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22 pages, 5055 KB  
Article
Structural and Mechanistic Insights into Dual Cholinesterase Inhibition by Marine Phytohormones
by Kumju Youn, Legie Mae Soriano and Mira Jun
Mar. Drugs 2026, 24(1), 35; https://doi.org/10.3390/md24010035 - 9 Jan 2026
Viewed by 201
Abstract
Cholinergic dysfunction is a hallmark of Alzheimer’s disease (AD), driven by elevated acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) activity that depletes acetylcholine and contributes to amyloid pathology. Current AD treatments face major challenges, including poor brain penetration, short effect duration and safety concerns, highlighting [...] Read more.
Cholinergic dysfunction is a hallmark of Alzheimer’s disease (AD), driven by elevated acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) activity that depletes acetylcholine and contributes to amyloid pathology. Current AD treatments face major challenges, including poor brain penetration, short effect duration and safety concerns, highlighting the need for compounds suitable for preventive or earlier-stage intervention. This study investigated marine phytohormones as modulators of cholinergic imbalance, using an integrative strategy encompassing enzymatic assays, QSAR and DFT calculations, molecular docking, molecular dynamics (MD) simulations, and ADMET profiling. Among them, isopentenyl adenine (IPA) and abscisic acid (ABA) showed inhibitory activity against cholinesterases. IPA inhibited both AChE and BChE through distinct mechanisms with noncompetitive inhibition of AChE and competitive inhibition of BChE, while ABA showed selective noncompetitive inhibition of AChE. DFT-based analysis revealed distinct electronic properties supporting differential reactivity. Moreover, IPA interacted with both catalytic and peripheral residues in AChE, and aligned with BChE’s active site, while ABA was bound more peripherally. MD simulations confirmed complex-specific conformational stability based on RMSD, RMSF, Rg, and hydrogen bonding analysis. Both compounds showed low off-target potential against serine proteases and favorable predicted ADMET profiles. These results support the potential of marine phytohormones as preventive modulators of cholinergic dysfunction in AD. Full article
(This article belongs to the Special Issue Marine Natural Products as Enzyme Inhibitors)
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26 pages, 5063 KB  
Article
Blocking ASIP to Protect MC1R Signaling and Mitigate Melanoma Risk: An In Silico Study
by Farah Maarfi, Mohammed Cherkaoui, Sana Afreen and Mohd Yasir Khan
Pharmaceuticals 2026, 19(1), 114; https://doi.org/10.3390/ph19010114 - 8 Jan 2026
Viewed by 183
Abstract
Background: Melanin protects skin and hair from the effects of ultraviolet (UV) radiation damage, which contributes to all forms of skin cancer, including melanoma. Human melanocytes produce two main types of melanin: eumelanin provides effective photoprotection, and pheomelanin offers less protection against UV-induced [...] Read more.
Background: Melanin protects skin and hair from the effects of ultraviolet (UV) radiation damage, which contributes to all forms of skin cancer, including melanoma. Human melanocytes produce two main types of melanin: eumelanin provides effective photoprotection, and pheomelanin offers less protection against UV-induced skin damage. The agouti signaling protein (ASIP) antagonizes the melanocortin-1 receptor (MC1R), hinders melanocyte signaling, and shifts pigmentation toward pheomelanin, promoting UV vulnerability. In this study, we aim to discover compounds that inhibit ASIP–MC1R interaction and effectively preserve eumelanogenic signaling. Methods: The ASIP–MC1R interface-based pharmacophore model from ASIP is implicated in MC1R receptor protein engagement. We performed virtual screening with a validated pharmacophore model for ~4000 compounds curated from ZINCPharmer and applied drug-likeness filters, viz. ADMET and toxicity profiling tests. Further, the screened candidates were targeted for docking to the ASIP C-terminal domain corresponding to the MC1R-binding moiety. Top compounds underwent a 100-nanosecond (ns) run of molecular dynamics (MD) simulations to assess complex stability and persistence of key contacted residues. Results: Sequential triage, including pharmacophore, ADME–toxicity (ADMET), and docking/ΔG, yielded a focused group of candidates against ASIP antagonists with a favorable fit value. The MD run for 100 ns supported pose stability at the targeted pocket. Based on these predictions and analyses, compound ZINC14539068 was screened as a new potent inhibitor of ASIP to preserve α-MSH-mediated signaling of MC1R. Conclusions: Our in silico pipeline identifies ZINC14539068 as a potent inhibitor of ASIP at its C-terminal interface. This compound is predicted to disrupt ASIP–MC1R binding, thereby maintaining eumelanin-biased signaling. These findings motivate experimental validation in melanocytic models and in vivo studies to confirm pathway modulation and anti-melanoma potential. Full article
(This article belongs to the Section AI in Drug Development)
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18 pages, 1943 KB  
Article
Thymol Derivatives as Antimalarial Agents: Synthesis, Activity Against Plasmodium falciparum, ADMET Profiling, and Molecular Docking Insights
by Amatul Hamizah Ali, Rini Retnosari, Siti Nur Hidayah Jamil, Nur Aqilah Zahirah Norazmi, Nabel Darwish Zuhaidi, Su Datt Lam, Sylvia Chieng, Hani Kartini Agustar, Kuhan Chandru, Nurhezreen Md Iqbal, Lau Yee Ling and Jalifah Latip
Biomedicines 2026, 14(1), 123; https://doi.org/10.3390/biomedicines14010123 - 8 Jan 2026
Viewed by 252
Abstract
Background: Thymol, a natural phenol with antimicrobial and antioxidant activities, and its derivatives offer promising scaffolds for antimalarial drug development, potentially helping overcome resistance. Materials and Methods: In this study, thymol derivatives were synthesized and assessed as antiplasmodial agents against both resistant and [...] Read more.
Background: Thymol, a natural phenol with antimicrobial and antioxidant activities, and its derivatives offer promising scaffolds for antimalarial drug development, potentially helping overcome resistance. Materials and Methods: In this study, thymol derivatives were synthesized and assessed as antiplasmodial agents against both resistant and sensitive strains of P. falciparum, as well as Plasmodium knowlesi. The ligand molecules were assessed with Plasmodium falciparum chloroquine resistance transporter (PfCRT)’s potential using in silico molecular docking and ADMET analysis. The parent compound, thymol, was chemically modified through esterification and conjugation with hydroxybenzoic acid and cinnamic acid derivatives to generate analogs with varied substitution patterns. Results: The findings showed that among seven successfully synthesized thymol derivatives, compounds 4 and 6 exhibited notable potency against Plasmodium falciparum 3D7 (EC50 = 6.01 ± 1.7 µM and 6.8 ± 1.1 µM, respectively) with high SI values (16.5 and 14.6, respectively), indicating improved selectivity relative to thymol. The cytotoxicity evaluation against HCF mammalian cells revealed that most thymol derivatives were non-toxic, with CC50 values greater than 99 µM, except for compound 3 (CC50 = 71.4 ± 4.5 µM) and compound 1 (CC50 = 58.4 ± 2.3 µM), which exhibited moderate cytotoxic effects. The molecular docking results showed that compounds 3 (−8.4 kcal/mol), 4 (−8.3 kcal/mol), and 6 (−8.3 kcal/mol) exhibited strong binding affinities toward the PfCRT protein. Conclusions: Therefore, thymol derivative compounds 4 and 6 exhibited stronger antiplasmodial activity in vitro against P. falciparum and P. knowlesi with safety profiles against mammalian cells, targeting PfCRT, highlighting their potential as lead antimalarial candidates. Full article
(This article belongs to the Section Cell Biology and Pathology)
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41 pages, 4841 KB  
Article
Rational Design, Synthesis and Pharmacological Evaluation of Chalcones as Dual-Acting Compounds—Histamine H3 Receptor Ligands and MAO-B Inhibitors
by Dorota Łażewska, Agata Doroz-Płonka, Kamil Kuder, Agata Siwek, Waldemar Wagner, Joanna Karnafał-Ziembla, Agnieszka Olejarz-Maciej, Małgorzata Wolak, Monika Głuch-Lutwin, Barbara Mordyl, Oktawia Osiecka, Michał Juszczak, Katarzyna Woźniak, Małgorzata Więcek, Gniewomir Latacz and Anna Stasiak
Int. J. Mol. Sci. 2026, 27(2), 581; https://doi.org/10.3390/ijms27020581 - 6 Jan 2026
Viewed by 252
Abstract
Chalcone-based derivatives were designed as dual-acting ligands targeting the histamine H3 receptor (H3R) and monoamine oxidase B (MAO-B), based on the lead compound DL76. Three series of compounds (118) were synthesised and characterised, including simple [...] Read more.
Chalcone-based derivatives were designed as dual-acting ligands targeting the histamine H3 receptor (H3R) and monoamine oxidase B (MAO-B), based on the lead compound DL76. Three series of compounds (118) were synthesised and characterised, including simple chalcones (19) and piperidinyl chalcones (1018). All piperidinyl derivatives exhibited nanomolar affinity for human H3R (hH3R), with compounds 1012 achieving Ki values ≤ 30 nM. Simple chalcones showed potent human MAO-B (hMAO-B) inhibition (IC50: 0.85–337 nM), especially 3,4-dichloro derivatives. Compound 15 was the most active hybrid, with a Ki of 46.8 nM for hH3R and an IC50 of 212.5 nM for hMAO-B. Molecular docking and 250 ns simulations revealed stabilising interactions at both binding sites and clarified structural features behind dual activity. Preliminary ADMET profiling showed low Caco-2 permeability and rapid microsomal metabolism, mainly via hydroxylation. Compound 15 exhibited micromolar cytotoxicity in SH-SY5Y and HepG2 cells, induced G2/M arrest, disrupted mitochondrial homeostasis, and was genotoxic in Peripheral Blood Mononuclear Cells (PBMCs). Additionally, for H3R ligands (15, DL76, pitolisant), the study reports the first use of Surface Plasmon Resonance Microscopy (SPRM) to assess their interactions with this receptor. Therefore, piperidinyl chalcones show promise as ligands with dual action on H3R and MAO-B, useful in the treatment of neurodegeneration and/or CNS cancers. Full article
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18 pages, 2618 KB  
Article
Computational Assessment of Lactobacillus helveticus and Bifidobacterium longum Metabolites for Perinatal Depression Therapy
by Oumaima Anachad, Wafaa Taha, Chaimaa Saadoune, Houssam Assioui, Imad Fenjar, Imane Thaifa, Faiza Bennis and Fatima Chegdani
Bacteria 2026, 5(1), 4; https://doi.org/10.3390/bacteria5010004 - 5 Jan 2026
Viewed by 190
Abstract
Perinatal depression (PND) is a severe mood disorder affecting mothers during pregnancy and postpartum, with implications for both maternal and neonatal health. Emerging evidence suggests that gut microbiota-derived metabolites play a critical role in neuroinflammation and neurotransmission. In this study, we employed an [...] Read more.
Perinatal depression (PND) is a severe mood disorder affecting mothers during pregnancy and postpartum, with implications for both maternal and neonatal health. Emerging evidence suggests that gut microbiota-derived metabolites play a critical role in neuroinflammation and neurotransmission. In this study, we employed an in silico approach to evaluate the pharmacokinetic and therapeutic potential of metabolites produced by Lactobacillus helveticus and Bifidobacterium longum in targeting key proteins implicated in PND, including BDNF, CCL2, TNF, IL17A, IL1B, CXCL8, IL6, IL10. The ADMET (Absorption, Distribution, Metabolism, Excretion, and Toxicity) profiles of selected microbial metabolites, including acetate, lactate, formate, folic acid, riboflavin, kynurenic acid, γ-aminobutyric acid, and vitamin B12 were assessed using computational tools to predict their bioavailability and safety. Enrichment analysis was performed to identify biological pathways and molecular mechanisms modulated by these metabolites, with a focus on neuroinflammation, stress response, and neurogenesis. Additionally, molecular docking studies were conducted to evaluate the binding affinities of these metabolites toward the selected PND-associated targets, providing insights into their potential as neuroactive agents. Our findings suggest that specific microbial metabolites exhibit favorable ADMET properties and strong binding interactions with key proteins implicated in PND pathophysiology. These results highlight the therapeutic potential of gut microbiota-derived metabolites in modulating neuroinflammatory and neuroendocrine pathways, paving the way for novel microbiome-based interventions for perinatal depression. Further experimental validation is warranted to confirm these computational predictions and explore the clinical relevance of these findings. Full article
(This article belongs to the Collection Feature Papers in Bacteria)
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34 pages, 6954 KB  
Article
Natural Fatty Acids as Dual ACE2-Inflammatory Modulators: Integrated Computational Framework for Pandemic Preparedness
by William D. Lituma-González, Santiago Ballaz, Tanishque Verma, J. M. Sasikumar and Shanmugamurthy Lakshmanan
Int. J. Mol. Sci. 2026, 27(1), 402; https://doi.org/10.3390/ijms27010402 - 30 Dec 2025
Viewed by 297
Abstract
The COVID-19 pandemic exposed critical vulnerabilities in single-target antiviral strategies, highlighting the urgent need for multi-mechanism therapeutic approaches against emerging viral threats. Here, we present an integrated computational framework systematically evaluating natural fatty acids as potential dual ACE2 (Angiotension Converting Enzyme 2)-inflammatory modulators; [...] Read more.
The COVID-19 pandemic exposed critical vulnerabilities in single-target antiviral strategies, highlighting the urgent need for multi-mechanism therapeutic approaches against emerging viral threats. Here, we present an integrated computational framework systematically evaluating natural fatty acids as potential dual ACE2 (Angiotension Converting Enzyme 2)-inflammatory modulators; compounds simultaneously disrupting SARS-CoV-2 viral entry through allosteric ACE2 binding while suppressing host inflammatory cascades; through allosteric binding mechanisms rather than conventional competitive inhibition. Using molecular docking across eight ACE2 regions, 100 ns molecular dynamics simulations, MM/PBSA free energy calculations, and multivariate statistical analysis (PCA/LDA), we computationally assessed nine naturally occurring fatty acids representing saturated, monounsaturated, and polyunsaturated classes. Hierarchical dynamics analysis identified three distinct binding regimes spanning fast (τ < 50 ns) to slow (τ > 150 ns) timescales, with unsaturated fatty acids demonstrating superior binding affinities (ΔG = −6.85 ± 0.27 kcal/mol vs. −6.65 ± 0.25 kcal/mol for saturated analogs, p = 0.002). Arachidonic acid achieved optimal SwissDock affinity (−7.28 kcal/mol), while oleic acid exhibited top-ranked predicted binding affinity within the computational hierarchy (ΔGbind = −24.12 ± 7.42 kcal/mol), establishing relative prioritization for experimental validation rather than absolute affinity quantification. Energetic decomposition identified van der Waals interactions as primary binding drivers (65–80% contribution), complemented by hydrogen bonds as transient directional anchors. Comprehensive ADMET profiling predicted favorable safety profiles compared to synthetic antivirals, with ω-3 fatty acids showing minimal nephrotoxicity risks while maintaining excellent intestinal absorption (>91%). Multi-platform bioactivity analysis identified convergent anti-inflammatory mechanisms through eicosanoid pathway modulation and kinase inhibition. This computational investigation positions natural fatty acids as promising candidates for experimental validation in next-generation pandemic preparedness strategies, integrating potential therapeutic efficacy with sustainable sourcing. The framework is generalizable to fatty acids from diverse biological origins. Full article
(This article belongs to the Section Molecular Informatics)
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26 pages, 3200 KB  
Article
A Novel Quinolone JH62 (E-2-(Tridec-4-en-1-yl)-quinolin-4(1H)-one) from Pseudomonas aeruginosa Exhibits Potent Anticancer Activity
by Qunyi Chen, Jianhe Wang, Xiaoyan Wu, Lantu Xiong, Lianhui Zhang and Zining Cui
Microorganisms 2026, 14(1), 78; https://doi.org/10.3390/microorganisms14010078 - 30 Dec 2025
Viewed by 358
Abstract
Cancer remains a leading cause of mortality worldwide, and new chemical leads are essential for developing potent anticancer therapies. Evidence suggests that Pseudomonas aeruginosa (Pa) may suppress tumorigenesis, although the underlying mechanisms remain largely unclear. This study characterized a novel small [...] Read more.
Cancer remains a leading cause of mortality worldwide, and new chemical leads are essential for developing potent anticancer therapies. Evidence suggests that Pseudomonas aeruginosa (Pa) may suppress tumorigenesis, although the underlying mechanisms remain largely unclear. This study characterized a novel small molecule quinolone, JH62 (E-2-(tridec-4-en-1-yl)-quinolin-4(1H)-one, C22H31NO), from Pa. JH62 exhibited broad-spectrum anticancer activity, inhibiting the proliferation of A549 lung cancer cells in a time- and dose-dependent manner with an IC50 of 15 μM, while showed low cytotoxicity toward normal cells. In xenograft mice model, treatment with JH62 (10 mg/kg) reduced tumor weight and volume by 73% and 79%, respectively. Mechanistically, treatment with JH62 induced structural and functional disruption of mitochondria in cancer cells, triggered autophagic cell death, and did not cause DNA damage. Genetic analysis confirmed that JH62 biosynthesis depends on the pqsABCDE gene cluster and that JH62 positively regulates its own production. ADMET profiling further indicated promising drug-like properties for future development. These findings establish JH62 as a promising anticancer lead compound derived from microbial metabolism. Full article
(This article belongs to the Section Medical Microbiology)
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19 pages, 762 KB  
Article
Therapeutic Potential and Predictive Pharmaceutical Modeling of Indole Kratom Alkaloids
by Md Harunur Rashid, Matthew J. Williams, Andres Garcia Guerra, Arunporn Itharat, Raimar Loebenberg and Neal M. Davies
J. Phytomed. 2026, 1(1), 1; https://doi.org/10.3390/jphytomed1010001 - 29 Dec 2025
Viewed by 350
Abstract
Kratom alkaloids are classified as aromatic pentacyclic indole and substituted carbonyl oxindole alkaloids. This study investigates the metabolism and interactions of indole alkaloids using in silico tools, including ADMET Predictor 13.0™, to assess pharmacokinetic and metabolic profiles. The analysis examined absorption, distribution, metabolism, [...] Read more.
Kratom alkaloids are classified as aromatic pentacyclic indole and substituted carbonyl oxindole alkaloids. This study investigates the metabolism and interactions of indole alkaloids using in silico tools, including ADMET Predictor 13.0™, to assess pharmacokinetic and metabolic profiles. The analysis examined absorption, distribution, metabolism, and excretion (ADME), focusing on cytochrome P450 (CYP) and UDP-glucuronosyltransferase (UGT) enzyme interactions, drug transporters, and clearance. Most indole alkaloids showed strong substrate interaction and inhibition of CYP3A4 (79–99% confidence) and induction of CYP1A2 (up to 94% confidence). Among UGT enzymes, UGT1A1 demonstrated the highest substrate affinity (97%), while none interacted with UGT2B15. All alkaloids showed strong P-glycoprotein (Pgp) interaction but minimal inhibition of BCRP. Mitralactonine exhibited the highest skin permeability, and Mitralactonal showed maximal jejunal permeability. Most indole alkaloids demonstrated significant blood–brain barrier penetration (up to 99% confidence) and compliance with Lipinski’s rule of five. Predictive modeling indicated notable effects on hepatic microsomal clearance parameters. This investigation offers the first comprehensive in silico ADMET profiling of kratom indole alkaloids, uncovering their CYP3A4 inhibition potential and metabolic liabilities to prioritize candidates for safer therapeutic development, though limited by model biases, applicability domain restrictions, and inability to fully capture biological complexity, stereochemistry, or interindividual variability necessitating experimental in vitro and in vivo validation. Full article
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18 pages, 2586 KB  
Article
Novel ACE-Inhibitory Peptides from Royal Jelly Proteins: Comprehensive Screening, Mechanistic Insights, and Endothelial Protection
by Wanyu Yang, Xinyu Zou, Tianrong Zhang, Qingqing Liu, Ziyan Liu, Fan Li, Yuhong Luo, Yiwen Wang, Zhijun Qiu and Bin Zhang
Foods 2026, 15(1), 84; https://doi.org/10.3390/foods15010084 - 26 Dec 2025
Viewed by 294
Abstract
This study aimed to identify novel angiotensin-converting enzyme (ACE)-inhibitory peptides from royal jelly proteins (RJPs) by integrating in silico digestion, virtual screening, and in vitro evaluation. Three major royal jelly proteins (MRJP1-3) were subjected to in silico digestion using 16 enzymatic systems, yielding [...] Read more.
This study aimed to identify novel angiotensin-converting enzyme (ACE)-inhibitory peptides from royal jelly proteins (RJPs) by integrating in silico digestion, virtual screening, and in vitro evaluation. Three major royal jelly proteins (MRJP1-3) were subjected to in silico digestion using 16 enzymatic systems, yielding 1411 unique peptides. Virtual screening based on predicted bioactivity, toxicity, water solubility, and ADMET profiles resulted in the selection of 27 candidate peptides. Molecular docking revealed strong binding affinities for these peptides compared with the positive control captopril, among which PYPDWSFAK and RPYPDWSF exhibited potent ACE-inhibitory activity, with IC50 values of 110 ± 1.02 μmol/L and 204 ± 0.61 μmol/L, respectively. Kinetic analysis indicated that PYPDWSFAK acts as a mixed-type ACE inhibitor. Docking visualization demonstrated that PYPDWSFAK forms multiple hydrogen bonds with key residues in the ACE active pocket and directly coordinates with the catalytic Zn2+ ion. Cellular assays showed that PYPDWSFAK was non-cytotoxic, suppressed Ang II–induced endothelial cell migration, restored NO and ET-1 balance, and enhanced SOD and GSH-Px activities. Overall, this study enriches the repertoire of ACE-inhibitory peptides derived from royal jelly proteins. Furthermore, PYPDWSFAK is identified as a promising ACE-inhibitory peptide with potential for incorporation into natural antihypertensive ingredients or functional foods. Full article
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21 pages, 7060 KB  
Article
Inhibitory Activity of LDT10 and LDT119, New Saturated Cardanols, Against Trypanosoma cruzi
by Renato Granado, Brenda de Lucena Costa, Cleonice Andrade Holanda, Daniel Carneiro Moreira, Luiz Antonio Soares Romeiro, Emile Santos Barrias and Wanderley de Souza
Pharmaceuticals 2026, 19(1), 30; https://doi.org/10.3390/ph19010030 - 22 Dec 2025
Viewed by 229
Abstract
Background/Objectives: Chagas disease, caused by Trypanosoma cruzi, remains a major neglected tropical disease with limited therapeutic options restricted to benznidazole and nifurtimox, both associated with significant toxicity and reduced efficacy during chronic infection. Seeking novel, safe, and sustainable chemotherapeutic candidates, two new [...] Read more.
Background/Objectives: Chagas disease, caused by Trypanosoma cruzi, remains a major neglected tropical disease with limited therapeutic options restricted to benznidazole and nifurtimox, both associated with significant toxicity and reduced efficacy during chronic infection. Seeking novel, safe, and sustainable chemotherapeutic candidates, two new saturated cardanol-derived phospholipid analogs—LDT10 and LDT119—were rationally designed based on the molecular scaffold of miltefosine and biosourced from cashew nut shell liquid (CNSL). This study aimed to evaluate the pharmacokinetic properties of these compounds in silico and assess their antiparasitic activity, cytotoxicity, and morphological and ultrastructural effects on all developmental forms of T. cruzi in vitro. Materials and Methods: In silico ADMET predictions (SwissADME, pkCSM) were performed to determine bioavailability, pharmacokinetic behavior, CYP inhibition, mutagenicity, and hepatotoxicity. Antiproliferative activity was evaluated in epimastigotes, trypomastigotes, and intracellular amastigotes using dose–response assays and flow cytometry. Cytotoxicity was assessed in HEPG2 and HFF-1 cells using resazurin-based viability assays. Morphological and ultrastructural alterations were investigated through scanning (SEM) and transmission (TEM) electron microscopy. Reactive oxygen species (ROS) generation was quantified with H2DCFDA after 4 h and 24 h of exposure. Results: In silico analyses indicated favorable drug-like profiles, high intestinal absorption (>89%), absence of mutagenicity or hepatotoxicity, and non-penetration of the blood–brain barrier. LDT10 was not a P-gp substrate, and LDT119 acted as a P-gp inhibitor, suggesting reduced efflux and higher intracellular retention. Both compounds inhibited epimastigote proliferation with low IC50 values (LDT10: 0.81 µM; LDT119: 1.2 µM at 48 h) and reduced trypomastigote viability (LD50 LDT10: 2.1 ± 2 µM; LDT119: 1.8 ± 0.8 µM). Intracellular amastigotes were highly susceptible (IC50 LDT10: 0.48 µM; LDT119: 0.3 µM at 72 h), with >90% inhibition at higher concentrations. No cytotoxicity was observed in mammalian cells up to 20 µM. SEM revealed membrane wrinkling, pore-like depressions, rounded cell bodies, and multiple flagella, indicating cell division defects. TEM showed Golgi disorganization, autophagic vacuoles, mitochondrial vesiculation, and abnormal kinetoplast replication, while host cells remained structurally preserved. Both compounds induced significant ROS production in trypomastigotes after 24 h in a dose-dependent manner. Conclusions: LDT10 and LDT119 exhibited potent and selective in vitro activity against all developmental stages of T. cruzi, with low micromolar to submicromolar IC50/LD50 values, minimal mammalian cytotoxicity, and extensive morphological and ultrastructural damage consistent with disruption of phospholipid biosynthesis pathways. Combined with favorable in silico pharmacokinetic predictions, these CNSL-derived phospholipid analogs represent promising candidates for future Chagas disease chemotherapy and warrant further in vivo evaluation. Full article
(This article belongs to the Section Biopharmaceuticals)
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33 pages, 7434 KB  
Article
From Deep-Sea Natural Product to Optimized Therapeutics: Computational Design of Marizomib Analogs
by Nasser Alotaiq and Doni Dermawan
Int. J. Mol. Sci. 2025, 26(24), 12159; https://doi.org/10.3390/ijms262412159 - 18 Dec 2025
Viewed by 275
Abstract
The proteasome β5 subunit plays a central role in protein degradation and is an established therapeutic target in glioblastoma. Marizomib (MZB), a natural β5 inhibitor, has shown promising anticancer activity, yet suboptimal pharmacological properties limit its clinical translation. Using a comprehensive computational approach, [...] Read more.
The proteasome β5 subunit plays a central role in protein degradation and is an established therapeutic target in glioblastoma. Marizomib (MZB), a natural β5 inhibitor, has shown promising anticancer activity, yet suboptimal pharmacological properties limit its clinical translation. Using a comprehensive computational approach, this study aimed to identify and characterize novel MZB analogs with improved binding affinity, stability, and drug-like profiles. An integrative in silico study was performed, including molecular docking, frontier molecular orbital (FMO) analysis, pharmacophore modeling, molecular dynamics (MD) simulations over 200 ns, MM/PBSA binding free energy calculations, and per-residue energy decomposition. ADMET profiling evaluated the pharmacokinetic and safety properties of MZB and top-performing analogs. Docking and pharmacophore modeling revealed strong complementarity between MZB analogs and the β5 catalytic pocket. MD simulations showed that MZBMOD-77 and MZBMOD-79 exhibited exceptional structural stability with low RMSD values (0.40–0.42 nm), persistent binding within the active site cavity, and significant disruption of hydrogen-bond networks in the active loop regions Ala19–Lys33 and Val87–Gly98. MM/PBSA analysis confirmed their superior binding free energies (−19.99 and −18.79 kcal/mol, respectively), surpassing native MZB (−6.26 kcal/mol). Per-residue decomposition highlighted strong contributions from Arg19, Ala20, Lys33, and Ala50. ADMET predictions indicated improved oral absorption, reduced toxicity, and favorable pharmacokinetics compared to native MZB. This integrative computational study identifies MZBMOD-77 and MZBMOD-79 as promising next-generation proteasome β5 inhibitors. These analogs mimic and enhance the inhibitory mechanism of native MZB, offering potential candidates for further optimization and preclinical development in glioblastoma therapy. Full article
(This article belongs to the Special Issue Latest Advances in Protein-Ligand Interactions)
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35 pages, 3818 KB  
Article
Machine Learning-Based QSAR Screening of Colombian Medicinal Flora for Potential Antiviral Compounds Against Dengue Virus: An In Silico Drug Discovery Approach
by Sergio Andrés Montenegro-Herrera, Anibal Sosa, Isabella Echeverri-Jiménez, Rafael Santiago Castaño-Valencia and Alejandra María Jerez-Valderrama
Pharmaceuticals 2025, 18(12), 1906; https://doi.org/10.3390/ph18121906 - 18 Dec 2025
Viewed by 423
Abstract
Background/Objectives: Colombia harbors exceptional plant diversity, comprising over 31,000 formally identified species, of which approximately 6000 are classified as useful plants. Among these, 2567 species possess documented food and medicinal applications, with several traditionally utilized for managing febrile illnesses. Despite the global [...] Read more.
Background/Objectives: Colombia harbors exceptional plant diversity, comprising over 31,000 formally identified species, of which approximately 6000 are classified as useful plants. Among these, 2567 species possess documented food and medicinal applications, with several traditionally utilized for managing febrile illnesses. Despite the global burden of dengue virus infection affecting millions annually, no specific antiviral therapy has been established. This study aimed to identify potential anti-dengue compounds from Colombian medicinal flora through machine learning-based quantitative structure–activity relationship (QSAR) modeling. Methods: An optimized XGBoost algorithm was developed through Bayesian hyperparameter optimization (Optuna, 50 trials) and trained on 2034 ChEMBL-derived activity records with experimentally validated anti-dengue activity (IC50/EC50). The model incorporated 887 molecular features comprising 43 physicochemical descriptors and 844 ECFP4 fingerprint bits selected via variance-based filtering. IC50 and EC50 endpoints were modeled independently based on their pharmacological distinction and negligible correlation (r = −0.04, p = 0.77). Through a systematic literature review, 2567 Colombian plant species from the Humboldt Institute’s official checklist were evaluated (2501 after removing duplicates and infraspecific taxa), identifying 358 with documented antiviral properties. Phytochemical analysis of 184 characterized species yielded 3267 unique compounds for virtual screening. A dual-endpoint classification strategy categorized compounds into nine activity classes based on combined potency thresholds (Low: pActivity ≤ 5.0, Medium: 5.0 < pActivity ≤ 6.0, High: pActivity > 6.0). Results: The optimized model achieved robust performance (Matthews correlation coefficient: 0.583; ROC-AUC: 0.896), validated through hold-out testing (MCC: 0.576) and Y-randomization (p < 0.01). Virtual screening identified 276 compounds (8.4%) with high predicted potency for both endpoints (“High-High”). Structural novelty analysis revealed that all 276 compounds exhibited Tanimoto similarity < 0.5 to the training set (median: 0.214), representing 145 unique Murcko scaffolds of which 144 (99.3%) were absent from the training data. Application of drug-likeness filtering (QED ≥ 0.5) and applicability domain assessment identified 15 priority candidates. In silico ADMET profiling revealed favorable pharmaceutical properties, with Incartine (pIC50: 6.84, pEC50: 6.13, QED: 0.83), Bilobalide (pIC50: 6.78, pEC50: 6.07, QED: 0.56), and Indican (pIC50: 6.73, pEC50: 6.11, QED: 0.51) exhibiting the highest predicted potencies. Conclusions: This systematic computational screening of Colombian medicinal flora demonstrates the untapped potential of regional biodiversity for anti-dengue drug discovery. The identified candidates, representing structurally novel chemotypes, are prioritized for experimental validation. Full article
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18 pages, 2942 KB  
Article
Structure-Based Identification of Ponganone V from Pongamia pinnata as a Potential KPC-2 β-Lactamase Inhibitor: Insights from Docking, ADMET, and Molecular Dynamics
by Himanshu Jangid, Chirag Chopra and Atif Khurshid Wani
Microbiol. Res. 2025, 16(12), 262; https://doi.org/10.3390/microbiolres16120262 - 18 Dec 2025
Viewed by 251
Abstract
Carbapenem-resistant Enterobacterales (CREs) pose a critical threat to global public health, largely driven by the enzymatic activity of Klebsiella pneumoniae carbapenemase-2 (KPC-2), a class A serine β-lactamase that hydrolyzes most β-lactam antibiotics. While β-lactamase inhibitors like avibactam offer temporary relief, emerging KPC variants [...] Read more.
Carbapenem-resistant Enterobacterales (CREs) pose a critical threat to global public health, largely driven by the enzymatic activity of Klebsiella pneumoniae carbapenemase-2 (KPC-2), a class A serine β-lactamase that hydrolyzes most β-lactam antibiotics. While β-lactamase inhibitors like avibactam offer temporary relief, emerging KPC variants demand novel, sustainable inhibitory scaffolds. This study aimed to identify and characterize potential natural inhibitors of KPC-2 from Pongamia pinnata, leveraging a comprehensive in silico workflow. A curated library of 86 phytochemicals was docked against the active site of KPC-2 (PDB ID: 3DW0). The top-performing ligands were subjected to ADMET profiling (pkCSM), and 100 ns molecular dynamics simulations (GROMACS) to evaluate structural stability and interaction persistence, using avibactam as control. Ponganone V exhibited the most favorable binding energy (−9.0 kcal/mol), engaging Ser70 via a hydrogen bond and forming π–π interactions with Trp105. Glabrachromene II demonstrated a broader interaction network but reduced long-term stability. ADMET analysis confirmed high intestinal absorption, non-mutagenicity, and absence of hERG inhibition for both ligands. Molecular dynamics simulations revealed that Ponganone V maintained compact structure and stable hydrogen bonding throughout the 100 ns trajectory, closely mirroring the behavior of avibactam, whereas Glabrachromene II displayed increased fluctuation and loss of compactness beyond 80 ns. Principal Component Analysis (PCA) further supported these findings, with Ponganone V showing restricted conformational motion and a single deep free energy basin, while avibactam and Glabrachromene II exhibited broader conformational sampling and multiple energy minima. The integrated computational findings highlight Ponganone V as a potent and pharmacologically viable natural KPC-2 inhibitor, with strong binding affinity, sustained structural stability, and minimal toxicity. This study underscores the untapped potential of Pongamia pinnata phytochemicals as future anti-resistance therapeutics and provides a rational basis for their experimental validation. Full article
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24 pages, 4983 KB  
Article
Phytochemical Profiling and Structure-Based Computational Characterization of Marrubium vulgare L. Compounds as Hsp90 Modulators
by Ilham Zarguan, Hanane Abbou, Razana Zegrari, Rihab Festali, Devan Buchanan, Abdelaziz Benjouad and Lamiae Belayachi
Int. J. Mol. Sci. 2025, 26(24), 12150; https://doi.org/10.3390/ijms262412150 - 17 Dec 2025
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Abstract
Marrubium vulgare L. is a medicinal plant widely used in traditional medicine, with emerging evidence of anticancer potential. This study investigated its bioactive compounds as inhibitors of Heat Shock Protein 90 alpha (Hsp90α), a molecular chaperone essential for oncogenic protein stability. Organic and [...] Read more.
Marrubium vulgare L. is a medicinal plant widely used in traditional medicine, with emerging evidence of anticancer potential. This study investigated its bioactive compounds as inhibitors of Heat Shock Protein 90 alpha (Hsp90α), a molecular chaperone essential for oncogenic protein stability. Organic and aqueous extracts were profiled using high-performance liquid chromatography–mass spectrometry (HPLC–MS), revealing a diverse phytochemical composition. Identified compounds were screened against the full-length crystal structure of Hsp90α using a structure-based computational workflow that included extra-precision and domain-specific molecular docking, molecular dynamics (MD) simulations, and MM/GBSA binding free energy calculations. Pharmacokinetic and toxicity profiles were evaluated through ADMET predictions. This study elucidated the chemical composition of the plant and identified two hit compounds: Forsythoside B bound preferentially to the middle domain, potentially interfering with client protein interactions, and chlorogenic acid targeted the C-terminal domain, which regulates dimerization and allosteric activity. Both ligands displayed stable protein–ligand interactions during MD and favorable ADMET properties. These findings provide the first integrated chemical and computational prediction framework, suggesting that some M. vulgare metabolites may interact with Hsp90, highlighting its potential as a source of novel anticancer scaffolds and laying the groundwork for experimental validation and drug development. Full article
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24 pages, 2507 KB  
Article
Equisetum hyemale L. Extracts: Phytochemistry, Biological Performance, ADMET Profiling, and Toxicity Predictions
by Yulianna Minutti-Calva, Karen Schürenkämper-Carrillo, Edwin E. Reza-Zaldívar, Oscar E. Del Razo-Rodríguez, Ian Vitola, Jorge Manuel Silva-Jara, José Daniel Lozada-Ramírez, Daniel A. Jacobo-Velázquez, Diego E. Navarro-López, Marco Chávez-Tinoco, Edgar R. López-Mena, Jorge L. Mejía-Méndez and Eugenio Sánchez-Arreola
Pharmaceuticals 2025, 18(12), 1901; https://doi.org/10.3390/ph18121901 - 17 Dec 2025
Viewed by 437
Abstract
Background: Equisetum hyemale L., commonly known as scouring rush or horsetail, is a perennial plant with significant applications in traditional medicine. Methods: The aerial parts of E. hyemale L. were macerated with hexane, chloroform, and ethyl acetate. The phytochemical profile of the [...] Read more.
Background: Equisetum hyemale L., commonly known as scouring rush or horsetail, is a perennial plant with significant applications in traditional medicine. Methods: The aerial parts of E. hyemale L. were macerated with hexane, chloroform, and ethyl acetate. The phytochemical profile of the extracts was investigated using chromatography approaches. The biological performance of the extracts was determined using antibacterial, antioxidant, anticancer, and toxicity in vitro and in vivo models. Molecular docking and ADMET analyses were employed to determine interactions with structural components of multidrug resistant bacteria and assess potential toxicological risks. Results: The extracts exert high scavenging activity against ABTS radicals (IC50 2.57–2.68 μg/mL), but poor antibacterial activity. It was evidenced that treatment with extracts exerts in moderate cytotoxicity on hepatocellular and colorectal cancer cell lines. Toxicity assays unveiled that the extracts decrease the survival rate of C. elegans nematodes after 2 h of exposure to treatment. In silico studies evidenced a high affinity of campesterol and calcitriol towards the DNA gyrase, and the oral bioavailability of farnesol and limonene. Conclusions: Our findings demonstrated the presence of biologically active secondary metabolites in hexane, chloroform, and ethyl acetate extracts from E. hyemale L. This work also demonstrated the biological performance of these extracts in in vitro and in vivo models, and validated the potential pharmacokinetic and pharmacodynamic profile of their phytoconstituents. Full article
(This article belongs to the Section Natural Products)
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