From structural insight to molecule: Integrative molecular simulations identify candidate pyruvate kinase activators
Doni Dermawan ,Nasser Alotaiq
Abstract
Pyruvate kinase (PKLR) is a key glycolytic enzyme that regulates red blood cell energy homeostasis. Although Mitapivat is the first approved allosteric activator for pyruvate kinase deficiency (PKD), its clinical utility is limited by metabolic and pharmacokinetic challenges, underscoring the need for improved analogues.
Introduction
Pyruvate kinase deficiency (PKD) is a rare but severe inherited red blood cell disorder caused by mutations in the pyruvate kinase (PKLR) gene, leading to impaired pyruvate kinase activity, reduced glycolytic ATP production, and compromised erythrocyte survival .Clinically, PKD manifests with chronic nonspherocytic hemolytic anemia, splenomegaly, and iron overload, often requiring lifelong transfusion support or splenectomy
Materials and methods
3D structure generation and MM2 energy minimization
The chemical derivatives of Mitapivat were retrieved from the ChEMBL database [24] (a curated repository of bioactive molecules with drug-like properties) using the SwissSimilarity platform [25]. The SMILES of Mitapivat (C1CC1CN2CCN(CC2)C(=O)C3 = CC = C(C = C3)NS(=O)(=O)C4 = CC = CC5 = C4N=CC = C5) was employed as the query input. The search was restricted to bioactive compound classes.
3D structure alignment and similarity analysis
To evaluate structural consistency and conformational variation among Mitapivat and its derivatives, 3D structure alignment was performed using the superimpose feature in BIOVIA Discovery Studio version 2024 (Dassault Systèmes, Vélizy-Villacoublay, France). To further assess structural relationships.
Results
To systematically explore the potential of Mitapivat analogues as novel PKLR activators, we performed structural alignment, molecular similarity analysis, and docking-based screening of the designed
Structure alignment and similarity analysis
A total of 190 Mitapivat derivatives were identified with a similarity score ≥ 0.90, indicating high structural conservation relative to the parent scaffold. This ensured that the derivatives retained the essential pharmacophoric elements of Mitapivat (the pyrrolidine amide core, the aryl sulfonamide moiety
Molecular docking results, binding pose, and binding affinity analysis
The docking simulations provided a comprehensive assessment of the binding affinity and interaction profiles of Mitapivat and its derivatives with the PKLR allosteric binding site. As shown Mitapivat exhibited a binding energy of −8.24 kcal/mol with a HADDOCK score of −40.1, confirming its strong and specific interaction with PKLR and validating the docking protocol.
Conclusions
In conclusion, this study demonstrates the effectiveness of an integrative computational framework in identifying promising next-generation derivatives of Mitapivat, the first-in-class allosteric activator of PKLR. Our results highlight that sulfonamide-containing derivatives, particularly CHEMBL3729403 and CHEMBL3729860, exhibit stronger binding affinities, enhanced conformational stability.
Citation: Dermawan D, Alotaiq N (2026) From structural insight to molecule: Integrative molecular simulations identify candidate pyruvate kinase activators. PLoS One 21(8): e0352669. https://doi.org/10.1371/journal.pone.0352669
Editor: Javed Iqbal, University of Sahiwal, PAKISTAN
Received: August 27, 2025; Accepted: June 14, 2026; Published: August 12, 2026
Copyright: © 2026 Dermawan, Alotaiq. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Data Availability: All relevant data are within the paper and its Supporting Information files. The custom code used for HOMO–LUMO analysis is publicly accessible without restriction via GitHub at: https://github.com/pritampanda15/Omixium_YouTube_Channel/tree/main/HOMO_LUMO (accessed on 14 May 2025). This ensures transparency, reproducibility, and reuse of the computational workflow described in this study.
Funding: This research received no external funding.
Competing interests: The authors have declared that no competing interests exist.
