TopFor: Automated Preparation of AMBER-Compatible Parameters for Noncanonical Amino Acids in Peptides
- 1Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)
Abstract
Peptides containing noncanonical amino acids (ncAAs) are becoming increasingly important in drug discovery, but their molecular dynamics (MD) simulation remains limited by labor-intensive residue parameterization and topology preparation. Here, we present TopFor (Topology and Residue Force-Field Parameter Preparation), an open-source, peptide-oriented workflow that automates the generation of ncAA residue templates and force-field parameter files for MD simulations with AMBER using established charge-derivation methods. TopFor supports single-residue, whole-peptide, and batch parameterization workflows. The workflow was validated using the MDM2-p53 complex by comparing native AMBER residue definitions with residues processed by TopFor using three charge-derivation methods, each evaluated in three independent 100 ns MD simulations. TopFor-generated residue definitions showed structural and conformational behavior comparable to the native AMBER representation. Applicability to more complex peptide architectures was demonstrated using the head-to-tail cyclic peptide cyclosporin A and the cyclic depsipeptide cyclohexylgriselimycin. At library scale, 1,138 of 1,214 cyclohexylgriselimycin derivatives (93.7%) successfully completed TopFor parameterization and the subsequent initial AMBER-based computational workflow across two derivatization campaigns. TopFor was further integrated into a structure-based peptide discovery workflow based on the DnaN-griselimycin complex. Six GM-derived peptides were computationally prioritized and experimentally evaluated, of which four produced SPR responses against Mycobacterium smegmatis (M. smegmatis) DnaN and three showed concentration-dependent responses. TopFor reduces the manual effort required to prepare ncAA-containing peptides for MD simulations and enables their integration into both library-scale computational screening and structure-based peptide discovery workflows. Keywords: noncanonical amino acids; peptide parameterization; molecular dynamics; AMBER; AmberTools; peptide design; high-throughput virtual screening
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BibTeX
@misc{buelbuel2026topfor,
title = {{TopFor: Automated Preparation of AMBER-Compatible Parameters for Noncanonical Amino Acids in Peptides}},
author = {E. F. Buelbuel and H. Gnanasekar and C. Benasolo and S. Rasheed and R. Mueller and O. V. Kalinina and K. A. J. Bozhueyuek},
howpublished = {bioRxiv},
year = {2026},
month = oct,
doi = {10.64898/2026.10.05.756260},
url = {https://www.biorxiv.org/content/10.64898/2026.10.05.756260v1},
note = {CC BY-NC-ND},
}
RIS
TY - UNPB
TI - TopFor: Automated Preparation of AMBER-Compatible Parameters for Noncanonical Amino Acids in Peptides
AU - E. F. Buelbuel
AU - H. Gnanasekar
AU - C. Benasolo
AU - S. Rasheed
AU - R. Mueller
AU - O. V. Kalinina
AU - K. A. J. Bozhueyuek
PY - 2026
DA - 2026/10/05
PB - bioRxiv
DO - 10.64898/2026.10.05.756260
UR - https://www.biorxiv.org/content/10.64898/2026.10.05.756260v1
AB - Peptides containing noncanonical amino acids (ncAAs) are becoming increasingly important in drug discovery, but their molecular dynamics (MD) simulation remains limited by labor-intensive residue parameterization and topology preparation. Here, we present TopFor (Topology and Residue Force-Field Parameter Preparation), an open-source, peptide-oriented workflow that automates the generation of ncAA residue templates and force-field parameter files for MD simulations with AMBER using established charge-derivation methods. TopFor supports single-residue, whole-peptide, and batch parameterization workflows. The workflow was validated using the MDM2-p53 complex by comparing native AMBER residue definitions with residues processed by TopFor using three charge-derivation methods, each evaluated in three independent 100 ns MD simulations. TopFor-generated residue definitions showed structural and conformational behavior comparable to the native AMBER representation. Applicability to more complex peptide architectures was demonstrated using the head-to-tail cyclic peptide cyclosporin A and the cyclic depsipeptide cyclohexylgriselimycin. At library scale, 1,138 of 1,214 cyclohexylgriselimycin derivatives (93.7%) successfully completed TopFor parameterization and the subsequent initial AMBER-based computational workflow across two derivatization campaigns. TopFor was further integrated into a structure-based peptide discovery workflow based on the DnaN-griselimycin complex. Six GM-derived peptides were computationally prioritized and experimentally evaluated, of which four produced SPR responses against Mycobacterium smegmatis (M. smegmatis) DnaN and three showed concentration-dependent responses. TopFor reduces the manual effort required to prepare ncAA-containing peptides for MD simulations and enables their integration into both library-scale computational screening and structure-based peptide discovery workflows. Keywords: noncanonical amino acids; peptide parameterization; molecular dynamics; AMBER; AmberTools; peptide design; high-throughput virtual screening
ER -