Recep Adiyaman
Weekly Digest March 06, 2026 · 22 min read

Weekly Digest: Mar 02 - Mar 06, 2026

A curated summary of the top protein engineering and structure prediction signals from Mar 02 - Mar 06, 2026.

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Daily curated signals from arXiv, PubMed, and BioRxiv.

🧬 Weekly Recap

Mar 02 - Mar 06, 2026

Missed a day? Here are the top research signals and tools from Monday to Friday, summarized in one place.


🏆 Top Signals of the Week

🗓️ Monday, Mar 02

Hybrid Computational Framework Integrating Ensemble Learning, Molecular Docking, and Dynamics for Predicting Antimalarial Efficacy of Malaria Box Compounds.

🧬 Abstract

The emergence of drug-resistant strains of Plasmodium falciparum continues to challenge global malaria control efforts, underscoring the urgent need for novel therapeutic strategies. In this study, we present an integrative computational framework that combines ensemble machine learning, molecular docking, and molecular dynamics simulations to predict and characterize the antimalarial activity of compounds from the Malaria Box database. Initially, topographical and quantum mechanical descriptors were used to construct regression models for predicting pEC 50 values, but due to the limited predictive performance in the global regression, a classification strategy was adopted, categorizing compounds into “active” and “very active” classes. The best ensemble classifier achieved robust performance (Acc 10 -fold = 0.738, Acc ext = 0.675), with good sensitivity and specificity over individual models. Subsequent regression modeling within each class yielded high predictive accuracy, with ensemble models reaching Q 2 10-fold values of 0.810 and 0.793 for the very active and active classes, respectively. To explore potential mechanisms of action, molecular docking was performed against P. falciparum Cytochrome B, revealing strong binding affinities for most compounds, particularly those forming π-π stacking and hydrogen bonds with Glu272. Molecular dynamics simulations over 200 ns confirmed the stability of several ligand-protein complexes, including unexpected behavior from compound M31, which demonstrated stable binding despite poor docking scores, suggesting a possible competitive inhibition mechanism. Binding free energy calculations further validated these findings, highlighting several promising candidates for future experimental evaluation. This integrative approach offers a powerful platform for accelerating antimalarial drug discovery by combining predictive modeling with mechanistic insights.

🗓️ Tuesday, Mar 03

Development of DHODH inhibitors incorporating virtual screening, pharmacophore modeling, fragment-based optimization methods, ADMET, molecular docking, molecular dynamics, PCA analysis, and free energy landscape.

🧬 Abstract

The overexpression of dihydroorotate dehydrogenase (DHODH) in various malignant tumor cells is significantly associated with ferroptosis, making DHODH inhibition a promising strategy for cancer therapy. In this study, we employed an integrated approach to screen and optimize DHODH inhibitor candidates. First, virtual screening of the FDA-approved drug library identified 20 potential compounds (with the positive control AG-636 as a benchmark, docking score: 133.166). Subsequent pharmacophore modeling (ROC curve value >0.8) further narrowed the candidates to six compounds, which underwent fragment displacement optimization. All optimized compounds were evaluated for absorption, distribution, metabolism, excretion, and toxicity (ADMET) properties. Molecular docking identified compounds 65:[(4S)-2,2-dimethyl-1,3-dioxolan-4-yl]methyl 3-(4-{[(2S)-2-hydroxypropyl]oxy}phenyl) (docking score: 197.362) and 66: [(4S)-2,2-dimethyl-1,3-dioxolan-4-yl]methyl 4-(4-{[(2S)-2-hydroxypropyl]oxy}phenyl) (docking score: 202.623) as high-affinity candidates. Molecular dynamics (MD) simulations, principal component analysis (PCA), and free energy landscape (FEL) analyses confirmed stable binding conformations for both compounds. Notably, compound 66: [(4S)-2,2-dimethyl-1,3-dioxolan-4-yl]methyl 4-(4-{[(2S)-2-hydroxypropyl]oxy}phenyl) exhibited minimal conformational changes, suggesting superior binding stability. This study advances compound 66: [(4S)-2,2-dimethyl-1,3-dioxolan-4-yl]methyl 4-(4-{[(2S)-2-hydroxypropyl]oxy}phenyl) as a promising DHODH inhibitor candidate through a multimodal workflow integrating structure-based pharmacophore design, fragment optimization, ADMET profiling, and advanced molecular simulations, providing a novel avenue for DHODH-targeted antitumor therapies.

Why it matters: Expands the searchable sequence space for novel folds and high-affinity binders.

🗓️ Wednesday, Mar 04

Anomalous Effect of Denaturant on Protein Unfolding Dynamics Revealed by Single Molecule Manipulation Experiments.

🧬 Abstract

High temperatures and chemical denaturants in bulk experiments, as well as mechanical forces in single-molecule studies, typically promote protein unfolding. In this study, we report an unexpected decrease in the unfolding rate of cold shock protein (Csp) at low concentrations of guanidine hydrochloride (GuHCl) in single-molecule magnetic tweezers experiments. This behavior contrasts with that of control protein GB1, which unfolds faster under the same denaturing conditions. Steered molecular dynamics (SMD) simulations indicate that stretching force applied to the N- and C-termini of Csp triggers an allosteric conformational change, converting loop regions into β-strands and reducing the solvent-accessible surface area (SASA). The combination of experimental and simulation data suggests that the unfolding transition state of Csp has a smaller SASA than that of the native state, providing a structural explanation for the observed kinetic anomaly. These results demonstrate that allosteric conformational or dynamical changes, triggered by mechanical or chemical perturbations, can render proteins resistant to denaturation by lowering their unfolding rates, thereby conferring resistance to environmental stress.

🗓️ Thursday, Mar 05

Investigation of the potential mechanism by which methylparaben induces psoriasis: an integrated study using network toxicology, molecular docking, molecular dynamics simulation, and eight machine learning algorithms.

🧬 Abstract

Psoriasis is a chronic inflammatory skin disease with limited safe and effective treatments. Methylparaben, a widely used preservative in cosmetics, pharmaceuticals, and food, is an emerging environmental pollutant linked to immune-related skin disorders, but its role and mechanism in psoriasis remain unclear. This study explored its potential mechanism using network toxicology, molecular docking, molecular dynamics simulation, and eight machine learning algorithms. Methylparaben targets were retrieved from GeneCards and TCMSP, and psoriasis-related targets from CTD and GeneCards. Overlapping targets were screened with Venny 2.1.0. A PPI network was constructed via STRING, and core targets identified using Cytoscape 3.10.2. GO and KEGG enrichment analyses were performed on DAVID. Molecular docking evaluated the binding affinity of methylparaben with key targets. A total of 138 compound-related and 5,592 psoriasis-related targets were identified. Core targets such as INS, HIF1A, and PPARG are involved in regulating immune-inflammatory responses, keratinocyte proliferation and differentiation, and oxidative stress. GO analysis revealed enrichment in xenobiotic metabolism, lipopolysaccharide response, and metal ion binding. KEGG analysis highlighted pathways related to cancer, chemical carcinogenesis from reactive oxygen species, and drug metabolism via cytochrome P450 enzymes. Molecular docking showed stable binding of methylparaben to INS (-4.5 kcal/mol), HIF1A (-5.9 kcal/mol), and PPARG (-5.5 kcal/mol), primarily through hydrogen bonds and hydrophobic interactions. Methylparaben may exert its effects on psoriasis via multi-target and multi-pathway mechanisms, influencing inflammation, oxidative stress, and cellular regulation. These findings provide valuable insight into its toxicological mechanism and potential therapeutic application.

Why it matters: Provides actionable mutations to enhance catalytic efficiency or thermostability.

🗓️ Friday, Mar 06

Identification of Bioactive Ingredients and Mechanistic Pathways of Xuefu Zhuyu Decoction in Ventricular Remodeling: A Network Pharmacology, Molecular Docking and Molecular Dynamics Simulations.

🧬 Abstract

Background Xuefu Zhuyu Decoction (XFZYD) is clinically used in China to promote blood circulation, resolve blood stasis, and alleviate ventricular remodeling (VR). However, its molecular mechanisms remain unclear. Objective This study investigates the active components and underlying molecular mechanisms of XFZYD in treating VR. Methods Targets of XFZYD’s active components and VR-related targets were identified. A protein-protein interaction (PPI) network and a drug-ingredient-target network were constructed. GO functional annotation and KEGG pathway enrichment analysis were performed to explore biological functions. Hub targets and their corresponding active ingredients were validated through molecular docking and molecular dynamics (MD) simulations. Results A total of 1,089 active ingredients with high gastrointestinal absorption (GI) and drug-likeness (DL ≥ 2) were identified. Five hundred and thirty-eight common targets were shared between XFZYD and VR, with 10 core targets, including AKT1, STAT3, TP53, EGFR, SRC, TNF, MAPK3, CTNNB1, IL6, and VEGFA. GO analysis revealed XFZYD’s influence on wound healing, oxygen response, epithelial cell proliferation, and receptor signaling. KEGG analysis highlighted key pathways such as PI3K-Akt signaling, lipid and atherosclerosis, and fluid shear stress. Molecular docking revealed that active ingredients display favorable interactions with the hub genes, with binding energies from -9.5 to -6.0 kcal/mol. These interactions were further validated through MD simulations, demonstrating stable binding throughout the 100 ns simulation period. Conclusion XFZYD exhibits therapeutic effects on VR through multiple active components and pathways, providing a scientific basis for its clinical application and further research.

Why it matters: Enhances small-molecule or peptide docking accuracy for targeted drug discovery.


📚 All Papers & Quick Reads

🗓️ Monday, Mar 02

🗓️ Tuesday, Mar 03

🗓️ Wednesday, Mar 04

🗓️ Thursday, Mar 05

🗓️ Friday, Mar 06


🛠️ Tools & Datasets

  • 🛠 Tool: Chai-1 - Multi-modal foundation model for molecular structure prediction.
  • 🛠 Tool: Boltz-1 - Open-source biomolecular structure prediction model.
  • 💾 Dataset: AlphaFold Structure Database - 200M+ predicted structures from DeepMind/EMBL-EBI.
  • 💾 Dataset: Uniprot Knowledgebase - The world’s most comprehensive resource for protein sequence and annotation.
  • 🛠 Tool: ProteinSolver - Graph-based neural network for protein sequence design.
  • 💾 Dataset: PDB-REDO - Optimized protein structure database with refined models.
  • 🛠 Tool: RFdiffusion - State-of-the-art generative model for de novo protein design.
  • 💾 Dataset: CATH - Hierarchical protein domain classification for structure and function.
  • 🛠 Tool: ProteinMPNN - High-speed sequence design optimized for fixed-backbone folding.
  • 💾 Dataset: SCOPe - Curated structural classification of proteins for fold analysis.
  • 🛠 Tool: OpenFold - Fast, trainable, and open implementation of AlphaFold2.
  • 💾 Dataset: Pfam - Protein families database with curated multiple sequence alignments.

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