Discovery, Development and Optimization of Protein Drugs Lecturer: Michael Jeltsch, Faculty of Pharmacy, University of Helsinki
Course: MPHARM-002A/PROV-105A
11. & 17. September 2025
Protein Drug Discovery & Development
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Table of contents
TOC
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Biology
Technologies
Protein hormones, growth factors & cytokines
Enzymes
Protein toxins
Protein vaccines (“recombinant vaccines”)
Antibodies
Protein drugs & biologicals
Examples of protein drugs
Discovery of protein drugs
Generation of protein drugs
today
next week
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Biologics
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Biologic = biological drug = biopharmaceutical =
A drug that is produced by/from living organisms or contains components of living organisms
Is this a good definition?
Think about the difference between synthetic and natural vitamins or the chemical synthesis of small proteins (Merrifield Solid‐Phase Peptide Synthesis)
…the definition is changing
The FDA definition of biologics includes meanwhile small peptides if they have >40 amino acids even if they are fully-synthetically produced.
…does it matter?
Yes, since the regulatory frameworks for small molecule drugs (SMDs) and biologics are different! E.g. semaglutide is officially not a biologic even though scientifically it is!
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Different types of biologics
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Vaccines
Cell therapy
Gene therapy
Proteins
Transplants
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Biologics
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Although biologics are the most rapidly growing drug class, they are not new,
but are among the oldest, truly effective medical interventions.
1st vaccination performed by Edward Jenner (1796), variolation perhaps as old as 500 AD
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Different types of biologics
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Vaccines
Gene therapy
Cell
therapy
Proteins
Transplants
Any unifying theme?
Almost all biologics need to be “injected” with the exception of viruses.
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Different types of biologics: Proteins
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Vaccines
Gene therapy
Cell
therapy
Proteins
Transplants
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The four major protein drug classes
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The four major protein drug classes
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The four major protein drug classes
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The four six major protein drug classes
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The four major protein drug classes
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(limited)
The six major protein drug classes
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Discovery vs. understanding
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(Most) early (protein) drugs:�1. Drug discovery → 2. Mechanistic understanding
Botox cleaves SNARE proteins, which mediate membrane fusion of vesicles that carry the neurotransmitter acetylcholine.
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Discovery vs. understanding
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(Most) current (protein) drugs:�1. Mechanistic understanding → 2. Drug discovery/development
10-15% of SCID (Severe Combined Immunodeficiency)�cases are caused by Adenosine deaminase (ADA) deficiency;
ADA deficiency is curable since 1990 by retroviral gene therapy (drug: Strimvelis)!
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Discovery vs. understanding
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Target identification and validation for protein drugs does not really differ much from other drug types:
Making sure that the target is instrumental in the disease process (not only a byproduct of the disease)!
Alzheimer’s disease: Are β-amyloid plaques cause or consequence?
#1 β-amyloid plaques
cell damage & death
#2 unknown process
cell damage & death
β-amyloid plaques
The antibodies lecanemab and donanemab “tag” the βA for removal, thus reducing plaques. While they successfully treat Alzheimer’s, #1 and #2 are not exclusive…
βA
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The four major protein drug classes
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drug discovery = basic biomedical research = understanding the molecular basis of disease
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Examples of protein drugs
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BOTOX
Bevacizumab
Avastin
Insulin
Erythropoietin
Interferon-ɑ
Herceptin
Trastuzumab
Aflibercept
Eylea
Aranesp
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Justinus Kerner (1786 – 1862)
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BOTOX®
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Botox® (OnabotulinumtoxinA)
Botulinum toxins (BTs)
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BOTOX®
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Unit definition
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1 unit = mouse LD50 (female Swiss-Webster mice after single intraperitoneal injection)
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Heydrich assassination
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Bundesarchiv, Bild 146-1969-054-16 / Hoffmann, Heinrich
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Insulin
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Insulin
*The fact that pancreatic insulin-containing extracts were able to treat diabetes had been discovered three times independently before (by George Ludwig Zuelzer in 1906, Israel Kleiner in 1915, Nicolae Paulescu in 1916).
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Isolation from natural sources vs. recombinant protein production
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Recombinant DNA technology (simplified)
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WHY?
Because a recombinant production cell produces a s***load of protein compared to what can be found in natural sources
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Recombinant DNA technology (aka “Cloning”)
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Protein drug examples
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Growth factors/cytokines/protein hormones/toxins
Antibodies (Abs)
PROV-409 & PROV-410 “Cloning Course” (Recombinant DNA technology in therapeutic protein engineering)
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Rapid-acting insulins by preventing dimerization/multimerization
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How are intermediate & long-acting insulins made?
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Insulin profiles
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Degludec Insulin (t½ = 17-25h)
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How to “optimize” a protein: In-vitro/directed evolution
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Modified from https://commons.wikimedia.org/wiki/File:DE_cycle.png
In-vitro evolution
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Example: Making a super vascular endothelial growth factor (super-VEGF)
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DNA shuffling
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Synthetic or natural insulin? Nomenclature confusion
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Synthetic, man-made, human insulin: unclear usage, has historically been used to designate recombinant insulin as opposed to insulin from animal sources
Biosynthetic insulin: recombinant insulin
Fully synthetic insulin: by chemical synthesis in-vitro (“test tube”)
Insulin analogs (lispro, aspart, glulisine): recombinant insulin with modifications
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Modifications to “improve” proteins
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Aranesp® (Darbepoetin alfa)
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Aranesp® (Darbepoetin alfa)
>sp|P01588|EPO_HUMAN Erythropoietin OS=Homo sapiens OX=9606 GN=EPO PE=1 SV=1
MGVHECPAWLWLLLSLLSLPLGLPVLGAPP
N T
RLICDSRVLERYLLEAKEAENITTGCAEHC
SLNENITVPDTKVNFYAWKRMEVGQQAVEV
VN T
WQGLALLSEAVLRGQALLVNSSQPWEPLQL
HVDKAVSGLRSLTTLLRALGAQKEAISPPD
AASAAPLRTITADTFRKLFRVYSNFLRGKL
KLYTGEACRTGDR
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Aranesp® (Darbepoetin alfa)
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Modifications to “improve” proteins
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Interferons
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The big IF (1980 US documentary film)
Link to the Flash Gordon comic strip
(due to copyright issues, the comic strip must not be embedded into this presentation)
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Consensus interferon
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Modifications to “improve” proteins
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Development of smaller E. coli-produced anti-VEGF-A protein drugs
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Statistics “Name one biological drug”
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Immune system
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Immune system
Cell-mediated immunity
Humoral immunity
(proteins in body fluids):
Innate immunity
Adaptive/Acquired immunity
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Antibodies: a part of our immune system
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Antibodies:
Highly specific protein drugs that the body generates on demand to fight everything non-self (mostly other non-self proteins)
Antigen: the molecule that the antibody targets
Immunogen: a molecule that can elicit an immune response (e.g. the generation of antibodies
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Antibodies: a part of our immune system
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Antiserum*
Blood without cells & clotting factors. Antibodies (= immunoglobulins) are the 2nd most abundant blood proteins after albumins, ~15mg/ml.
Polyclonal antibody
All immunoglobulins that react with a specific antigen
Monoclonal antibody
One specific Ig protein with a defined amino acid sequence
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And the 2025 winner is …
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| Drug | Target | Indication | INN drug name | Brand names | Votes |
1 | Monoclonal antibodies | CGRP (calcitonin gene-related peptide)/CGRP receptor | Migraine | eptinezumab, fremanezumab, erenumab, galcanezumab | Emgality,Aimovig, Vyepti, Ajovy | 5 |
2 | Monoclonal antibodies | TNF-alpha | Inflammatory diseases (rheumatoid arthritis, Crohn’s disease, proriasis) | adalimumab, infliximab | Humira, Hyrimoz, Remsima | 5 |
3 | GLP-1 agonists | GLP-1 receptor | Diabetes, obesity | semaglutide, liraglutide | Ozempic, Rybelsus, | 4 |
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Antibody (Immunoglobulin) structure (IgG)
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100-120
amino acids
antigen
binding
site
(paratope)
hinge region
Light chain
Heavy chain
C = constant
V = variable
complementary determing regions (CDR) 1-3
FC region
(effector
function)
Fab region
(antigen
binding)
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Antibody in action
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antigen
antigen
Fc receptor
Effector cell (lymphocyte, mast cell, etc.)
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Antibody in action
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Neutralization of toxins and pathogens (“neutralizing/blocking” antibody)
Primary function of antibodies
SARS-CoV-2
Host cell membrane
ACE2
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Antibody classes
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IgG
secretory IgA
IgE
IgM
IgD
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Generation of antibody diversity
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V-D-J recombination (heavy chain, simplified)
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V-D-J recombination & class switching (heavy chain)
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Human heavy chain:
50 V�25 D
6 J
9 C
Human lambda light chain:
30 V�4 J
7 C
Human kappa light chain:
40 V�5 J
1 C
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Methods to generate antibody diversity
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Antibody drugs are not new!
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Illustration by Fritz Gehrke (1905)
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How are antibodies generated?
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Polyclonal antibody (“antiserum”) production
Ingredients for immunization (more or less unchanged for the last 100 years)
1. Antigen: (highly) purified protein, synthetic peptides (up to� ~100 aa)
2. Host: Rabbit, Mouse, Goat, Horse, Human (“convalescent� serum”)
3. Adjuvants (Freund’s complete adjuvant (FCA)*, aluminium� salts): to be mixed (mostly emulgated) with the antigen to� boost the immune response
4. Injection syringe for subq (intradermal, intraperitoneal,� footpad, intramuscular) injection
5. Pre-immune serum sample
6. Repeat injection (“booster”): e.g. up to 5 times in rabbits in 3-week-intervals, many different protocols
7. “Test bleeds” (e.g. starting from 2 weeks after 2nd booster) for analysis
8. For small hosts mostly “final bleed”, for larger animals (incl. humans): repeated blood donation/plasmapheresis
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How to make monoclonals?
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mouse (murine) mAbs
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What happens if you inject mouse monoclonal antibodies (mAbs) into humans?
They are eliminated by an immune response!
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How to make human monoclonals?
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How to make human monoclonals?
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B cell receptor
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B cell receptor =
membrane-bound version of IgM
Igα
Igβ
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Engineered antibody formats
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Phage display of scFv fragments
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Phage display work-flow
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Drawbacks of phage display antibodies
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Ig-humanized mice
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Ig-humanized mice
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Eliminating immune response to therapeutic mAbs
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How to make human monoclonals?
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Big Business
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Judah Folkman (1933 – 2008)
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Folkman, Dvorak, Ferrara
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1997
1971
Judah Folkman proposes the concept
of antiangiogenic tumor therapy
1992
1983
Napoleone Ferrara generates neutralizing
mouse antibodies against VEGF
Harold Dvorak isolates Vascular Endothelial Growth Factor (VEGF)
Clinical trials start with the humanized
anti-VEGF antibody (“bevacizumab”)
2004
Bevacizumab receives FDA approval
for treatment of colon cancer
©
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Avastin®
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Avastin® (Bevacizumab)
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Avastin®
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VEGF growth factors and receptors
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Antibody fusion proteins: Eylea®
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Eylea® (Aflibercept)
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Antibody fusion proteins: Eylea®
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Herceptin®
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Herceptin® (Trastuzumab)
Antibody against ERBB2 (HER2)
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Herceptin®
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Biosimilars
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Herceptin - The first personalized drug?
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Stratified medicine/Precision medicine
“One-size-fits-all” medicine
Personalized medicine
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What happens after a ligand or an antibody binds a receptor?
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What happens after an activating ligand has bound to a receptor?
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Attaching a “payload” to an antibody
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Problem:
All of these
groups occur
multiple�times in�most�proteins!
→Site-specific
conjugation!
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Trastuzumab → Trastuzumab emtansine (Kadcyla)
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Kadcyla = Herceptin + toxic payload
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m-maleimidobenzoyl-N-hydroxysuccinimide ester (MBS, links to N-terminal amino group and lysines side chains on one end and cysteines at the other end, typical use: antibody-enzyme linking, heterobifunctional
�Example of heterobifunctional linker use in antibody production use: ADC trastuzumab emtansine (T-DM1, Kadcyla®, price ~70000 €/14 treatment cycles à 3 weeks).
Fair use
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Popular biologics
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Neurogenic or vasculogenic origin of migraine?
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Anti-CGRP monoclonal antibodies prevent migraine by blocking the calcitonin gene–related peptide (CGRP) pathway, which is a key driver of pain signaling and neurogenic inflammation in the trigeminovascular system.
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CGRP is one of several targets
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Antibodies against migraine
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Calcitonin gene-related peptide (CGRP)-blocking monoclonal antibodies
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More to read and watch
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Questions, contact
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