Jul 2026· Clinical Cancer Research· Vol 32, pp. B089-B089· 0 citations
TL;DR
These findings establish mitochondrial malic enzymes, particularly ME2/ME3, as tractable metabolic targets for cancer therapy, and provide a strong foundation for rational optimization of potency and isoform selectivity.
Abstract
Cancer remains a major global health challenge and urgently requires therapies that improve clinical outcomes and patient quality of life. Tumor cells frequently reprogram metabolism to sustain proliferation and survival, notably by increasing glutamine dependence and upregulating mitochondrial malic enzyme 2 (ME2), which generates pyruvate and NAD(P)H. ME2 is overexpressed in pancreatic, melanoma, and lung cancers, making it a compelling yet underexplored therapeutic target.
Recombinant human ME1, ME2, and ME3 were expressed and kinetically characterized in the presence and absence of inhibitors. We solved a complete set of X-ray crystal structures for all three isoforms bound to a potent malic enzyme inhibitor, defining ligand and metal coordination and capturing an unexpected enzyme conformation. These structures guided virtual screening of a curated library of ∼14 million drug-like and fragment molecules to identify novel malic enzyme inhibitors. Biochemical hits were advanced to cellular assays; lead compounds NPD-389 and FLA were evaluated for antiproliferative activity in melanoma and triple-negative breast cancer cell lines.
Kinetic analyses revealed distinct activity and inhibition profiles across ME isoforms. X-ray crystallography visualized the isoform-nonselective inhibitor NPD-389 bound in a metal-coordinating mode and stabilizing an unanticipated malic enzyme conformation. Structure-based virtual screening against this conformation yielded multiple novel scaffolds with biochemical inhibitory activity. One scaffold, FLA, displayed a unique selectivity profile and was found bound to ME2 in a previously cryptic pocket that rearranges upon ligand engagement and lies adjacent to the NAD+ cofactor and malate-binding site. In melanoma and triple-negative breast cancer models, both NPD-389 and FLA reduced proliferation, supporting their potential as chemical leads.
These findings establish mitochondrial malic enzymes, particularly ME2/ME3, as tractable metabolic targets for cancer therapy. Structural elucidation of NPD-389’s metal-binding mode and FLA’s cryptic/allosteric pocket provides a strong foundation for rational optimization of potency and isoform selectivity. Selective ME inhibitors, either isoform-specific or mitochondrially targeted, represent promising candidates for combination strategies with checkpoint inhibitors or chemotherapy to more effectively disrupt metabolic dependencies in cancer.
Ben Krinkel, Yuliana Yosaatmadja, Mark Slayton, Jin Heon Jeon, Jack Flanagan, Sofia Merajver, Christopher Squire, Kerry Loomes. Targeting metabolic vulnerabilities in cancer through structure-guided discovery of novel malic enzyme inhibitors [abstract]. In: Proceedings of AACR Drug Discovery and Development (AACR D3) Conference; 2026 Jul 21-24; Boston, MA. Philadelphia (PA): AACR; Clin Cancer Res 2026;32(14_Suppl):Abstract nr B089.
Glioblastoma (GBM) is a malignant brain tumor frequently driven by mutations in isocitrate dehydrogenase (IDH1 and IDH2) enzymes, which promote neomorphic synthesis of the oncometabolite 2-hydroxyglutarate (2-HG) and subsequent metabolic dysfunction. Although these mutations are associated with different clinical outcomes, therapeutic intervention remains challenging due to tumor heterogeneity, cellular plasticity, restricted blood-brain barrier permeability, drug efflux mechanisms, and effective DNA repair pathways. Therefore, this study aims to identify selective inhibitors of mutant IDH proteins by overcoming these challenges.
10,309 compounds from ChemFaces and MedChemExpress libraries are used for large-scale virtual screening and multi-level ADMET filtering, uncovering 19 lead compounds with favourable drug-likeness. Further, molecular docking followed by 300 ns of molecular dynamics simulations, PCA analysis, and MM-PBSA calculations were performed to explore conformational dynamics.
Molecular docking revealed strong binding affinities of PubChem ID 91457 (I1Hit1) as −7.57 kcal/mol and PubChem ID 4946 (I1Hit2) as −6.82 kcal/mol against IDH1, and PubChem ID 71550939 (I2Hit1) as −11.23 kcal/mol and PubChem ID 4946 (I2Hit2) as −7.87 kcal/mol against IDH2, by outperforming the standard (−6.17 kcal/mol). Molecular dynamics simulations, PCA analysis, and MM-PBSA calculations confirmed complex stability and inhibitory potential. Notably, I1Hit1 and I2Hit1 exhibited enhanced binding free energies of −20.67 ± 2.32 kcal/mol against IDH1 and -28.78 ± 2.67 kcal/mol against IDH2 respectively, compared to the standard, as further supported by computational pharmacophore evaluation.
Collectively, these findings highlight I1Hit1 and I2Hit1 as novel therapeutic compounds with efficient IDH-target inhibition to address epigenetic modification in GBM, and further experimental validation of these compounds is required to demonstrate potential inhibitors of IDH-driven metabolism in GBM.
Nivedhitha Tamilazhagan, S. Arumugam· Frontiers in Bioinformatics· 0 citations
Findings highlight Withaferin A as a promising natural inhibitor of UBE2J1 and provide a foundation for future experimental validation aimed at developing targeted therapies against ovarian cancer.
Zujaja Rehman, Ejaz Rasul, Wisha Asif et al.· In Silico Pharmacology· 0 citations
Neuroblastoma (NB) remains a major cause of pediatric cancer mortality for which new therapeutic strategies are needed. Exploitation of reprogrammed metabolic pathways offers an opportunity for cell-type specific anticancer therapeutics. To identify pediatric solid tumors with an enhanced susceptibility to targeting the nicotinamide adenine dinucleotide (NAD
+
) salvage pathway, we performed an unbiased high-throughput screen of over 200 cancer cell line models using inhibitors of nicotinamide phosphoribosyltransferase (NAMPT), the rate limiting enzyme in the NAD
+
salvage pathway. Our analysis identified NB as one of the most sensitive solid tumor types, prompting further investigation of NAMPT inhibition as a potential therapeutic strategy in this disease.
Using two early phase clinical NAMPT inhibitors (OT-82 and KPT-9274), we validated screen results using assays of proliferation and survival in a panel of molecularly diverse NB cell lines. Effects on proliferation, survival, NAD
+
abundance, adenosine triphosphate (ATP) levels, and energy-related metabolites were quantified, and downstream consequences of NAD
+
-consuming enzymatic pathways were examined. Tolerability, antitumor activity and pharmacodynamic effects of OT-82 were evaluated in three orthotopic NB mouse models.
In the drug screen, NB models ranked among the most sensitive pediatric solid tumor cells lines to NAMPT inhibition. OT-82 and KPT-9274 potently suppressed proliferation and viability across multiple molecularly diverse NB models in an on-target manner. Mechanistically, NAMPT inhibition resulted in rapid depletion of NAD
+
and ATP, disruption of energy metabolism, accumulation of DNA damage, and induction of irreversible non-apoptotic cellular death. In vivo, OT-82 was well tolerated and produced marked antitumor activity, including tumor regressions in orthotopic NB models, including several with regional liver metastases. Pharmacodynamic analysis confirmed intratumoral NAD
+
depletion during treatment, demonstrating on-target pathway inhibition in vivo.
These findings identify NB as a highly NAMPT inhibitor-sensitive pediatric solid tumor and establish NAMPT-dependent NAD
+
biosynthesis as a targetable metabolic vulnerability in this disease. By integrating an unbiased discovery screen with mechanistic and orthotopic in vivo validation using clinically relevant inhibitors, this study provides a strong translational rationale for clinical investigation of NAMPT inhibitors in NB.
Sophia Varriano, Amy Yu, Abantika Chakraborty et al.· Journal of Experimental &...· 0 citations
Beyond enabling the discovery of several new potent and selective small molecules, these studies have allowed us to elucidate key parameters for potency, selectivity, and metabolic stability that should aid future efforts in RBP drug discovery.
G. M. Scherer, Jacob P. Sorrentino, A. K. Jaiswal et al.· Journal of Medicinal Chemist...· 0 citations
Cancer cells show accelerated glucose metabolism, a
significant hallmark, supporting their growth and
survival. The first rate-limiting step of glycolysis is
catalyzed by an enzyme Hexokinase-2 (HK2) and is
commonly overexpressed in many cancers compared to
normal cells. Our previous microarray and validation
by qPCR showed overexpression of HK2 in
transformed fibroblast cells, generated by cellmediated adhesion, as well as in the generated tumors.
An epigenetic modification in the promoter region of
HK2 and its release into the bloodstream was also
observed in the clinical samples of cancer (unpublished
data). Because of its strong association with cancer
progression and tissue-specific expression, the present
study considered HK2 as a promising target for
anticancer strategies.
A structure-based virtual screening procedure and
300ns MD simulations were used to identify potential
lead molecules to inhibit HK2 activity in cancer cells
by screening a large in-house library of 1.28 million
compounds. Identified lead molecules were evaluated
based on XPG docking score, MM/GBSA analysis,
ADMET and MD simulations across the selected three
HK2 co-crystal structures with open and closed
conformation states. Among the several lead molecules
obtained, lead 1 of each target exhibited favourable
XPG and MM/GBSA scores, steady binding
trajectories and sustained interactions.
Mythreyi Jannu, B. Krishnan, U. Amineni et al.· Research journal of biotechn...· 0 citations
Therapy-induced lineage plasticity is a major mechanism of resistance in advanced prostate cancer, enabling tumor progression despite androgen receptor (AR)-directed therapies and promoting emergence of lethal neuroendocrine prostate cancer (NEPC). Our prior studies identified the pseudokinase Tribbles homolog 2 (TRIB2) as a key regulator of therapy resistance, lineage plasticity, and neuroendocrine (NE) differentiation. Despite strong biological rationale, TRIB2 remains difficult to target because pseudokinases lack catalytic activity and often possess shallow or poorly defined ligand-binding pockets. However, structural analyses indicate that TRIB2 retains a conserved ATP-binding pocket involved in regulating protein stability and scaffolding functions, suggesting a tractable therapeutic vulnerability.
We employed a structure-guided drug discovery workflow integrating computational docking, biochemical validation, thermal shift assay (TSA), cellular thermal shift assay (CETSA), and functional screening to identify compounds targeting the TRIB2 pseudokinase domain. Lead compounds were evaluated for target engagement, selectivity, and biologic activity in enzalutamide-resistant and NEPC models. Mechanistic studies assessed downstream signaling, lineage-plasticity markers, apoptosis, and viability in antiandrogen-resistant and engineered TRIB2-expressing systems.
Structure-guided optimization identified TBI-001 as a bioactive TRIB2-directed small molecule with favorable pharmacologic properties. TSA and CETSA confirmed direct interaction between TBI-001 and TRIB2 in biochemical and cellular contexts. TBI-001 induced TRIB2 destabilization and suppressed downstream survival signaling, including AKT and BCL2 pathways. Treatment reduced expression of TRIB2 regulated lineage-plasticity and NE regulators, including MYCN, EZH2, ASCL1, BRN2 and SOX2. Mechanistically, TRIB2 actively suppresses AR signaling to facilitate resistance; accordingly, TRIB2 inhibition restored AR pathway activity and resensitized resistant cells to enzalutamide. Functionally, TBI-001 selectively reduced viability and induced apoptosis in enzalutamide-resistant and NEPC models while sparing nonmalignant prostate epithelial cells. In xenograft studies, TBI-001 inhibited tumor growth, reduced NE marker expression, and was well tolerated without overt toxicity. Human liver microsomal stability assays demonstrated low intrinsic clearance and prolonged microsomal half-life, supporting favorable drug-like pharmacokinetic properties.
These findings establish TRIB2 as a druggable vulnerability in enzalutamide-resistant and NE prostate tumors despite the inherent challenges of targeting pseudokinases. Pharmacologic disruption of TRIB2 signaling using TBI-001 suppresses oncogenic and lineage-plasticity programs, restores sensitivity to AR-directed therapy, and selectively impairs survival of resistant tumor cells. This work provides a framework for development of first-in-class TRIB2-directed therapeutics for aggressive prostate cancer subtypes.
JITENDER MONGA, Sang-Yoon Lee, Deepak Rohila, Sharad K. Suthar, Shirish Gadgeel, Craig Rogers. Structure-guided discovery of first-in-class TRIB2 small-molecule inhibitors for therapy-resistant neuroendocrine prostate cancer [abstract]. In: Proceedings of AACR Drug Discovery and Development (AACR D3) Conference; 2026 Jul 21-24; Boston, MA. Philadelphia (PA): AACR; Clin Cancer Res 2026;32(14_Suppl):Abstract nr A079.
J. Monga, Sang-Yoon Lee, Deepak Rohila et al.· Clinical Cancer Research· 0 citations
