrogen result in down-

regulation of their production

Lecture 4 / Slide 3


Ligands

Example of partial agonist drug: Buprenorphine/Suboxone ®- opioid partial agonist with analgesic effects- produces pain relief by stimulating opioid receptors- much lower risk for inducing respiratory depression as compared to a full

agonist (morphine) because of overdose or abuse.

Lecture 4 / Slide 4


Ligands

Example of inverse agonist: Volinanserin (tested in clinical trials for treatment for insomnia) - highly selective inverse agonist of serotonin (5-HT2A) receptor

Risperidone ( antipsychotic, used to treat schizophrenia, bipolar disorder)- antagonist of serotonin receptors subtypes 5-HT1, 5-HT5, and 5-HT6

- inverse agonist of serotonin receptors subtypes 5-HT2A, 5-HT2B, and 5-HT2C

- inverse agonist of dopamine receptor D3 and histamine receptors H1 and H2

Lecture 4 / Slide 5


LigandsExample of ligand modifications that result in a variety of activity levels: Superagonist, Full Agonist, Partial Agonist, and Antagonist Actions of Arylguanidines at 5-Hydroxytryptamine-3 (5-HT3) Subunit A Receptors, ACS Chemical Neuroscience, 2016Link to the paper• Agonist- super – above natural activity- full – 100% of natural activity- partial – below natural activity

• Antagonist• Inverse Agonist- partial – below basal activity- full – complete deactivation

Lecture 4 / Slide 6

https://canvas.chapman.edu/courses/26037/modules/items/775140


Ligands and ReceptorsSuperagonist, Full Agonist, Partial Agonist, and Antagonist Actions of Arylguanidines at 5-Hydroxytryptamine-3 (5-HT3) Subunit A Receptors, ACS Chemical Neuroscience, 2016Link to the paper

1. Ligands: o Chemical structureo Modes of activity

2. Describe 5-HT3 receptor: Type / Natural ligand

3. Similar receptors by o Structure and Functiono Natural Ligand

4. Questions? Lecture 4 / Slide 7



Ligands

Chemistry of ligand interaction with a target• Electrostatic (including Van der Waals forces)• Hydrophobic• Covalent binding

Phenoxybenzamine Scopolamine

APR-246

Lecture 4 / Slide 8


Receptor

A cellular molecule or macromolecule (a complex or assembly of molecules) that is involved directly and specifically in chemical signaling.

• Physically associated with a cell

• Functionally associated with specific cell type(s)

• Localization:

Ø Cell surface receptors

Ø Intracellular receptorsAccessibility for drugs

Lecture 4 / Slide 9


Receptor


Direct interaction of receptors with ligands – directly involved in signalingSpecific interaction of receptors with ligands

– provide ligand-specific (signal-specific) response

Lecture 4 / Slide 10


Receptor


• Binds signaling molecule (ligand)• Transforms the signal according to the type of a receptor• Transmits the signal further through a pathway

Do we know any non-molecule signals?



Receptor

Transforms the signal according to the type of a receptor

Three major types of cell surface receptors:1. G-protein-coupled receptors2. Ion channel receptors3. Enzyme-linked receptors



Receptor G-protein-coupled receptors

Pharmacological importance• Almost 30% of FDA-approved medications target GPCRs • Expressed in most of the body’s tissues• Involved in cellular communication• GPCR-mediated signal transduction is crucial for

virtually all aspects of human physiology• GPCR druggability – the binding pockets have

beneficial physiochemical properties that facilitate the design of drug-like small molecules



G-protein-coupled receptors

IUPHAR classificationFive main families: • Rhodopsin (class A) • Secretin (class B) • Glutamate (class C) • Frizzled/Taste (class F)• Adhesion

From: The GPCR Network: a large-scale collaboration to determine human GPCR structure and function. R.C. Stevens, V. Cherezov, V. Katritch, R. Abagyan, P. Kuhn, H. Rosen & K. Wüthrich. Nature Reviews Drug Discovery 2013, 12:25-34. © 2013 Macmillan Publishers Ltd Lecture 4 / Slide 14



IUPHAR classificationFive main families: • Rhodopsin• Secretin• Glutamate• Frizzled/Taste• Adhesion

From: Hitchhiking on the heptahelical highway: structure and function of 7TM receptor complexes. J.J.G. Tesmer. Nature Reviews Molecular Cell Biology 2016, 17:439-450. © 2016 Macmillan Publishers Ltd Lecture 4 / Slide 15



Prominent therapeutic applications • opioid analgesics (agonists of μ opioid receptors) • allergy drugs (antagonists of histamine receptors) • anticholinergics (antagonists of cholinergic receptors) • typical and atypical antipsychotics (antagonists of

D2 dopamine receptor) • antimigraine drugs (agonists of serotonergic receptors) • asthma drugs (agonists of β2-adrenergic receptor), • anti-hypertensives (antagonists of α1-adrenergic and

angiotensin II receptors)




Almost 30% of FDA-approved medications target GPCRs

Distribution of approved therapeutic applications among GPCR families

From: How Ligands Illuminate GPCR Molecular Pharmacology D. Wacker, R. C. Stevens, and B. L. RothCell, 2017 170:414-427, © 2017 Elsevier Inc.




Frequent off-targets for drugs that aim at kinases and other molecular targets

Fenfluramine (anti-obesity):• association with valvular heart disease • legal damages totaling > $10 billion

Metabolite (norfenfluramine) activated cardiac 5-HT2B receptors

Fenfluramine NorfenfluramineLecture 4 / Slide 18



Frequent off-targets for drugs that aim at kinases and other molecular targets

Nowadays, compounds are typically profiled against large numbers of GPCRs prior to clinical trials

Potent actions of many approved and investigational drugs on GPCRs were discovered via profiling

From: How Ligands Illuminate GPCR Molecular Pharmacology D. Wacker, R. C. Stevens, and B. L. RothCell, 2017 170:414-427, © 2017 Elsevier Inc.



G-protein-coupled receptorsSignal transduction by GPCRsCanonical pathways1. Activation by a receptor-specific ligand

• Glutamate / Dopamine / Light / etc.2. Interaction with inactive G-protein assembly

• Complex of Ga-GDP with Gb-Gg3. G-protein activation

• Exchange of GDP to GTP at Ga• Dissociation into Ga-GTP and Gb-Gg

4. Initiation of signaling through specific pathways • Ga-GTP: enzymes, i.e. adenylate cyclase• Gb-Gg: ion channels, i.e. GIR K+ channels



G-protein-coupled receptorsSignal transduction by GPCRs1. Activation by a receptor-specific ligand

• Glutamate / Dopamine / Light / etc.2. Interaction with

a. G-protein complexb. G-protein associated receptor kinasec. Arrestin

3. Initiation of signaling through specific pathways • Ga-GTP: enzymes, i.e. adenylate cyclase• Gb-Gg: ion channels, i.e. GIR K+ channels• GRK: phosphorylation of other proteins• Arrestin: MAP kinase activation or

Clatrin-mediated endocytosis of GPCR



G-protein-coupled receptorsSignal transduction by GPCRs

1. Activation by a receptor-specific ligand• Glutamate / Dopamine / Light / etc.

Conformational change

2. Interaction with inactive G-protein assembly• Complex of Ga-GDP with Gb-Gg



G-protein-coupled receptors Home reading

Activation by a receptor-specific ligand• Glutamate / Dopamine / Light / etc.

Allosteric site(s)

Orthosteric site?

Bitopic ligand?

Link for the paper

From: How Ligands Illuminate GPCR Molecular Pharmacology D. Wacker, R. C. Stevens, and B. L. Roth. Cell, 2017 170:414-427, © 2017 Elsevier Inc. Lecture 4 / Slide 23



Ion Channel Receptors

Pharmacological importance• Control active flow of ions through the membrane• Involved in numerous processes: cognition, nerve

and muscle relaxation, regulation of blood pressure, cell proliferation, etc.

• Change in functionality of ion channels is linked to: cardiac disorders, kidney failure, abnormal pain sensitivity, deafness and blindness, neurological disorders, etc.

• More than 60 diseases are directly linked to mutationsin Ion Channels




Classification and diversity• More than 200 genes in human• Two major classes

• Voltage-gated• Ligand-gated

• Two classes different in• Gating mechanism • Structure• Origin

From: S.K. Bagal; A.D. Brown; P.J. Cox; K. Omoto; R.M. Owen; D.C. Pryde; B. Sidders; S.E. Skerratt; E.B. Stevens; R.I. Storer; N.A. Swain; J. Med. Chem. 2013, 56, 593-624. Copyright © 2012 American Chemical Society Lecture 4 / Slide 25



Similarity• Multi-subunit Topology

Ø Voltage sensor domain (VSD, 4 TM)

Ø Pore domain (PD, 2 TM)• Ion selectivity: K+, Na+, Ca2+

6TM

Cys-loop

K2P and Kir

ASIC and P2XLecture 4 / Slide 26



Difference• Structure of Subunits

Number of TMs:2 TM, 4 TM, 6 TM, 12 TM, 24 TM

• Number of Subunits• Auxiliary Subunits

6TM

Cys-loop

K2P and Kir

ASIC and P2XLecture 4 / Slide 27



Voltage-gated Ion Channels• Structural diversity

Ø 2 TM, 4 TM, 6 TM, 12 TM, 24 TMØ Auxiliary subunits

• Structural similarityØ Voltage sensor domain

(VSD, 4 TM)Ø Pore domain (PD, 2 TM)

• Ion selectivity: K+, Na+, Ca2+

From: Miceli F. et al. Front. Cell. Neurosci. 2015, 9:259. Lecture 4 / Slide 28



Activation• Receptor-specific ligand – ligand-gated- Acetylcholine- Gamma-aminobutyric acid- Membrane Lipids- Amino acids – Glycine, Glutamate, Aspartate- Gbg-proteins

• Transmembrane potential – voltage-gated• Membrane deformation – mechanosensitive




Channel Opening

From: Frank H. Yu et al. Pharmacol Rev 2005;57:387-395. Copyright © 2005 The American Society for Pharmacology and Experimental Therapeutics Lecture 4 / Slide 30



1. Activation• Receptor-specific ligand – ligand-gated• Transmembrane potential – voltage-gated• Membrane deformation – mechanosensitive

2. Structural change in the channel Gate• “Opening” the Gate and access to the Pore• Stabilization of the Channel in “open” state

3. Influx of specific ion(s)• Uses electrochemical gradient• Very fast process – up to 108 ions/s• High fidelity – K+:Na+ ~ 10000:1 in K+-channels




Important note on “Activation”• Ion Channel states: Closed / Resting / Open

• No ligands / no stimuli

• With a ligand / stimulus

ClosedOpen

OpenClosed

ClosedOpen

OR




Ligand interactionsites

Kv1.2 PDB: 3LUT

P-loop Toxin binding

site

Pore

Linker helix

Voltagesensordomain




Ligand interactionsites

Kv1.2 PDB: 3LUT

P-loopToxin

binding site

Pore

Linker helix

Voltagesensordomain

Localanesthetics

site



Key points to remember:

• Ligands: Agonist, Antagonist, Inverse Agonist, Full/Partial Agonist• Competitive/Non-competitive, Reversible/Irreversible• Activator, Inhibitor, Modulator, Allosteric ligand• Affinity, Potency, Efficacy, Selectivity/Specificity, Therapeutic Index• Chemistry of ligand-target interaction: Electrostatic, Hydrophobic, Covalent• Receptors: Ionotropic, Metabotropic• G-protein coupled receptors: Topology, Classes, Signal Transduction• Ion channel receptors: Topology, Classes/Types, Ion Transduction


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PHS602 DRUG DISCOVERY AND DEVELOPMENT