PACAP-38: brain signaling peptide linked to stress, pain, and migraine
A natural nervous-system peptide that regulates stress responses, fear, and pain signaling in the brain; studied for its role in PTSD and migraine, used as a lab research tool.
A researcher, an agent, or an algorithm wrote down the sequence and picked a target to hit.
An AI model like OpenFold3 or AlphaFold built a 3D structure and scored how well it fits the binding site.
A second contributor repeated the computation on their own hardware and the scores matched.
A chemistry service or a researcher ordered the sequence, it was manufactured, and mass spectrometry confirmed the right molecule was produced.
A binding or activity measurement confirmed that it actually does what the computer predicted — or didn't.
What this is
Pituitary adenylate cyclase-activating polypeptide-38 (PACAP-38) is a 38-amino-acid signaling peptide found in the nervous system of virtually all vertebrates. It belongs to the secretin/glucagon/VIP peptide family and was first isolated in 1989 by Miyata and colleagues from ovine hypothalamic extracts, identified by its ability to stimulate cyclic AMP production in pituitary cells. PACAP-38 is the dominant naturally occurring form of the peptide; a shorter 27-amino-acid variant, PACAP-27, arises from the same precursor through internal cleavage. The sequence stored here was characterized from a chicken gene that encodes both PACAP and growth hormone-releasing hormone (GHRH) on the same locus — a single-gene arrangement unique to birds that was resolved in mammals through gene duplication (McRory et al., DNA and Cell Biology, 1997). Native PACAP-38 carries a C-terminal amide group not represented in the raw stored sequence; research has shown this modification is not required for PAC1 receptor activation (Bourgault et al., 2016).
History
PACAP was discovered in 1989 when Miyata and Arimura screened ovine hypothalamic fractions for their capacity to stimulate cAMP in anterior pituitary cells, identifying a factor roughly 1,000-fold more potent than the related peptide VIP. Two years of structural work yielded both the 38-residue and 27-residue forms. The peptide's remarkable evolutionary stability — differing by only one residue between chicken and most mammals — pointed to fundamental biological importance, and by the early 1990s its receptors had been cloned and characterized in humans and rats (Ogi et al., Biochemical and Biophysical Research Communications, 1993; Hosoya et al., Biochemical and Biophysical Research Communications, 1993). The avian gene encoding PACAP was characterized by McRory and colleagues in 1997, revealing that in chickens the PACAP and GHRH sequences reside on a single co-expressed gene — a feature that in mammals became two separate genes after a stem-mammalian duplication. The 2000s brought detailed work on PAC1 receptor splice variants and intracellular signaling diversity (Pisegna et al., Journal of Biological Chemistry, 1996), and by the 2010s PACAP had been identified as a central player in stress circuitry, fear memory, and migraine — making it one of the most pleiotropic neuropeptides known.
What it does
PACAP-38 acts on neurons and glial cells throughout the brain to adjust the intensity of cellular responses to stress and sensory input. In the hippocampus it enhances the excitability of dentate gyrus granule cells and supports the type of synaptic strengthening that underlies learning and memory (Johnson et al., Frontiers in Cellular Neuroscience, 2020). In stress and fear circuits — particularly the amygdala and bed nucleus of the stria terminalis — elevated PACAP activity amplifies the startle response and can impair the brain's ability to distinguish genuine danger signals from safe ones. In the trigeminovascular system, PACAP-38 dilates meningeal blood vessels and sensitizes second-order pain-processing neurons in a manner that closely replicates the delayed headache and central sensitization seen in migraine attacks (Rubio-Beltrán et al., Journal of Headache and Pain, 2018). Beyond the nervous system, PACAP-38 regulates hormone secretion from the pituitary and pancreas, modulates immune responses, and has been proposed as a neuroprotective factor after ischemic injury (Hashimoto, Yakugaku Zasshi, 2002).
Evidence
- Human: Intravenous infusion of PACAP-38 in healthy volunteers and migraine patients provoked headache in the large majority of participants, with migraine-like attacks developing with a delayed onset of several hours in susceptible individuals (Rubio-Beltrán et al., 2018). Elevated PACAP-38 blood levels predict PTSD symptom severity in women; a specific single-nucleotide polymorphism in the PAC1 receptor gene (ADCYAP1R1 rs2267735) associates with PTSD and with impaired fear discrimination, with the effect driven by females (Ressler et al., 2011). A Phase 2 trial of AMG 301, a monoclonal antibody targeting the PAC1 receptor, did not separate from placebo for migraine prevention in 343 patients (Ashina et al., Cephalalgia, 2021). A subsequent Phase 2 trial of LY3451838, an antibody neutralizing PACAP-38 itself, showed numerical reductions in monthly migraine days in treatment-resistant patients but likewise did not reach statistical significance (Johnson et al., Cephalalgia, 2025).
- Animal: PAC1 receptor knockout mice show impaired long-term potentiation in the dentate gyrus and deficits in contextual fear conditioning (Johnson et al., 2020). Fear conditioning increases PAC1 receptor mRNA in the mouse amygdala; estrogen replacement selectively elevates PACAP transcripts in the bed nucleus of the stria terminalis, linking sex-specific stress vulnerability to PACAP tone (Ressler et al., 2011). Preclinical studies with the PAC1 antibody AMG 301 reduced evoked nociceptive activity in the trigemino-cervical complex comparably to sumatriptan (Rubio-Beltrán et al., 2018).
- In vitro: PACAP-38 activates multiple intracellular pathways downstream of PAC1, including adenylyl cyclase/cAMP, phospholipase C, and MEK/ERK; in dentate gyrus granule cells, PAC1 receptor endosomal recruitment of the MEK/ERK pathway — not the cAMP cascade — is the primary driver of excitability changes (Johnson et al., 2020). The receptor's signaling profile is further shaped by which of several splice variants is expressed, including forms with or without "Hip" and "Hop" inserts in the third intracellular loop (Pisegna et al., 1996).
Known effects
- Fear sensitization and PTSD vulnerability — Human genetic and biomarker evidence (Ressler et al., 2011); preclinical circuit mapping in amygdala and BNST
- Migraine provocation — Human infusion studies showing delayed headache and central sensitization; mechanistic evidence via trigeminovascular PAC1 activation
- Hippocampal neuroplasticity and memory consolidation — Preclinical (LTP and fear conditioning data in knockout and pharmacological models)
- Stress hormone regulation — Preclinical; PACAP drives CRH and ACTH release in hypothalamic–pituitary–adrenal axis models
- Growth hormone secretion (avian) — Demonstrated in grass carp and chicken pituitary cells via cAMP and Ca²⁺ signaling (Wong et al., Endocrinology, 2005; McRory et al., 1997)
Safety signals
PACAP-38 is an endogenous neuropeptide with no approved therapeutic application; safety data come from controlled infusion studies and early-phase antibody trials. Human PACAP-38 infusions reproducibly induce headache and, in migraine-susceptible individuals, migraine-like attacks with autonomic features; premonitory symptoms were reported in 48% of migraine patients versus 9% with CGRP infusions (Rubio-Beltrán et al., 2018), suggesting a stronger central component than CGRP-mediated migraine. No serious adverse events were attributed to PACAP-38 itself in published provocation studies. In the Phase 2 AMG 301 antibody trial, adverse-event rates were similar between active and placebo groups (Ashina et al., 2021). The Phase 2 LY3451838 trial reported one serious adverse event (primary CNS lymphoma) assessed as unrelated to the investigational antibody (Johnson et al., 2025).
Regulatory status
- US: Not approved for any therapeutic indication. Used as a research peptide and in controlled human provocation studies. No FDA IND status publicly registered for PACAP-38 as a therapeutic agent.
- WADA: No specific listing identified for PACAP-38 on the WADA Prohibited List; as an endogenous peptide with no established performance-enhancing use, it does not currently appear on published prohibited substance schedules.
Mechanism
PACAP-38 signals through three class B GPCRs: PAC1 (encoded by ADCYAP1R1), VPAC1, and VPAC2. PAC1 is roughly 100-fold more selective for PACAP over the structurally related VIP, accounting for PACAP's distinct biological profile relative to VIP at the same tissues (Liao et al., Current Topics in Medicinal Chemistry, 2019). Canonical PAC1 activation stimulates adenylyl cyclase (raising intracellular cAMP) and phospholipase C; the receptor also recruits MEK/ERK signaling after clathrin-mediated endosomal internalization, and in hippocampal dentate gyrus granule cells this endosomal ERK pathway — not the cAMP arm — is the dominant driver of neuronal excitability (Johnson et al., 2020). PAC1 exists in multiple splice isoforms defined by the presence or absence of Hip and Hop cassette inserts in the third intracellular loop; in the mammalian CNS, PAC1-Null and PAC1-Hop predominate, and the ratio of these variants influences downstream signaling bias. In stress circuits, PACAP-expressing terminals in the amygdala and BNST synapse onto PAC1-expressing neurons; elevated PACAP tone in these circuits increases threat-reactivity and can impair extinction of conditioned fear (Ressler et al., 2011; Johnson et al., 2020). In the trigeminovascular system, PAC1 receptors on second-order neurons in the trigeminocervical complex mediate delayed central sensitization after PACAP-38 exposure — an effect not replicated by VIP or by PACAP-38 acting at VPAC1/VPAC2, pointing to PAC1 as the therapeutically relevant migraine target (Rubio-Beltrán et al., 2018).
Open questions
- Why did both Phase 2 trials targeting the PACAP-PAC1 axis (AMG 301 and LY3451838) fail to separate from placebo in migraine prevention, despite compelling human provocation data implicating PACAP-38?
- Does the sex-specific PTSD association reflect estrogen-dependent regulation of ADCYAP1R1 expression, and would PAC1 antagonism show differential efficacy by sex in clinical anxiety or trauma trials?
- What is the functional consequence of the avian co-localization of GHRH and PACAP on a single gene, and do co-expression patterns in chicken tissue differ meaningfully from mammalian PACAP distribution?
- PAC1 splice-variant selectivity: can isoform-selective ligands dissociate the neuroprotective and pain-sensitizing arms of PACAP signaling?
Related peptides
- PACAP-27 — the 27-residue N-terminal fragment of PACAP-38, arising from the same precursor via internal cleavage at Gly28–Lys29–Arg30; shares identical potency at PAC1 but lacks the C-terminal 11 residues present in PACAP-38
- VIP (vasoactive intestinal peptide) — closest structural relative; acts at VPAC1 and VPAC2 but has roughly 100-fold lower affinity for PAC1 than PACAP-38, making it the key contrast peptide for isolating PAC1-specific biology in pharmacological experiments
Research directions for this peptide, selected from the current sources — hypotheses you can explore and model. None of it is proven yet; tap any one to see the full thinking.
Could PACAP-38 cause migraines through VPAC receptors instead of PAC1R?
If true, new migraine drugs could target VPAC1 or VPAC2 instead of PAC1R, potentially helping patients who do not respond to current PAC1R-blocking therapies. This would redirect years of drug development toward a more precise target.
Could PACAP-38 change how immune cells in the brain behave, not just nerve cells?
If true, PACAP-38 could be tested for diseases like multiple sclerosis or brain injury where overactive immune cells cause damage, giving an old peptide new jobs beyond pain and migraine.
Could the starting histidine make PACAP-38 more active in acidic, inflamed areas like the brain during a migraine?
If true, scientists could design PACAP drugs that turn on only where tissue is inflamed, reducing side effects in healthy parts of the body and making treatments safer and more precise.
Could short bursts of PACAP-38 protect brain cells while long-term exposure causes migraines?
If true, doctors could use PACAP-38 to protect the brain after a stroke or injury, but only for a short time, and avoid chronic use that might trigger or worsen headaches. This would clarify when the peptide helps versus harms.
Could the missing C-terminal amide make PACAP-38 break down faster while still working fine?
If true, doctors could adjust whether a synthetic version includes that tag based on whether they need a short burst or a long-lasting effect, making treatments more flexible and possibly cheaper to produce.
▸full evidence table2 metrics
| metric | value | tool |
|---|---|---|
| ipTM | 0.76238614320755 | openfold3-mlx |
| ranking score | 0.8443729877471924 | openfold3-mlx |
▸structural qualityopenfold3
| metric | value | note |
|---|---|---|
| gpde | 0.836 | global PDE — lower = better |
| disorder | 0.190 | fraction disordered |
| chain pair ipTM (A, B) | 0.762 | interface quality |
▸3-letter notation
▸recipeopenfold3-mlx 0.3.1
| parameter | value |
|---|---|
| model | openfold3-mlx 0.3.1 |
| weights | aedd8f3eb814e392… |
| hardware | apple_m4_base_16gb |
| mlx version | 0.31.1 |
| python | 3.14.3 |
| random seed | 42 |
| msa strategy | colabfold |
| diffusion samples | 1 |
| runtime | 450s |
| predicted by | mlx@peptide |
| predicted at | 2026-04-23 |
python3 openfold3/run_openfold.py predict --query_json {query.json} --runner_yaml examples/example_runner_yamls/mlx_runner.yml --output_dir {output_dir} --num_diffusion_samples 1 ▸citationbibtex
@peptide{pep10581,
sequence = {HIDGIFTDSYSRYRKQMAVKKYLAAVLGKRYKQRVKNK},
target = {pac1r},
author = {peptidemodel},
year = {2026},
status = {synthesized}
}