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Targeting Epigenetic Complexes and Alternative Protein Degradation Pathways in Medicinal Chemistry

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Biochemistry".

Deadline for manuscript submissions: 20 June 2026 | Viewed by 2904

Special Issue Editor


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Guest Editor
Faculdade de Ciências Farmacêuticas (FCFAR), Universidade Estadual Paulista, Sao Paulo, Brazil
Interests: new drugs; drug design; drug discovery; infectious disease; medicinal chemistry

Special Issue Information

Dear Colleagues,

The development of novel therapeutic strategies that modulate intracellular protein homeostasis and epigenetic regulation is opening unprecedented avenues in medicinal chemistry. Beyond classical PROTACs and HDAC inhibitors, recent efforts have unveiled emerging platforms such as LYTACs, AUTACs, ATTECs, and small-molecule modulators of chromatin remodeling complexes (e.g., NuRD, SWI/SNF, PRC2). These non-canonical degradation mechanisms and epigenetic regulators play critical roles in the progression of cancer, infectious diseases, and neurological disorders.

This Special Issue aims to highlight advances in the discovery and development of small molecules, hybrid compounds, conjugates, or molecular tools targeting either non-proteasomal degradation pathways or epigenetic protein complexes. Submissions may focus on molecular design, synthesis, SAR studies, mechanistic investigations, or therapeutic evaluation.

This Special Issue invites contributions that explore innovative small molecules, conjugates, and biologically active compounds designed to target these underexplored systems. We welcome original research and review articles covering:

  • Inhibitors and degraders targeting chromatin remodeling complexes (e.g., CHD4, HDACs, EZH2, BRD proteins);
  • Non-proteasomal degradation strategies: lysosome-targeting chimeras (LYTACs), autophagy-tethering compounds (AUTACs/ATTECs);
  • Molecular mechanisms linking epigenetic control and protein stability;
  • Rational design, synthesis, SAR studies, and degradation kinetics;
  • Therapeutic applications in cancer, neurodegeneration, infectious and neglected diseases;
  • Delivery systems or conjugates enabling selective engagement of epigenetic or degradation targets.

Dr. Jean Leandro Dos Santos
Guest Editor

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Keywords

  • protein degradation
  • LYTAC
  • AUTAC
  • ATTEC
  • epigenetics
  • NuRD
  • HDAC
  • BRD
  • SWI/SNF
  • PRC2
  • chromatin
  • conjugates
  • lysosome
  • autophagy
  • drug discovery

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Published Papers (2 papers)

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Review

35 pages, 2122 KB  
Review
From Epigenetic Regulation to Protein Degradation: Emerging Strategies for Anti-Infective Drug Discovery
by Andressa Francielli Bonjorno, Diogo Boreski, Ana Luísa Rodriguez Gini, Pamela Souza Tada da Cunha, Jhonnathan Alves Moura, Chung Man Chin, Cauê Benito Scarim and Jean Leandro Dos Santos
Int. J. Mol. Sci. 2026, 27(9), 3977; https://doi.org/10.3390/ijms27093977 - 29 Apr 2026
Abstract
Infectious diseases remain a major global health challenge, driven by antimicrobial resistance, pathogen persistence, and the limited integration of mechanistically innovative therapeutic approaches. Emerging evidence indicates that epigenetic regulation is fundamental to host–pathogen interactions, influencing transcriptional programmes associated with virulence, immune evasion, stress [...] Read more.
Infectious diseases remain a major global health challenge, driven by antimicrobial resistance, pathogen persistence, and the limited integration of mechanistically innovative therapeutic approaches. Emerging evidence indicates that epigenetic regulation is fundamental to host–pathogen interactions, influencing transcriptional programmes associated with virulence, immune evasion, stress adaptation, and phenotypic plasticity. In organisms such as bacteria, parasites, and intracellular pathogens, including Mycobacterium tuberculosis and Plasmodium falciparum, chromatin-associated regulators and DNA-modifying enzymes have been identified as dosage-sensitive determinants of infection outcomes. Traditional strategies focus primarily on occupancy-driven enzymatic inhibition. In contrast, targeted protein degradation (TPD) introduces an event-driven pharmacological paradigm in which transient ligand engagement triggers sustained depletion of regulatory proteins. Platforms such as proteolysis-targeting chimeras (PROTACs) and BacPROTACs exemplify the ability to exploit host and pathogen proteolytic systems, thereby expanding the druggable proteome beyond conventional small-molecule targets. This review examines the relationship between epigenetic regulation and pathogen survival, highlights recent advances in degradation technologies, and discusses conceptual and translational challenges in implementing TPD in antimicrobial and antiparasitic drug discovery. Full article
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24 pages, 2985 KB  
Review
Targeted RNA Degradation as a Promising Therapeutic Strategy
by Sivakumar Komachankandy and Yeongju Lee
Int. J. Mol. Sci. 2025, 26(21), 10767; https://doi.org/10.3390/ijms262110767 - 5 Nov 2025
Cited by 3 | Viewed by 2506
Abstract
RNAs have recently emerged as versatile therapeutic targets, broadening the scope of drug discovery beyond the conventional protein-centered paradigm. Small-molecule-induced RNA degradation has been established as a promising approach, with novel modalities such as Ribonuclease-Targeting Chimeras (RIBOTACs), bleomycin-conjugated degraders, and imidazole-based RNA degrader [...] Read more.
RNAs have recently emerged as versatile therapeutic targets, broadening the scope of drug discovery beyond the conventional protein-centered paradigm. Small-molecule-induced RNA degradation has been established as a promising approach, with novel modalities such as Ribonuclease-Targeting Chimeras (RIBOTACs), bleomycin-conjugated degraders, and imidazole-based RNA degrader demonstrating strong potential. These strategies selectively eliminate disease-associated RNAs by harnessing endogenous ribonucleases, redirecting the nucleic acid-cleaving activity of natural products, or incorporating catalytic warheads. Recent studies have validated therapeutic applications across cancer, neurodegenerative disorders, and viral infections, underscoring the wide-ranging impact of this strategy. Nevertheless, key challenges remain, including the development of more potent recruiters, diversification of degradation mechanisms, optimization of linker chemistry, and overcoming pharmacokinetic limitations. With continued innovation, RNA degraders are expected to evolve into a robust therapeutic platform that expands the druggable space and enables new treatment opportunities for diseases once considered untreatable. Full article
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