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KDM1A

KDM1A, also known as LSD1 (lysine-specific demethylase 1), is a gene located on chromosome 1p36.12 in humans that encodes a flavin adenine dinucleotide (FAD)-dependent histone demethylase enzyme critical for epigenetic regulation of gene expression. The protein product, lysine-specific histone demethylase 1A, specifically removes methyl groups from mono- and di-methylated lysine 4 (H3K4me1/2) and lysine 9 (H3K9me1/2) residues on histone H3, thereby acting as either a transcriptional coactivator or corepressor depending on the cellular context and associated protein complexes. First identified in 2004 as a nuclear amine oxidase homolog, KDM1A plays essential roles in chromatin remodeling, embryonic development, stem cell differentiation, and neuronal function, while its dysregulation is implicated in various cancers and neurodevelopmental disorders. Structurally, the KDM1A protein features an N-terminal SWIRM domain for binding, a central amine oxidase-like () domain responsible for its demethylase activity, and a TOWER domain that inserts into the AOL to facilitate cofactor binding and substrate specificity. It commonly interacts with multiprotein complexes such as CoREST and NuRD, which enhance its recruitment to target genes and coordinate deacetylation with demethylation to fine-tune accessibility. Beyond histones, KDM1A can demethylate non- substrates like and , expanding its influence on cellular processes including and tumor suppression. In development, KDM1A is vital for maintaining identity in hematopoiesis and , as well as for and cardiac formation, with knockout studies in mice revealing embryonic lethality due to impaired . In disease contexts, KDM1A is frequently overexpressed in solid tumors and hematologic malignancies, such as , , and , where it promotes oncogenic processes like , , and by repressing tumor suppressor genes. Its role in maintenance and therapy resistance has positioned KDM1A as a promising therapeutic target, with selective inhibitors like ORY-1001 (in clinical trials as of 2025) and GSK-LSD1, which have shown efficacy in preclinical models and early clinical studies by restoring epigenetic balance and sensitizing cells to . As of 2025, inhibitors such as iadademstat are in phase II/III trials, often combined with standard therapies, showing promising results in AML and . Additionally, germline mutations in KDM1A have been linked to rare neurodevelopmental syndromes, including cleft palate and , underscoring its broader physiological importance.

Gene Overview

Genomic Location and Organization

The KDM1A gene, encoding lysine demethylase 1A (also known as LSD1), is situated on the short arm of at cytogenetic band 1p36.12. In the GRCh38 reference assembly, it spans approximately 64 kb, extending from genomic position 23,019,468 to 23,083,689 on the forward strand. The gene comprises 21 exons, with the majority encoding the functional protein domains, and its intron-exon structure supports the production of a primary of 2,556 that translates into an 852-amino-acid protein. Evolutionary analysis reveals high conservation of KDM1A across metazoans, reflecting its essential role in modification. Orthologs are present in mammals, including the (Mus musculus Kdm1a, Gene ID: 99982, located on 4qE2), and in teleost fish such as the (Danio rerio kdm1a, Gene ID: 558450, on 17). Sequence alignments indicate that the oxidase-like and associated motifs are particularly well-preserved, with over 90% identity in key catalytic residues between human and rodent orthologs, enabling functional studies in these model organisms. The promoter region upstream of the KDM1A transcription start site features CpG islands, characterized by high and unmethylated CpG dinucleotides in cells, which facilitate basal transcriptional activity and responsiveness to developmental cues. These regulatory elements, spanning several hundred base pairs, lack tissue-specific enhancers but integrate with core promoter motifs to maintain widespread expression. across and shows conservation of these CpG islands, suggesting their role in preventing aberrant silencing. Alternative splicing of KDM1A transcripts yields multiple isoforms, primarily through variable inclusion of microexons in the 3' region. The canonical full-length isoform (LSD1) retains all s and localizes predominantly to the , while shorter variants, such as those lacking exon 8a or with truncated C-termini (e.g., LSD1ΔTSS), exhibit altered interactions and subcellular distribution, influencing processes like neuronal . Ensembl annotates 64 splice variants, though only a subset are protein-coding and functionally characterized, with tissue-specific patterns emerging in neural and hematopoietic contexts.

Expression Patterns and Regulation

KDM1A displays ubiquitous basal expression across most human tissues, reflecting its broad role in cellular processes, though levels vary significantly. According to RNA sequencing data, expression is particularly elevated in the testis (RPKM 45.8), brain regions such as the and , and hematopoietic cells including those in and lymphoid tissues, where it supports maintenance and differentiation. Lower expression is noted in tissues like liver and skeletal muscle, underscoring tissue-specific demands for its demethylase activity. Transcriptional regulation of KDM1A involves key factors that fine-tune its levels in response to cellular signals. E2F1 acts as a positive regulator, promoting KDM1A transcription through RNA polymerase II-mediated mechanisms during cell cycle progression. In contrast, p53 exerts inhibitory control, directly suppressing KDM1A expression to modulate DNA damage responses and prevent oncogenic transformation, particularly in cells with wild-type p53. Additionally, feedback loops with microRNAs contribute to post-transcriptional control; for instance, miR-137 directly targets KDM1A mRNA, leading to its suppression and thereby limiting excessive demethylase activity in contexts like neuronal development and cancer. Epigenetic mechanisms further govern KDM1A expression at its own locus, with 4 (H3K4) states playing a pivotal role in promoter accessibility. Elevated H3K4 correlates with active transcription of KDM1A, while demethylation—potentially mediated by KDM1A itself or cooperating factors—can repress it, establishing a self-regulatory circuit that maintains balanced expression during development and stress responses. This dynamic interplay ensures precise control over landscapes influenced by KDM1A. In pathological contexts, KDM1A expression patterns are often dysregulated, with upregulation observed in various tumors under hypoxic conditions mediated by hypoxia-inducible factor 1α (HIF-1α). HIF-1α signaling enhances KDM1A transcription to support glycolytic adaptation and tumor progression, as evidenced by correlated expression signatures in hypoxic tumor microenvironments.

Protein Structure and Function

Domain Architecture

The KDM1A protein consists of 852 and has a calculated molecular weight of 92.9 . This single polypeptide chain adopts a modular essential for its role as a flavin-dependent demethylase, with distinct domains organized along its length to support association, substrate specificity, and enzymatic catalysis. The N-terminal SWIRM domain spans 172–270 and forms a compact six-helix bundle that mediates binding, facilitating the protein's recruitment to . Adjacent to this is the Tower domain ( 418–522), a protruding composed of two extended antiparallel α-helices that plays a critical role in substrate recognition by interacting with tails and positioning them for demethylation; this domain inserts into the amine oxidase-like () domain, dividing it into two subdomains. The domain ( 271–417 and 523–833) encompasses the catalytic core and binds the () cofactor non-covalently; it features a Rossmann fold for FAD accommodation. The amino-terminal region (approximately residues 1–171) includes nuclear localization signals (NLS), such as the basic motif at residues 112–117 (RRKRAK), which ensure nuclear import via interaction with importin-α, and a flexible loop that aids in cofactor binding by allowing conformational adjustments during catalysis. Crystal structures, including PDB entry 2H94 resolved at 2.9 , illustrate the overall fold with the amine oxidase domain exhibiting multiple helical bundles surrounding a central β-sheet core, while the SWIRM and Tower domains extend outward to form an elongated, asymmetric shape suited for engagement. These structural elements collectively enable KDM1A's integration into larger complexes, though their precise interactions are detailed elsewhere.

Catalytic Mechanism and Activity

KDM1A, also known as lysine-specific demethylase 1A (LSD1), functions as a (FAD)-dependent amine oxidase that catalyzes the oxidative demethylation of mono- and dimethylated residues on tails. Specifically, it targets H3K4me1 and H3K4me2 to repress transcription or H3K9me1 and H3K9me2 to activate transcription in a context-dependent manner determined by its associated cofactors and cellular environment. The reaction proceeds through a flavin-dependent oxidative process that removes methyl groups, producing as a byproduct and leaving the unmethylated residue. The catalytic mechanism begins with the substrate , typically in its neutral form at physiological , positioning within the enzyme's . A proton is abstracted from the methylated , facilitating the subsequent direct transfer from the α-carbon of the to the N5 atom of , which reduces the cofactor to FADH₂ and generates a positively charged intermediate. This then undergoes non-enzymatic , yielding the demethylated and . The overall reaction can be represented as: \text{R-CH}_2\text{-NH-CH}_3 + \text{H}_2\text{O} + \text{E-[FAD](/page/Fad)} \rightarrow \text{R-CH}_2\text{-NH}_2 + \text{[HCHO](/page/Formaldehyde)} + \text{E-FADH}_2 where R denotes the protein backbone, E- is the enzyme-bound flavin, is , and the reduced FADH₂ is reoxidized by molecular oxygen to regenerate and produce . KDM1A activity is strictly dependent on as a cofactor, with the enzyme exhibiting optimal performance at physiological around 7.5–8.0. Kinetic studies indicate high substrate affinity for H3K4me2 peptides. The enzyme is inhibited by reducing agents such as (GSH), which interferes with reduction, and by irreversible inhibitors like tranylcypromine (), which forms a covalent with the flavin cofactor, blocking access. Beyond histones, KDM1A exhibits non-canonical demethylase activity on select non-histone proteins, modulating their stability and function. For instance, it demethylates at 142, enhancing DNMT1 stability and promoting global maintenance. Similarly, KDM1A targets the tumor suppressor at 370, reducing its transcriptional and pro-apoptotic effects.

Molecular Interactions

Key Protein Partners

KDM1A, also known as LSD1, forms a tight complex with the corepressor CoREST through its Tower domain, which interacts with the linker region of CoREST (residues 286–482), exhibiting a (Kd) of approximately 16 nM as determined by . This interaction is mediated by the structure of the Tower domain protruding from KDM1A's amine oxidase domain, enabling stable assembly that contributes to the nuclear retention of KDM1A. CoREST binding enhances the overall stability of KDM1A in the . KDM1A associates with histone deacetylases HDAC1 and HDAC2 primarily through scaffold proteins like CoREST or RCOR1, forming a multiprotein unit where /2 bind indirectly to KDM1A via the ELM2-SANT domain of CoREST. Additionally, KDM1A integrates into the NuRD complex via direct interactions with components such as MTA1, where KDM1A's association with MTA1 occurs through its Tower domain, facilitating proximity for synergistic deacetylation activities. These associations with /2 and MTA1/NuRD elements position KDM1A within repressive chromatin-modifying modules. KDM1A interacts with transcription factors including the (AR) and (ER) through specific motifs in their ligand-binding domains, particularly the AF-2 region, allowing recruitment to hormone-responsive promoters. For AR, KDM1A binds via a region encompassing helices 11 and 12, while for ERα, the interaction involves the C-terminal helix 12 motif, enabling context-dependent coregulator functions. KDM1A also interacts with SMAD1 and SMAD5 through its Tower domain, with the MH2 domain of SMAD1 binding KDM1A to recruit it to BMP-responsive enhancers in embryonic stem cells, promoting H3K4 demethylation and repression of differentiation genes. Other notable binding partners include the SNAG domain-containing transcription factors Gfi1 and Gfi1b, which engage KDM1A's substrate-binding cleft—mimicking the tail—to form a repressive interface critical for hematopoietic gene control. KDM1A also associates with CtBP1, a corepressor involved in viral latency mechanisms, such as in herpes simplex virus type 1 (HSV-1), where CtBP1 bridges KDM1A to viral immediate-early promoters for epigenetic silencing.

Functional Complexes

KDM1A primarily functions within multi-subunit complexes that integrate its demethylase activity with other chromatin-modifying enzymes to regulate . The most characterized of these is the CoREST complex, composed of KDM1A, corepressor 1 (RCOR1, also known as CoREST), and histone deacetylases and HDAC2. This complex facilitates the demethylation of at 4 (H3K4me1/2) in conjunction with deacetylation of nearby residues, thereby promoting transcriptional repression at target promoters. Structural studies reveal that CoREST stabilizes KDM1A and positions it for efficient engagement, with the complex forming an asymmetric assembly where KDM1A and HDACs bind distinct faces of the . Paralogs such as RCOR2 and RCOR3 can substitute for RCOR1, modulating the complex's repressive efficiency, though RCOR1 remains the predominant scaffold in most cellular contexts. In neuronal contexts, KDM1A integrates into the REST supercomplex, which incorporates the REST , the CoREST complex, and the Sin3A-HDAC corepressor assembly to enforce silencing of neuronal differentiation genes. This supercomplex coordinates H3K4 demethylation by KDM1A with H3K9 methylation and deacetylation mediated by associated enzymes, maintaining repressive chromatin states in non-neuronal cells and during early neural development. Disruption of this integration impairs REST-dependent gene repression, highlighting KDM1A's role as a central hub for multi-layered epigenetic silencing. The of the supercomplex allows dynamic recruitment to RE1 silencing elements in target gene promoters, ensuring context-specific neuronal gene control. KDM1A also assembles into complexes with the (AR) in prostate cells, where it is recruited to AR-bound enhancers and promoters alongside coactivators like SRC-1 and corepressors such as NCoR to regulate androgen-responsive genes. In this context, KDM1A shifts its substrate specificity from H3K4 to H3K9 demethylation, relieving repressive marks to facilitate AR-dependent transcriptional activation and progression. The complex's composition enables KDM1A to act dually as a coactivator by derepressing while coordinating with SRC-1 for acetylation and NCoR for initial corepressor functions prior to ligand-induced remodeling. This AR-KDM1A interaction is ligand-dependent and critical for maintaining oncogenic gene programs in castration-resistant . The assembly and disassembly of these KDM1A-containing es are dynamically regulated by post-translational modifications, particularly at serine 112 (S112) by the ERK signaling pathway. ERK-mediated at S112 enhances KDM1A's , binding, and interaction with scaffolds like CoREST, thereby promoting formation and sustaining repressive or activating functions in response to mitogenic signals. Conversely, or competing modifications facilitate disassembly, allowing KDM1A redistribution to alternative partners. This phosphorylation-dependent toggling is essential for cellular adaptability, such as during epithelial-mesenchymal transition or response to growth factors, and its dysregulation contributes to aberrant persistence in diseases like cancer.

Biological Roles

Epigenetic Gene Regulation

KDM1A, also known as lysine-specific demethylase 1 (LSD1), plays a central role in epigenetic regulation by catalyzing the removal of methyl groups from specific lysine residues, thereby modulating structure and transcriptional output. As a (FAD)-dependent amine oxidase, KDM1A primarily targets mono- and dimethylated at 4 (H3K4me1/2) and, in certain contexts, at 9 (H3K9me1/2), influencing the balance between active and repressive states. This enzymatic activity was first demonstrated in a seminal study identifying KDM1A as the initial demethylase capable of reversing H3K4 . In its repressive function, KDM1A demethylates H3K4me1/2 at active promoters, leading to compaction and diminished recruitment of (Pol II), which suppresses gene transcription. By erasing these activating marks, KDM1A facilitates the transition to a heterochromatic state, often in association with corepressor complexes that further enforce silencing. This mechanism is critical for maintaining transcriptional repression at developmental genes, ensuring proper cellular identity. KDM1A exhibits context-dependent activation roles, particularly through demethylation of H3K9me2 at enhancer regions or in non-histone substrates, often requiring cofactors such as the (). In hormone-responsive cells, KDM1A acts as a coactivator, promoting -mediated transcription of target genes like () by facilitating enhancer activation and Pol II pausing release. This bidirectional functionality—serving as a corepressor during or a coactivator in signaling pathways like androgen response—allows KDM1A to fine-tune based on cellular context and interacting partners. Genome-wide followed by sequencing (ChIP-seq) analyses reveal KDM1A enrichment at bivalent domains in embryonic s (ESCs), where it balances activating and repressive marks to poise genes for timely activation during . These binding profiles highlight KDM1A's broad influence on enhancer and promoter landscapes, contributing to the epigenetic plasticity essential for maintenance.

Developmental and Differentiation Processes

KDM1A plays a critical role in early embryonic development, particularly during and formation. In models, Kdm1a embryos exhibit severe defects, arresting development around embryonic day 6.5 to 7.5 (E6.5–E7.5) due to failure in and improper specification, primarily from derepression of endogenous retroviral elements that disrupt the epigenetic landscape required for proper cell fate transitions. Similarly, in , loss of Lsd1/Kdm1a impairs hemangioblast , a -derived lineage, by failing to downregulate the endothelial Etv2, thereby hindering the transition to primitive hematopoietic cells essential for mesodermal patterning during . In hematopoietic development, KDM1A regulates differentiation by repressing primitive programs, including embryonic , to facilitate the switch to adult expression. During erythroid maturation, KDM1A collaborates with factors like GFI1B to silence embryonic and fetal loci (such as HBE and HBG), promoting the expression of adult β- (HBB) and ensuring proper oxygen transport capacity in differentiated red blood cells. This repressive function is evident in conditional studies where Lsd1 in hematopoietic progenitors leads to persistent expression of primitive signatures, blocking full maturation and adult dominance. KDM1A is integral to neuronal , particularly through its integration into the REST-CoREST complex, which silences proneural genes to coordinate timely lineage commitment and cortical organization. In neural progenitors, the REST-CoREST-KDM1A complex targets RE1 elements in proneural genes like Neurogenin1 (Neurog1) and Ascl1, maintaining repression until differentiation cues trigger complex disassembly and gene activation for neuronal specification. This regulated silencing is crucial for cortical layering, as disruption of the CoREST-KDM1A interaction in mouse models delays radial of newborn pyramidal neurons, resulting in disorganized cortical and impaired layer formation by altering the balance of versus in the ventricular zone. In embryonic stem cells (ESCs), KDM1A is poised at bivalent promoters and enhancers of pluripotency genes such as Oct4 (Pou5f1), where its demethylase activity is inhibited by histone acetylation during self-renewal. Upon signals, KDM1A becomes active to remove H3K4me1/2 marks, coordinating with H3K9 methyltransferases to repress pluripotency genes and facilitate of lineage-specific programs. KDM1A knockout in mouse ESCs does not impair self-renewal but leads to defects in cell growth and , underscoring its role in transitioning from pluripotency to committed states.

Disease Associations

Role in Cancer

KDM1A is overexpressed in approximately 50% of cancer types analyzed through (TCGA), including many solid tumors such as (BRCA), (PRAD), and (LUAD, LUSC) cancers, where elevated levels correlate with poor prognosis, including reduced overall survival in cancers like LUAD, though associations vary in (better OS but worse relapse-free survival). This overexpression promotes aggressive disease phenotypes by driving and across these malignancies. In cancer stem cell (CSC) maintenance, KDM1A enhances epithelial-to-mesenchymal transition (EMT) and self-renewal, particularly in breast CSCs, through interaction with Slug to enable H3K4 demethylation at the E-cadherin promoter, repressing its expression and facilitating metastasis. Knockdown of KDM1A reduces the CD44+/CD24- CSC population, impairs mammosphere formation, and limits tumor growth in xenograft models, underscoring its role in sustaining stemness and chemoresistance. KDM1A contributes to metabolic reprogramming in hypoxic tumors by demethylating hypoxia-inducible factor-1α (HIF-1α) at residues 32 and 391, stabilizing the protein and upregulating glycolytic genes to support energy demands under low oxygen conditions. This mechanism sustains tumor growth, as seen in where KDM1A depletion shifts toward mitochondrial , reducing glucose uptake and proliferation. In , KDM1A overexpression is prominent in poorly differentiated tumors and cooperates with amplified MYCN at the 1p36 locus to repress tumor suppressor genes like CDKN1A and CLU, driving aggressive progression in high-risk subtypes. This interaction enhances epigenetic silencing and cell viability, with combined inhibition showing synergistic effects on tumor suppression.

Links to Neurodevelopmental Disorders

Mutations in the KDM1A gene have been identified in cases of s characterized by cleft palate, , and distinctive facial dysmorphisms. Specifically, heterozygous missense mutations were reported in three unrelated individuals, leading to impaired demethylase activity and disrupted binding to transcription factors such as GFI1B and CTBP1. These variants, including p.Glu403Lys, p.Asp580Gly, and p.Tyr785His, affect residues in the or substrate-binding , resulting in partial loss of function and alongside the core phenotypic features. The , known as cleft palate, , and distinctive facial features (CPRF; OMIM #616728), highlights KDM1A's critical role in craniofacial and . Recent characterizations expand this to a dominant KDM1A-related spectrum, incorporating , seizures, and variable (as of 2025). Dysregulation of KDM1A contributes to disorders () through its involvement in repressing synaptic genes, as evidenced by studies using (iPSC) models. In patients with Helsmoortel-Van der Aa syndrome, a monogenic form of caused by ADNP mutations, disruption of the ADNP-KDM1A-GTF2I impairs neural and synaptic in iPSC-derived cortical organoids. This normally maintains repressive states at synaptic loci; its alteration leads to aberrant , reduced neuronal maturation, and ASD-like phenotypes, underscoring KDM1A's role in . Additionally, pharmacological inhibition of KDM1A in models restores H3K4 at synaptic genes, ameliorating social and repetitive behaviors. Links between KDM1A and involve altered expression in the , impacting signaling via H3K4 demethylation. Reduced KDM1A levels contribute to dysregulated modifications at promoters of -related genes, such as those in the /CoREST complex, leading to impaired neuronal gene repression and cognitive deficits characteristic of the disorder. This dysregulation affects H3K4 methylation balance, influencing monoamine signaling pathways implicated in .

Genetic Mutations

Germline Variants

Germline variants in the , encoding lysine-specific demethylase 1A (LSD1), are rare and primarily associated with autosomal dominant predisposition to , as well as neurodevelopmental disorders characterized by developmental delays. These variants often lead to loss of enzymatic function, disrupting demethylation at H3K4me1/2 sites and altering programs critical for and . Population-level data indicate that predicted loss-of-function (pLOF) variants in KDM1A occur at a low frequency, approximately 0.14% in healthy controls, but are enriched in MM patients at around 1.23%, conferring a of 9.08 (95% : 1.97–41.95). Rare mutations in KDM1A confer susceptibility to through , where heterozygous loss reduces LSD1 activity and promotes expansion via upregulation of target genes such as CCND2. Identified variants include truncating mutations like c.805_806delAG (p.Arg269Aspfs7), c.707delA (p.Gln236Hisfs3), and c.517+1G>A (p.?), which eliminate key functional domains including the and SWIRM domains essential for demethylase activity; these were found in familial and early-onset cases, with affected individuals showing lower KDM1A transcript levels in compared to normal controls. Missense variants, such as c.1424T>C (p.Leu475Pro) and c.2003G>C (p.Arg668Pro), also impair by disrupting or interactions, further supporting an autosomal dominant observed in pedigrees. In neurodevelopmental contexts, germline heterozygous missense variants in KDM1A cause a syndrome featuring , , and distinctive facial features, often resembling . Examples include mutations like c.1207G>A (p.Glu403Lys) and c.2353T>C (p.Tyr785His), which reduce LSD1 demethylase activity and lead to elevated H3K4 , impairing neural ; affected individuals exhibit delayed motor milestones (e.g., walking after 2–3 years) and speech delays in family cases or occurrences. Frameshift and mutations are less commonly reported in developmental pedigrees but align with the model, as evidenced by heterozygous Kdm1a knockout mice displaying no overt phenotypes yet subtle changes consistent with mild tolerance to reduced dosage. Recent studies as of 2025 have expanded the phenotypic spectrum to include features such as cleft palate and, in rare cases, primary bilateral macronodular adrenal hyperplasia.

Somatic Alterations

Somatic alterations in KDM1A, which encodes the lysine-specific demethylase 1A (LSD1), are uncommon in human cancers, with mutations occurring at low frequencies and often linked to specific malignancies such as chronic myeloid leukemia (CML). Whole-exome sequencing studies have identified somatic missense mutations in KDM1A in approximately 4% of newly diagnosed CML cases, typically affecting the catalytic amine oxidase domain and potentially impairing its demethylase activity, as these mutations correlate with disease state and resolve upon treatment response. Copy number variations at the KDM1A locus on 1p36 have been reported in , with gains at 1p36.3 observed in up to 30% of cases in small cohorts, potentially contributing to KDM1A overexpression and tumor progression. In neuroblastomas, while 1p36 deletions are more common and associated with poor , Epigenetic alterations, including promoter changes, also influence KDM1A expression in cancer. In colorectal tumors, the KDM1A promoter is frequently hypomethylated, leading to overexpression.

Therapeutic Targeting

Inhibitor Development

Development of small-molecule inhibitors targeting KDM1A (also known as LSD1) has primarily focused on disrupting its -dependent demethylase activity through covalent or non-covalent mechanisms, with preclinical evaluations emphasizing potency, selectivity, and efficacy in cellular and animal models of hematologic malignancies. Early efforts leveraged the structural similarity between KDM1A and monoamine oxidases (MAOs), adapting known MAO inhibitors to target the enzyme's catalytic pocket. Irreversible inhibitors, such as derivatives, covalently bind the cofactor, forming an adduct with the cysteine residue (Cys374), thereby permanently inactivating the . ORY-1001 (iadademstat), a prototypical derivative, exhibits subnanomolar potency (IC50 ≈ 30 nM) and induces differentiation of leukemic blasts in (AML) models by accumulating H3K4me2 marks on target genes. Preclinical studies in AML xenografts demonstrated that ORY-1001 reduces tumor burden and prolongs survival, highlighting its therapeutic potential when combined with standard chemotherapies. To address limitations of irreversible inhibition, such as potential from covalent modification, reversible inhibitors have been designed to occupy the substrate-binding channel without forming permanent bonds, allowing for tunable . Compounds like GSK-LSD1, which binds the substrate channel proximal to the site, achieve an IC50 of 16 against KDM1A while maintaining over 1,000-fold selectivity against related FAD-dependent enzymes, including MAO-A and MAO-B. Similarly, NCD38, a phenylcyclopropylamine optimized for direct delivery to the KDM1A , inhibits the with an IC50 of approximately 0.59 μM and has shown preclinical efficacy in reducing viability and inducing in glioblastoma stem cells and models. These substrate-channel targeting agents, with IC50 values typically in the 20-100 range for optimized analogs, promote H3K4me2 accumulation and disrupt oncogenic gene repression without broad . Proteolysis-targeting chimeras (PROTACs) represent an advanced strategy for KDM1A inhibition by inducing ubiquitin-mediated degradation rather than enzymatic blockade, potentially overcoming resistance from non-catalytic scaffolding functions. dBET1-like PROTACs, such as MS9117, conjugate a KDM1A-binding (e.g., a derivative) to an E3 ligase recruiter (e.g., for ), achieving near-complete KDM1A depletion at low nanomolar concentrations in AML cells. In preclinical AML models, these degraders demonstrate superior efficacy over small-molecule inhibitors, with enhanced blast differentiation, reduced leukemic engraftment in xenografts, and synergy with hypomethylating agents, attributed to comprehensive removal of KDM1A protein complexes. A major challenge in KDM1A inhibitor development has been off-target inhibition of MAO-A and MAO-B, which share the FAD-binding motif and can lead to neuropsychiatric side effects like . Structural optimizations, including incorporation of bicyclic scaffolds such as triazole-fused pyrimidines, have improved selectivity by >100-fold over MAOs while retaining low-nanomolar KDM1A potency (IC50 ≈ 10-50 nM). These modifications sterically hinder MAO binding and enhance interactions with KDM1A-specific residues in the substrate channel, as validated in crystallographic studies and cellular assays. Ongoing efforts continue to refine these scaffolds to minimize liability and improve oral bioavailability for preclinical translation.

Clinical Applications and Trials

KDM1A (also known as LSD1) inhibitors have entered clinical evaluation primarily for hematologic malignancies and select solid tumors, with several phase trials assessing , , and pharmacodynamic markers. Iadademstat (ORY-1001), a covalent irreversible KDM1A inhibitor, has shown promising activity in (AML). In the first-in-human phase I trial (EudraCT 2013-002447-29), iadademstat monotherapy in relapsed/refractory AML patients demonstrated a manageable profile and preliminary signs of clinical activity, including partial responses in a subset of patients. More recent combination strategies have improved outcomes; a phase Ib (NCT06357182) combining iadademstat with and in newly diagnosed, unfit AML patients reported an overall response rate of 100% among the first eight enrollees, with 88% achieving complete remission, based on 2025 updates. In neuroendocrine tumors, seclidemstat (SP-2577), a reversible , has been investigated in phase I/II trials for relapsed/refractory (NCT03600649 and NCT03895684). Among five first-relapse patients, 40% achieved an objective response rate, while 60% experienced disease control, including stable disease with one complete response and one partial response. Thirteen patients evaluable after two cycles showed seven with stable disease as the best response, indicating potential stabilization in advanced disease. For solid tumors such as small cell lung cancer (SCLC), iadademstat is under evaluation in ongoing phase I/II trials, often in combination with inhibitors (e.g., NCT06287775). As of November 2025, the trial is ongoing with no efficacy data reported yet; standard SCLC treatments yield median PFS around 5 months, and early iadademstat combinations aim to extend this benchmark. Across KDM1A inhibitor trials, common adverse effects include grade 3/4 (up to 20-46%) and (up to 13-45%), often reversible and linked to hematopoietic effects of KDM1A inhibition. Pharmacodynamic biomarkers, such as elevated H3K4me2 levels in peripheral mononuclear cells, correlate with engagement and may predict response, as observed in AML cohorts where increased H3K4me2 preceded clinical benefit.

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