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Discovery of a pyrazolopyridine alkaloid that mitigates neuronal ER stress and age-related decline.

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The 1 match
  1. [1] § Materials and methods › Phytochemical compound virtual screening ↔ run_virtual_screening.sh, lines 92–157 · score 0.77 · prepare_ligand4.py, prepare_receptor4.py, unique compounds, pdbqt format, AutoDockTools, virtual

Paper

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The authors' code

Shell · 157 lines · 5.7 KB · no license · 1 match

  2. ### Shell Script (`run_screening_workflow.sh`)
  4. This version is a single, continuous script without functions or the re-run logic, as requested.
  6. ```bash
  7. #!/bin/bash
  8. set -e -o pipefail
  10. #================================================================================================
  11. # HIGH-THROUGHPUT VIRTUAL SCREENING WORKFLOW (Linear Execution)
  12. #
  13. # This script automates a full virtual screening pipeline in a sequential manner:
  14. # 1. Ligand Preparation: Prepares 3D ligands from a SMILES file using Gypsum-DL.
  15. # 2. Protein Preparation: Prepares a receptor PDB file for docking.
  16. # 3. Virtual Screening: Runs a high-throughput screen using POAP.
  17. #================================================================================================
  19. #------------------------------------------------------------------------------------------------
  20. # SECTION 1: CONFIGURATION
  21. # !! EDIT THESE VARIABLES TO MATCH YOUR SYSTEM AND PROJECT !!
  22. #------------------------------------------------------------------------------------------------
  24. # --- Project and File Paths ---
  25. MAIN_DIR="${HOME}/Downloads/Drug_screening/AUTODOCK"
  26. PROTEIN_PDB="${HOME}/Downloads/SWISS_model/ERO1B_HUMAN.pdb"
  27. MASTER_SMILES_FILE="${HOME}/Downloads/Drug_screening/COCONUT_DB.smi"
  28. POAP_SCRIPT_DIR="${HOME}/Downloads/Drug_screening/POAP_CMUTEAM-main/scripts_v1_1_conda/"
  29. GRID_PARAM_FILE="${HOME}/Downloads/Drug_screening/test/protein/3AHQ.txt"
  30. MGLTOOLS_PREP_PATH="${HOME}/miniconda3/envs/autodock/bin/"
  32. # --- File Naming ---
  33. PROTEIN_NAME="ERO1B"
  35. # --- Parallel Processing Parameters ---
  36. NTASKS=125
  37. LIGANDS_PER_SPLIT=125
  39. # --- Conda Environments ---
  40. CONDA_ENV_GYPSUM="gypsum"
  41. CONDA_ENV_AUTODOCK="autodock"
  42. CONDA_ENV_POAP="poap"
  44. # --- Directory Names (Script will create these inside MAIN_DIR) ---
  45. GYPSUM_OUTPUT_DIR="COCONUT_PDB"
  46. PDBQT_OUTPUT_DIR="COCONUT_PDBQT"
  47. SPLIT_SMI_DIR="SPLIT_INPUT"
  48. PREPARED_PROTEIN_DIR="PREPARED_PROTEIN"
  49. PREPARED_LIGAND_DIR="PREPARED_LIGANDS"
  50. POAP_WORKING_DIR="WORKING_POAP"
  52. #------------------------------------------------------------------------------------------------
  53. # SECTION 2: SCRIPT EXECUTION
  54. # The script will now run from top to bottom.
  55. #------------------------------------------------------------------------------------------------
  57. echo "INFO: Creating main working directory at ${MAIN_DIR}"
  58. mkdir -p "${MAIN_DIR}"
  59. cd "${MAIN_DIR}"
  61. # --- Step 1: Ligand Preparation with Gypsum-DL ---
  62. echo "INFO: Activating conda environment: ${CONDA_ENV_GYPSUM}"
  63. source activate "${CONDA_ENV_GYPSUM}"
  65. echo "INFO: Splitting master SMILES file into chunks of ${LIGANDS_PER_SPLIT}..."
  66. mkdir -p "${SPLIT_SMI_DIR}"
  67. split --additional-suffix=".smi" -l "${LIGANDS_PER_SPLIT}" "${MASTER_SMILES_FILE}" "${SPLIT_SMI_DIR}/CO_"
  69. echo "INFO: Running Gypsum-DL in parallel with ${NTASKS} tasks..."
  70. mkdir -p "${GYPSUM_OUTPUT_DIR}"
  71. for smi in "${SPLIT_SMI_DIR}"/*.smi; do
  72. echo "INFO: Processing input file >>> $(basename "$smi")"
  73. mpirun -n "${NTASKS}" python -m mpi4py run_gypsum_dl.py \
  74. --source "${smi}" \
  75. --output_folder "../${GYPSUM_OUTPUT_DIR}" \
  76. --add_pdb_output \
  77. -m 1 \
  78. --job_manager mpi \
  79. --num_processors "${NTASKS}"
  80. done
  82. echo "INFO: Renaming output PDB files for simplicity..."
  83. cd "${GYPSUM_OUTPUT_DIR}"
  84. for f in *_output_1.pdb; do
  85. mv -- "$f" "${f%_output_1.pdb}.pdb"
  86. done
  87. cd ..
  89. echo "INFO: Deactivating conda environment."
  90. conda deactivate
  92. # --- Step 2: Convert Ligand PDB to PDBQT ---
  93. echo "INFO: Activating conda environment: ${CONDA_ENV_AUTODOCK}"
  94. source activate "${CONDA_ENV_AUTODOCK}"
  96. echo "INFO: Converting ligand PDB files to PDBQT format..."
  97. mkdir -p "${PDBQT_OUTPUT_DIR}"
  98. cd "${GYPSUM_OUTPUT_DIR}"
  99. for fname in *.pdb; do
  100. python2 "${MGLTOOLS_PREP_PATH}prepare_ligand4.py" -l "${fname}" -v -o "../${PDBQT_OUTPUT_DIR}/${fname%.pdb}.pdbqt"
  101. done
  102. cd ..
  104. echo "INFO: Deactivating conda environment."
  105. conda deactivate
  107. # --- Step 3: Prepare Protein Receptor ---
  108. echo "INFO: Activating conda environment: ${CONDA_ENV_AUTODOCK}"
  109. source activate "${CONDA_ENV_AUTODOCK}"
  111. echo "INFO: Preparing protein receptor ${PROTEIN_NAME}..."
  112. pdb2pqr30 --ff=AMBER --with-ph=7.4 "${PROTEIN_PDB}" "${PROTEIN_NAME}.pqr"
  113. python2 "${MGLTOOLS_PREP_PATH}prepare_receptor4.py" -r "${PROTEIN_NAME}.pqr" -v -o "${PROTEIN_NAME}.pdbqt"
  115. echo "INFO: Deactivating conda environment."
  116. conda deactivate
  118. # --- Step 4: Organize Files for POAP Screening ---
  119. echo "INFO: Organizing final ligand and protein files for POAP..."
  120. mkdir -p "${PREPARED_PROTEIN_DIR}" "${PREPARED_LIGAND_DIR}"
  121. cp "${PDBQT_OUTPUT_DIR}"/*.pdbqt "${PREPARED_LIGAND_DIR}/"
  122. cp "${PROTEIN_NAME}.pdbqt" "${PREPARED_PROTEIN_DIR}/"
  123. cp "${GRID_PARAM_FILE}" "${PREPARED_PROTEIN_DIR}/${PROTEIN_NAME}.txt"
  125. # --- Step 5: Run POAP Virtual Screening ---
  126. echo "INFO: Activating conda environment: ${CONDA_ENV_POAP}"
  127. source activate "${CONDA_ENV_POAP}"
  129. echo "INFO: Starting POAP virtual screening..."
  130. bash "${POAP_SCRIPT_DIR}/POAP_vs.bash" -s <<EOF
  131. 1
  132. ${MAIN_DIR}/${PREPARED_LIGAND_DIR}
  133. ${MAIN_DIR}/${PREPARED_PROTEIN_DIR}
  134. ${MAIN_DIR}/${POAP_WORKING_DIR}
  135. 8
  136. 8
  137. 1
  138. 2000
  139. EOF
  141. echo "INFO: Deactivating conda environment."
  142. conda deactivate
  144. # --- Workflow Complete ---
  145. echo "------------------------------------------------------"
  146. echo "SCRIPT COMPLETE."
  147. echo "Final results are located in: ${MAIN_DIR}/${POAP_WORKING_DIR}/Results"
  148. echo "------------------------------------------------------"
  150. # --- Optional Commands for Analysis ---
  151. #
  152. # To move completed ligands from an interrupted run (run this manually if needed):
  153. # for i in `cut -f1 WORKING_POAP/Results/output.txt`; do mv PREPARED_LIGANDS/${i}.pdbqt PREPARED_LIGANDS/COMPLETED_RUN/; done
  154. #
  155. # To count total unique compounds from multiple combined runs:
  156. # cat WORKING_POAP_RUN1/Results/output.txt WORKING_POAP_RUN2/Results/sorted.txt | cut -f1 | sort | uniq | wc -l
  157. #

run_virtual_screening.sh at commit 170bd01, no license · at the source

Overview

Authors: Salinee Jantrapirom1,2, Apiwat Sangphukieo3, Natsinee U-on3, Pattaporn Poonsawas4, Wasinee Wongkumool3, Ranchana Yeewa3, Chansunee Panto2, Puttachat Poound2, Ester Zito5,6, Alice Marrazza5, Luca Lo Piccolo3
ORCID iDs: Pattaporn Poonsawas, Wasinee Wongkumool, Ester Zito, Luca Lo Piccolo
  1. Department of Pharmacology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
  2. Drosophila Centre for Human Diseases and Drug Discovery (DHD), Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
  3. Center of Multidisciplinary Technology for Advanced Medicine (CMUTEAM), Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
  4. Faculty of Pharmaceutical Sciences, Khon Kaen University, Khon Kaen, Thailand
  5. Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Milan, Italy
  6. Department of Biomolecular Sciences, University of Urbino Carlo Bo, Urbino, Italy
Institutions: Chiang Mai University (Thailand); Khon Kaen University (Thailand); University of Urbino (Italy); Mario Negri Institute for Pharmacological Research (Italy)
Journal: Communications biology, volume 9, issue 1, article 964
Dates: received 2 November 2025; accepted 28 April 2026; published online 8 May 2026
Type: Research article · Language: English
License: CC BY-NC-ND
Identifiers: DOI 10.1038/s42003-026-10226-8 · PMID 42104039 · PMCID PMC13369832 · OpenAlex W7160598820
Open access: gold, a free copy (OpenAlex)
Status: code verified
Categories: human (organism), other condition (population)
Methods: Spectral & time-frequency, Statistics, Evoked potentials
Keywords: Amyotrophic lateral sclerosis, Neurodegeneration
MeSH: Aging*, Alkaloids*, Endoplasmic Reticulum Stress*, Neurons*, Pyrazoles*, Pyridines*, Animals, Humans (* major topic)
Topic: Endoplasmic Reticulum Stress and Disease (Cell Biology, Biochemistry, Genetics and Molecular Biology), according to OpenAlex
Funding: CMU | Faculty of Medicine, Chiang Mai University (139/2567); Chiang Mai University (CMU) (FF66/061, FF68/207569, FF67/044); National Research Council of Thailand (NRCT) (N42A670768); Health Systems Research Institute (HSRI) (66-124, 68-060)
Citations: cited by 1 paper (Europe PMC); 67 references in the paper

Abstract

The abstract is not reproduced here: the paper's license (CC BY-NC-ND) does not allow it. Read it in the paper, at the publisher or on Europe PMC.

Repository

Its files are read in the Code ↔ Paper reader above, with 1 match between paragraphs and lines of code.

asangphukieo/Phytochem_screening

License: none: the authors keep all their rights
State: the link answers, verified on 28 September 2026
Evidence: files inventoried
Commit: 170bd015b2e675a6d879dc0ad4c19a2a8d5a097b, 19 July 2025
Languages: Shell (1)
Size: 4 files, 1 script
Software Heritage: not archived
Found in: “Code availability”
Holds: README
Not found: license file, CITATION.cff, environment file, tests, continuous integration, documentation
Availability: 1 check, the latest on 28 September 2026: the link answers
  • 28 September 2026: the link answers
2 files
At the source: github.com/asangphukieo/Phytochem_screening

Code availability statement

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Read it in the paper: doi.org/10.1038/s42003-026-10226-8.

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  • 1 match between paragraphs of the paper and lines of the code (method lexical-v1);
  • neither the text of the paper nor the code itself.

Its JSON (tracing-map.json) is deposited on Zenodo with its DOI once the map is validated.

Data

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Data availability statement

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  • it says that the data are available on request

Read it in the paper: doi.org/10.1038/s42003-026-10226-8.

Versions

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Version 1, 28 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 11 authors, 2 keywords, 8 MeSH terms, 4 funders, 67 references.

Cite

This paper

Jantrapirom, S., Sangphukieo, A., U-on, N., Poonsawas, P., Wongkumool, W., Yeewa, R., Panto, C., Poound, P., Zito, E., Marrazza, A., & Lo Piccolo, L. (2026). Discovery of a pyrazolopyridine alkaloid that mitigates neuronal ER stress and age-related decline. Communications biology, 9(1), 964. https://doi.org/10.1038/s42003-026-10226-8

BibTeX

@article{jantrapirom2026discovery,
author = {Jantrapirom, Salinee and Sangphukieo, Apiwat and U-on, Natsinee and Poonsawas, Pattaporn and Wongkumool, Wasinee and Yeewa, Ranchana and Panto, Chansunee and Poound, Puttachat and Zito, Ester and Marrazza, Alice and Lo Piccolo, Luca},
title = {{Discovery of a pyrazolopyridine alkaloid that mitigates neuronal ER stress and age-related decline}},
journal = {Communications biology},
year = {2026},
month = may,
volume = {9},
number = {1},
pages = {964},
publisher = {Nature Publishing Group},
issn = {2399-3642},
doi = {10.1038/s42003-026-10226-8},
url = {https://doi.org/10.1038/s42003-026-10226-8},
pmid = {42104039},
pmcid = {PMC13369832}
}

RIS

TY - JOUR
AU - Jantrapirom, Salinee
AU - Sangphukieo, Apiwat
AU - U-on, Natsinee
AU - Poonsawas, Pattaporn
AU - Wongkumool, Wasinee
AU - Yeewa, Ranchana
AU - Panto, Chansunee
AU - Poound, Puttachat
AU - Zito, Ester
AU - Marrazza, Alice
AU - Lo Piccolo, Luca
TI - Discovery of a pyrazolopyridine alkaloid that mitigates neuronal ER stress and age-related decline
T2 - Communications biology
J2 - Commun Biol
PY - 2026
DA - 2026/05/08
VL - 9
IS - 1
SP - 964
SN - 2399-3642
PB - Nature Publishing Group
DO - 10.1038/s42003-026-10226-8
UR - https://doi.org/10.1038/s42003-026-10226-8
LA - en
ER -

CSL-JSON

{
"id": "10.1038/s42003-026-10226-8",
"type": "article-journal",
"title": "Discovery of a pyrazolopyridine alkaloid that mitigates neuronal ER stress and age-related decline",
"container-title": "Communications biology",
"author": [
{
"family": "Jantrapirom",
"given": "Salinee"
},
{
"family": "Sangphukieo",
"given": "Apiwat"
},
{
"family": "U-on",
"given": "Natsinee"
},
{
"family": "Poonsawas",
"given": "Pattaporn"
},
{
"family": "Wongkumool",
"given": "Wasinee"
},
{
"family": "Yeewa",
"given": "Ranchana"
},
{
"family": "Panto",
"given": "Chansunee"
},
{
"family": "Poound",
"given": "Puttachat"
},
{
"family": "Zito",
"given": "Ester"
},
{
"family": "Marrazza",
"given": "Alice"
},
{
"family": "Lo Piccolo",
"given": "Luca"
}
],
"container-title-short": "Commun Biol",
"volume": "9",
"issue": "1",
"page": "964",
"DOI": "10.1038/s42003-026-10226-8",
"PMID": "42104039",
"PMCID": "PMC13369832",
"ISSN": "2399-3642",
"publisher": "Nature Publishing Group",
"URL": "https://doi.org/10.1038/s42003-026-10226-8",
"language": "en",
"issued": {
"date-parts": [
[
2026,
5,
8
]
]
}
}

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