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VDLIN: A Deep Learning-Based Platform for Methylcobalamin-Inspired Immunomodulatory Compound Screening.

Xuefei Guo¹, Yang Zhao¹, Xianle Rong²

¹Institute of Systems Biomedicine, Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, NHC Key Laboratory of Medical Immunology, Peking University Health Science Center, Beijing, 100191, China.

Advanced Science (Weinheim, Baden-Wurttemberg, Germany)

|October 27, 2025

Summary

Methylcobalamin (MCB) reduces inflammation but weakens innate immunity. A new compound, Co7, balances these effects, offering a promising therapeutic for inflammatory diseases and COVID-19.

Keywords:

EGR1 NF‐κB TLR4 Vitamin B12 (VB12)convolutional neural network inflammatory response innate immunity

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Area of Science:

Immunology
Molecular Biology
Computational Biology

Background:

Methylcobalamin (MCB), an active Vitamin B12 (VB12) form, showed anti-inflammatory potential during COVID-19.
MCB treatment may impair macrophage-mediated innate immune responses, despite its anti-inflammatory benefits.

Purpose of the Study:

To investigate MCB's impact on innate immunity and develop a strategy to overcome its limitations.
To identify novel compounds with both anti-inflammatory and immune-boosting properties.

Main Methods:

Comprehensive analyses including RNA-seq, ATAC-seq, and CUT&Tag to understand MCB's mechanism.
Development of a deep learning model, VDLIN (Vitamin B12-derived Deep Learning for Innate Immunity), for compound screening.
Identification and characterization of a novel compound, Co7.

Main Results:

MCB reduces inflammation by limiting chromatin accessibility at NF-κB and EGR1 binding sites, decreasing IFNB1 production and enhancing viral immune evasion.
VDLIN successfully identified Co7, which retains MCB's anti-inflammatory effects.
Co7 enhances immune activation through the TLR4 signaling pathway, unlike MCB.

Conclusions:

MCB's dual effect on inflammation and innate immunity is mediated by chromatin dynamics.
Co7 represents a promising therapeutic candidate, balancing anti-inflammatory and immune-stimulatory functions for inflammatory diseases and SARS-CoV-2 infection.
This study highlights new therapeutic opportunities by understanding the interplay between chromatin and immune regulation.