Design of peptide-based PAC1 antagonists combining molecular dynamics simulations and a biologically relevant cell-based assay Article Swipe
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· 2025
· Open Access
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· DOI: https://doi.org/10.1101/2025.04.16.649181
The PACAP receptor PAC1 is a G s -coupled family B1 GPCR for which the highest-affinity endogenous peptide ligands are the pituitary adenylate cyclase-activating peptides PACAP38 and PACAP27, and whose most abundant endogenous ligand is PACAP38. PACAP action at PAC1 is implicated in neuropsychiatric disorders, atherosclerosis, pain chronification, and protection from neurodegeneration and ischemia. As PACAP also interacts with two related receptors, VPAC1 and VPAC2, highly selective ligands, both agonists and antagonists, for PAC1 have been sought. To date, the peptide PACAP(6-38) and polypeptide M65, which is related to maxadilan, a sandfly vasodilator peptide, have been identified as selective for PAC1. Several non-peptide small molecule compounds (SMOLs) have been reported to be specific antagonists at PAC1, albeit their specificities have not been rigorously documented. Here, we present a platform of cellular assays for the screening of biologically relevant antagonists at PAC1 and show that some currently proposed SMOL antagonists do not have activity in this cell reporter assay, while we confirm that PACAP(6-38) and M65 are competitive antagonists. We have used this assay system to explore other peptide antagonists at PAC1, guided by molecular dynamics analysis of the PACAP-PAC1 interaction based on cryo-EM structural models of PAC1 complexed with a number of biologically active ligands. The affinity-trap model for the PAC1-ligand interaction successfully predicts the engagement behavior of PACAP27 and PACAP38 peptide-based PAC1 inhibitors. In particular, C-terminal deletants of PACAP(6-38) that maintain equipotency to PACAP(6-38) allow the shorter sequence to function as a scaffold for further peptide-based antagonist exploration.
Related Topics
- Type
- preprint
- Language
- en
- Landing Page
- https://doi.org/10.1101/2025.04.16.649181
- https://www.biorxiv.org/content/biorxiv/early/2025/04/22/2025.04.16.649181.full.pdf
- OA Status
- green
- References
- 86
- Related Works
- 10
- OpenAlex ID
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Raw OpenAlex JSON
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https://openalex.org/W4409727086Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.1101/2025.04.16.649181Digital Object Identifier
- Title
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Design of peptide-based PAC1 antagonists combining molecular dynamics simulations and a biologically relevant cell-based assayWork title
- Type
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preprintOpenAlex work type
- Language
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enPrimary language
- Publication year
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2025Year of publication
- Publication date
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2025-04-22Full publication date if available
- Authors
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Wenqin Xu, Abigail M Keith, Wenjuan Ye, Xin Hu, Noel Southall, M. Alarcon Juan, Marc Ferrer, Mark J. Henderson, Patrick M. Sexton, Giuseppe Deganutti, Lee E. EidenList of authors in order
- Landing page
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https://doi.org/10.1101/2025.04.16.649181Publisher landing page
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https://www.biorxiv.org/content/biorxiv/early/2025/04/22/2025.04.16.649181.full.pdfDirect link to full text PDF
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YesWhether a free full text is available
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greenOpen access status per OpenAlex
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https://www.biorxiv.org/content/biorxiv/early/2025/04/22/2025.04.16.649181.full.pdfDirect OA link when available
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0Total citation count in OpenAlex
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86Number of works referenced by this work
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10Other works algorithmically related by OpenAlex
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| referenced_works | https://openalex.org/W4405242687, https://openalex.org/W2068480672, https://openalex.org/W2049064554, https://openalex.org/W4206527713, https://openalex.org/W1998448862, https://openalex.org/W2120631068, https://openalex.org/W2083539885, https://openalex.org/W2040585119, https://openalex.org/W2117576447, https://openalex.org/W2046390054, https://openalex.org/W3194546463, https://openalex.org/W4286587717, https://openalex.org/W4312095457, https://openalex.org/W1899381300, https://openalex.org/W2150319500, https://openalex.org/W44602424, https://openalex.org/W3005682500, https://openalex.org/W3009563971, https://openalex.org/W4309475330, https://openalex.org/W2792717414, https://openalex.org/W4210367784, https://openalex.org/W4226158523, https://openalex.org/W2460044225, https://openalex.org/W2991255948, https://openalex.org/W2102160446, https://openalex.org/W4381613830, https://openalex.org/W963618461, https://openalex.org/W1970837549, https://openalex.org/W2114897128, https://openalex.org/W3158738611, https://openalex.org/W2978309801, https://openalex.org/W4400875039, https://openalex.org/W3003982436, https://openalex.org/W2132629607, https://openalex.org/W2097775366, https://openalex.org/W2109154308, https://openalex.org/W2296686360, https://openalex.org/W2029667189, https://openalex.org/W2047399603, https://openalex.org/W2330799739, https://openalex.org/W2739440454, https://openalex.org/W1976499671, https://openalex.org/W2082586732, https://openalex.org/W1978189250, https://openalex.org/W1994941561, https://openalex.org/W2100561975, https://openalex.org/W2035687084, https://openalex.org/W2003949305, https://openalex.org/W1968984443, https://openalex.org/W1989857487, https://openalex.org/W2041479810, https://openalex.org/W2296644869, https://openalex.org/W1975470137, https://openalex.org/W2111407966, https://openalex.org/W2543675020, https://openalex.org/W2972120114, https://openalex.org/W3137285709, https://openalex.org/W4394795164, https://openalex.org/W3039478115, https://openalex.org/W2093818683, https://openalex.org/W1970186130, https://openalex.org/W2902726772, https://openalex.org/W2047635540, https://openalex.org/W3013404124, https://openalex.org/W4283320970, https://openalex.org/W3008303042, https://openalex.org/W2049326326, https://openalex.org/W2013236826, https://openalex.org/W2885895791, https://openalex.org/W2956753841, https://openalex.org/W4210328822, https://openalex.org/W4407031925, https://openalex.org/W1984030577, https://openalex.org/W4321996988, https://openalex.org/W4381951938, https://openalex.org/W4380322672, https://openalex.org/W3127425425, https://openalex.org/W2037435728, https://openalex.org/W2111112233, https://openalex.org/W1981502096, https://openalex.org/W2973504822, https://openalex.org/W2765091532, https://openalex.org/W3204197854, https://openalex.org/W2772059359, https://openalex.org/W3141989181, https://openalex.org/W2937469079 |
| referenced_works_count | 86 |
| abstract_inverted_index.G | 7 |
| abstract_inverted_index.a | 6, 91, 128, 200, 243 |
| abstract_inverted_index.s | 8 |
| abstract_inverted_index.As | 55 |
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| abstract_inverted_index.To | 78 |
| abstract_inverted_index.We | 169 |
| abstract_inverted_index.as | 98, 242 |
| abstract_inverted_index.at | 39, 115, 140, 180 |
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| abstract_inverted_index.is | 5, 35, 41, 87 |
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| abstract_inverted_index.to | 89, 111, 175, 234, 240 |
| abstract_inverted_index.we | 126, 160 |
| abstract_inverted_index.M65 | 165 |
| abstract_inverted_index.The | 1, 206 |
| abstract_inverted_index.and | 27, 29, 49, 53, 64, 71, 83, 142, 164, 220 |
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| abstract_inverted_index.not | 121, 151 |
| abstract_inverted_index.the | 15, 21, 80, 134, 188, 210, 215, 237 |
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| abstract_inverted_index.M65, | 85 |
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| abstract_inverted_index.also | 57 |
| abstract_inverted_index.been | 76, 96, 109, 122 |
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| abstract_inverted_index.used | 171 |
| abstract_inverted_index.with | 59, 199 |
| abstract_inverted_index.Here, | 125 |
| abstract_inverted_index.PAC1, | 116, 181 |
| abstract_inverted_index.PAC1. | 101 |
| abstract_inverted_index.PACAP | 2, 37, 56 |
| abstract_inverted_index.VPAC1 | 63 |
| abstract_inverted_index.allow | 236 |
| abstract_inverted_index.assay | 173 |
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| abstract_inverted_index.date, | 79 |
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| abstract_inverted_index.which | 14, 86 |
| abstract_inverted_index.while | 159 |
| abstract_inverted_index.whose | 30 |
| abstract_inverted_index.VPAC2, | 65 |
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| abstract_inverted_index.albeit | 117 |
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| abstract_inverted_index.number | 201 |
| abstract_inverted_index.system | 174 |
| abstract_inverted_index.(SMOLs) | 107 |
| abstract_inverted_index.PACAP27 | 219 |
| abstract_inverted_index.PACAP38 | 26, 221 |
| abstract_inverted_index.Several | 102 |
| abstract_inverted_index.confirm | 161 |
| abstract_inverted_index.cryo-EM | 193 |
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| abstract_inverted_index.peptide | 18, 81, 178 |
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| abstract_inverted_index.related | 61, 88 |
| abstract_inverted_index.sandfly | 92 |
| abstract_inverted_index.shorter | 238 |
| abstract_inverted_index.sought. | 77 |
| abstract_inverted_index.-coupled | 9 |
| abstract_inverted_index.Abstract | 0 |
| abstract_inverted_index.PACAP27, | 28 |
| abstract_inverted_index.PACAP38. | 36 |
| abstract_inverted_index.abundant | 32 |
| abstract_inverted_index.activity | 153 |
| abstract_inverted_index.agonists | 70 |
| abstract_inverted_index.analysis | 186 |
| abstract_inverted_index.behavior | 217 |
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| abstract_inverted_index.dynamics | 185 |
| abstract_inverted_index.function | 241 |
| abstract_inverted_index.ligands, | 68 |
| abstract_inverted_index.ligands. | 205 |
| abstract_inverted_index.maintain | 232 |
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| abstract_inverted_index.peptide, | 94 |
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| abstract_inverted_index.platform | 129 |
| abstract_inverted_index.predicts | 214 |
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| abstract_inverted_index.compounds | 106 |
| abstract_inverted_index.currently | 146 |
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| abstract_inverted_index.interacts | 58 |
| abstract_inverted_index.ischemia. | 54 |
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| abstract_inverted_index.PACAP-PAC1 | 189 |
| abstract_inverted_index.antagonist | 248 |
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| abstract_inverted_index.maxadilan, | 90 |
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| abstract_inverted_index.vasodilator | 93 |
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| abstract_inverted_index.antagonists. | 168 |
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| abstract_inverted_index.specificities | 119 |
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| abstract_inverted_index.atherosclerosis, | 46 |
| abstract_inverted_index.highest-affinity | 16 |
| abstract_inverted_index.neuropsychiatric | 44 |
| abstract_inverted_index.neurodegeneration | 52 |
| abstract_inverted_index.cyclase-activating | 24 |
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| citation_normalized_percentile.is_in_top_10_percent | False |