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Daily Signal January 21, 2026 · 7 min read

Issue #27: AlphaFold can help African researchers to do cutting-edge structural biology.

Protein Design Digest - 2026-01-21 - Mechanistic Investigation of Astragalus Root in the Management of T2DM-NAFLD Comorbidity: An Integrated Network Pharmacology, Molecular Docking, Molecular Dynamics Simulation, and In Vitro Study

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AlphaFold can help African researchers to do cutting-edge structural biology.

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Exploring the mechanism of Kemofang in treating idiopathic membranous nephropathy based on LC-MS/MS combined with network pharmacology, molecular docking, and molecular dynamics simulation.

Idiopathic membranous nephropathy (IMN), an autoimmune glomerular disease, arises from in situ immune complex deposition in the glomerular subepithelial spaces, triggering complement activation and podocyte injury. Although the Kemo Formula shows therapeutic potential for IMN, its mechanisms remain unclear. This study employed LC-MS/MS, network pharmacology, molecular docking, and dynamic simulations to elucidate the mechanism of action. LC-MS/MS and the TCMSP database identified 83 bioactive components from 267 chemicals detected in the Kemo Formula. Using PubChem, Swiss Target Prediction, and GeneCards, 827 drug targets and 2581 IMN-related targets were screened, yielding 336 overlapping targets linked to 81 components. Network analysis prioritized 15 key components ( baicalein and quercetin) and 36 core targets (TP53, IL6, and AKT1). Functional enrichment revealed involvement in hormone response, MAPK cascade regulation, and kinase binding with pathways including lipid metabolism, PI3K/Akt, and MAPK signaling. Molecular docking indicated strong binding affinities between the active components and targets, while dynamic simulations predicted the stability of the galangin-AKT1 complex. The Kemo Formula likely mitigates IMN by multi-target modulation, ameliorating lipid dysregulation, suppressing podocyte apoptosis, and attenuating immune-inflammatory and oxidative stress via PI3K/Akt and MAPK pathways. This integrative approach highlights its multicomponent, multitarget therapeutic strategy against IMN, providing a foundation for further mechanistic and clinical exploration.

Discovery of ActRIIB antagonistic peptides from in vitro-digested chicken breast meat via an integrated Peptidomics and molecular docking approach.

Sarcopenia and obesity are major global health challenges. This study investigated peptides from chicken breast meat via in vitro digestion as potent ActRIIB antagonists to promote myogenesis. The intestinal-phase digest collected at 120 min showed the highest degree of hydrolysis (65.99 % ± 4.00 %) and enhanced C2C12 proliferation (128.15 % ± 9.90 %). Peptidomics identified peptides mainly from myofibrillar proteins and metabolic enzymes. Molecular docking revealed key hydrogen-bonding residues, including Glu 95 , Pro 117 , Glu 94 , Thr 93 , Asn 96 (Chain A), Ser 97 (Chain L), and Ser 59 (Chain H). Surface plasmon resonance showed that KEKLHVYKHIEK, EIKKEEKKEER, and DLENDKQQLDEK exhibited strong ActRIIB-binding affinity (K D : 0.514, 0.813, 1.91 μM). These peptides enhanced cell proliferation, inhibited myostatin signaling by reducing Smad2/3 phosphorylation, and upregulated MyoD expression. Molecular dynamics simulations (100 ns) indicated that DLENDKQQLDEK-ActRIIB and EIKKEEKKEER-ActRIIB complexes maintained a stable average number of 6 and 10 hydrogen bonds, respectively. Chicken breast-derived peptides thus represent promising functional food ingredients for combating muscle-wasting disorders.

Rational discovery of testosterone-enhancing peptide (AGNYGLPT) from sea cucumber: targeting T-type calcium channels through docking, molecular dynamics simulations, and cellular validation.

Calcium ions (Ca 2+ ) are a crucial signaling factor in testosterone synthesis. This study employed computer-guided peptide screening and mechanism exploration to elucidate how sea cucumber peptide (SCP) promotes testosterone synthesis via Cacna1g (T-type calcium channel). Ca 2+ treatment alone significantly upregulated the expression of Cacna1g, protein kinase C (PKC), protein kinase A (PKA), and testosterone synthase genes (StAR, Hsd17b3, Cyp17a1); these effects were further enhanced by SCP co-treatment. Molecular docking combined with correlation analysis pinpointed the peptide’s isoelectric point as a critical determinant governing its binding affinity to Cacna1g. SCP was subsequently fractionated into three components via ion-exchange chromatography, among which the fraction 1 (F1) elevated intracellular Ca 2+ levels and enhanced testosterone synthesis. Moreover, molecular docking results for the F1 sequences also showed a positive linear relationship between binding affinity and isoelectric point. Peptide AGNYGLPT in F1 stabilizes Cacna1g (with the strongest binding ability) via hydrogen bonding, and participates in ion channel formation (Charge = -2, Radius = 2.8 Å). In vitro, AGNYGLPT increased intracellular Ca 2+ levels and enhanced testosterone synthesis, but this effect was abolished by inhibition of T-type calcium channels. This study provided mechanistic insights into peptide-channel interactions and offered new ideas for computer-assisted screening of active peptides.

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Deciphering the pharmacological mechanisms of salidroside in cervical cancer by combining network pharmacology, molecular docking, and in vitro studies.

Cervical cancer is one of the major and serious risks to women. Read more →

Exploring the Mechanism of 2,4-Dichlorophenoxyacetic Acid in Causing Neurodegenerative Diseases Based on Network Toxicology and Molecular Docking.

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Molecular docking and MD simulations predicted quercetin as a potent human interleukin-1 beta (hIL1β) inhibitor for improved endodontic disease management.

IL1β, a pro-inflammatory cytokine, is a key mediator in the inflammatory processes linked to endodontic disorders. Read more →

Identification of diagnostic genes and drug prediction of allergic asthma by integrated bioinformatics analysis, machine learning, and molecular docking.

Background Allergic asthma is a heterogeneous inflammatory airway disease with limited biomarkers and unclear immune mechanisms, complicating diagnosis and treatment. Read more →

Non-standard proteins in the lens of AlphaFold3 - a case study of amyloids

While three-dimensional structures of globular and transmembrane forms are available for many amyloid proteins, structures of their amyloid forms are scarce in the PDB. Read more →

AI-powered literature mining reveals the therapeutic significance of GLP-1 receptor: Simulation of natural agonist candidates based on molecular dynamics.

Glucagon-like peptide-1 (GLP-1), a pivotal incretin hormone modulating glycemic homeostasis, has emerged as a clinically validated target for the treatment of type 2 diabetes and obesity. Read more →

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Deep learning is not a magic wand, but a powerful lens for structural biology. — Recep Adiyaman

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