OPLS4: Improving Force Field Accuracy on Challenging Regimes of Chemical Space

Pyridine indole hybrids as novel potent CYP17A1 inhibitors

Prostate cancer (PCa) is one of the most prevalent malignancies affecting men worldwide, and androgen deprivation therapy (ADT) is a primary treatment approach. CYP17A1 inhibitors like abiraterone target the steroidogenic pathway to reduce androgen levels, but their clinical efficacy is limited by drug resistance and adverse effects. This study reports the synthesis and evaluation of novel CYP17A1 inhibitors derived from a previously identified hit compound. Several analogs were synthesised, including an unexpected di-cyano derivative, which demonstrated increased potency against CYP17A1 compared to abiraterone. Biological assays revealed that these compounds significantly inhibited CYP17A1 enzymatic activity and altered steroid biosynthesis. Among the newly synthesised inhibitors, compound 11 showed the highest potency (IC50 = 4 nM) and the related compound 14 presented a template for further development. A combined docking and molecular dynamics approach was used to identify the possible target binding modes of the compounds.

Biparatopic binding of ISB 1442 to CD38 in trans enables increased cell antibody density and increased avidity

ISB 1442 is a bispecific biparatopic antibody in clinical development to treat hematological malignancies. It consists of two adjacent anti-CD38 arms targeting non-overlapping epitopes that preferentially drive binding to tumor cells and a low-affinity anti-CD47 arm to enable avidity-induced blocking of proximal CD47 receptors. We previously reported the pharmacology of ISB 1442, designed to reestablish synthetic immunity in CD38+ hematological malignancies. Here, we describe the discovery, optimization and characterization of the ISB 1442 antigen binding fragment (Fab) arms, their assembly to 2 + 1 format, and present the high-resolution co-crystal structures of the two anti-CD38 Fabs, in complex with CD38. This, with biophysical and functional assays, elucidated the underlying mechanism of action of ISB 1442. In solution phase, ISB 1442 forms a 2:2 complex with CD38 as determined by size-exclusion chromatography with multi-angle light scattering and electron microscopy. The predicted antibody-antigen stoichiometries at different CD38 surface densities were experimentally validated by surface plasmon resonance and cell binding assays. The specific design and structural features of ISB 1442 enable: 1) enhanced trans binding to adjacent CD38 molecules to increase Fc density at the cancer cell surface; 2) prevention of avid cis binding to monomeric CD38 to minimize blockade by soluble shed CD38; and 3) greater binding avidity, with a slower off-rate at high CD38 density, for increased specificity. The superior CD38 targeting of ISB 1442, at both high and low receptor densities, by its biparatopic design, will enhance proximal CD47 blockade and thus counteract a major tumor escape mechanism in multiple myeloma patients.

Design, synthesis and characterization of aryl bis-guanyl hydrazones as RNA binders of C9orf72 G4C2 extended repeats

Expanded G4C2 repeats derived from mutations of the C9orf72 gene are causative factors in amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) patients, leading to multiple pathological events. Bis thiophene para dinicotinimidamide 2a was reported to preferentially stabilize G-quadruplex G4C2 RNA structures at sub-micromolar concentrations. We replaced its amidine groups with BBB-compliant guanyl hydrazones, and carried out scaffold variations to improve water solubility. An eight-membered array was built around bis-thiophene- (4b-6a), bis-oxazole- (7b), diphenylurea diamide- (8b) and phenyldioxy ditriazolephenyl scaffolds (9a,b). Biological profiling of the array identified 4b as a promising, drug-like hit, active in cellular assays on ALS patient-derived cells.

Harnessing computational tools for drug discovery: An integrated computational approach to identify potential BACE-1 inhibitors

The hallmark of Alzheimer's disease (AD), a progressive neurodegenerative condition, is the buildup of amyloid-beta (Aβ) plaque, which is mainly caused by β-secretase 1 (BACE-1) activity. BACE-1 inhibition is a potentially effective treatment strategy to lower the progression of AD. In order to find possible BACE-1 inhibitors using a drug repurposing technique, this study uses an integrated computational approach that includes pharmacophore modelling, virtual screening, molecular docking, MM-GBSA, molecular dynamics (MD) simulations, in-silico ADMET profiling, and PBPK modelling. A pharmacophore model, was created with known BACE-1 inhibitors to enable virtual screening of both novel and FDA-approved chemical libraries. Top candidates with good free energy scores and strong binding affinities were found using molecular docking and MM-GBSA calculations. The stability of shortlisted Hits inside the BACE-1 active site was further validated using MD simulations, which showed that some of the important interactions were maintained across a period of 50ns. ADMET and PBPK studies predicted favorable pharmacokinetic and safety profiles for the shortlisted hits, particularly for B2 and B9. These findings identify potential candidates for future experimental validation, offering an inexpensive approach for identification of compounds as potential BACE-1 inhibitors.

Discovery of natural MCL1 inhibitors using pharmacophore modelling, QSAR, docking, ADMET, molecular dynamics, and DFT analysis

Mcl-1, a member of the Bcl-2 family, is a crucial regulator of apoptosis, frequently overexpressed in various cancers, including lung, breast, pancreatic, cervical, ovarian cancers, leukemia, and lymphoma. Its anti-apoptotic function allows tumor cells to evade cell death and contributes to drug resistance, making it an essential target for anticancer drug development. This study aimed to discover potent antileukemic compounds targeting Mcl-1. We selected diverse molecules from the BindingDB database to construct a structure-based pharmacophore model, which facilitated the virtual screening of 407,270 compounds from the COCONUT database. An e-pharmacophore model was developed using the co-crystallized inhibitor, followed by QSAR modeling to estimate IC50 values and filter compounds with predicted values below the median. The top hits underwent molecular docking and MMGBSA binding energy calculations against Mcl-1, resulting in the selection of two promising candidates for further ADMET analysis. DFT calculations assessed their electronic properties, confirming favorable reactivity profiles of the screened compounds. Predictions for physicochemical and ADMET properties aligned with expected bioactivity and safety. Molecular dynamics simulations further validated their strong binding affinity and stability, positioning them as potential Mcl-1 inhibitors. Our comprehensive computational approach highlights these compounds as promising antileukemic agents, with future in vivo and in vitro validation recommended for further confirmation.

Repurposing the amino-3,5-dicyanopyridine scaffold from adenosine receptor ligands to carbonic anhydrase activators

We are repurposing a set of imidazole-containing amino-3,5-dicyanopyridines, previously reported as adenosine receptor ligands, in the role of activators of human-expressed carbonic anhydrase isoenzymes (hCA I, II, VA, and VII) considered relevant to controlling brain functions. Our focus has been to identify new carbonic anhydrase activators (CAAs) as pharmacological tools useful to investigate the CA role in psychiatric and neurodegenerative disorders. All tested compounds were inactive at hCA II, highlighting a trend similar to that of the reference activator histamine. On the contrary, most of them showed different activation profiles at the other CAs tested. In particular, while compounds 13 and 24 had the lowest KA values at hCA VII (KA = 0.8 μM) and I (KA = 0.7 μM), respectively, derivatives 14 and 17 displayed the most effective and balanced activation profile at hCA I, VA, and VII, with KA values in the low micromolar range. The binding mode of compound 14 was investigated in silico using X-ray solved (hCA I and VII) and homology built (hCA VA) structures. Focusing our attention on drug-like compounds to find new pharmacological tools, the ADME properties of all derivatives were in silico calculated to investigate their drug-like behavior. Compound 17 emerged as a candidate, as it showed high oral availability and permeability of the gut-blood barrier, together with a good potential to cross the BBB.

Redesigning oxazolidinones as carbonic anhydrase inhibitors against vancomycin-resistant enterococci

The rise of vancomycin-resistant enterococci (VRE) as a leading cause of hospital-acquired infections underscores the urgent need for new treatment strategies. In fact, resistance has developed not only to vancomycin but also to other clinically used agents, such as daptomycin and linezolid. We propose a novel drug design approach merging tedizolid, a second-generation oxazolidinone used as an unapproved salvage therapy in clinical settings, with carbonic anhydrase inhibitors (CAIs) recently validated as functioning decolonization agents. These sulfonamide derivatives showed potent inhibition of the carbonic anhydrases from Enterococcus faecium, with KI values in the range of 14.6-598 nM and 63.2-798 nM against EfCAα and EfCAγ. Computational simulations elucidated the binding mode of these dual-action antibiotics to the peptidyl transferase center (PTC) of the 50S ribosome subunit and bacterial CAs. A subset of six derivatives showed potent PTC-related anti-enterococcal effects against multidrug-resistant E. faecalis and E. faecium strains with some compounds outperforming both the oxazolidinone and CA inhibitor drugs (MIC values in the range 1-4 μg/mL).

2-(Phenylamino)-7,8-dihydroquinazolin-5(6H)-one, a promising scaffold for MAO-B inhibitors with potential GSK3β targeting

Neurodegenerative disorders, such as Parkinson's disease and Alzheimer's disease, constitute pathological conditions of great relevance on health span and quality of life. The identification of novel therapeutic options, able to modulate the processes involved in the insurgence and progression of neurodegenerative disorders, represents an intriguing challenge of current research. Herein, a library of 36-membered 2-(phenylamino)-7,8-dihydroquinazolinone derivatives was synthesized and biologically evaluated as human MAO inhibitors. Some compounds able to inhibit MAO-B potently and selectively (Ki in the nanomolar range) were identified, and robust structure-activity relationships were drawn, supported by computational studies. Further biological assays revealed a safe profile for all derivatives and, for compounds selected as the best MAO-B inhibitors (4, 5, 13, 14) the following properties also emerged: (i) the ability to inhibit MAO-B activity in whole cells, with an effectiveness comparable or slight lower with respect to the reference safinamide; (ii) physicochemical parameters suggesting drug-likeness properties; (iii) the ability to inhibit, albeit weakly, GSK3β kinase (for compound 4). Within the whole series, compound 4 stood out as a promising lead for future optimization campaigns aimed to obtain useful drugs for the treatment of Alzheimer's and Parkinson's diseases.

A deep learning model for structure-based bioactivity optimization and its application in the bioactivity optimization of a SARS-CoV-2 main protease inhibitor

Bioactivity optimization is a crucial and technical task in the early stages of drug discovery, traditionally carried out through iterative substituent optimization, a process that is often both time-consuming and expensive. To address this challenge, we present Pocket-StrMod, a deep-learning model tailored for structure-based bioactivity optimization. Pocket-StrMod employs an autoregressive flow-based architecture, optimizing molecules within a specific protein binding pocket while explicitly incorporating chemical expertise. It synchronously optimizes all substituents by generating atoms and covalent bonds at designated sites within a molecular scaffold nestled inside a protein pocket. We applied this model to optimize the bioactivity of Hit1, an inhibitor of the SARS-CoV-2 main protease (Mpro) with initially poor bioactivity (IC50 : 34.56 μM). Following two rounds of optimization, six compounds were selected for synthesis and bioactivity testing. This led to the discovery of C5, a potent compound with an IC50 value of 33.6 nM, marking a remarkable 1028-fold improvement over Hit1. Furthermore, C5 demonstrated promising in vitro antiviral activity against SARS-CoV-2. Collectively, these findings underscore the great potential of deep learning in facilitating rapid and cost-effective bioactivity optimization in the early phases of drug development.

Structure based prediction of selective MraY inhibitors

Antibiotic resistance is becoming a growing concern of public health and hence there is an increasing demand for developing better antibiotic strategies. One such strategy includes targeting the bacterial cell wall, thereby killing the bacteria. A bacterial transmembrane enzyme MraY (Phospho-N-acetylmuramoyl-pentapeptide translocase), is considered to be a promising target for developing new antibiotics since it is involved in cell wall synthesis. Tunicamycin is an antibiotic known to inhibit the function of MraY. However, it shows cross-reactivity with the structurally homologous human enzyme hGPT (GlcNAc-1-P-transferase), which therefore calls for antibiotics with MraY selectivity. In the present computational work, we identified selective MraY inhibitors, where virtual screening of 45,411 compounds was carried out, followed by molecular dynamics simulations to check the stability of key inhibitory interactions across MraY and hGPT. From five shortlisted tentative inhibitors, comparative structural interaction analysis for both MraY and hGPT suggested three compounds as potential selective MraY inhibitors.

Gardenin A alleviates alcohol-induced oxidative stress and inflammation in HepG2 and Caco2 cells via AMPK/Nrf2 pathway

Chronic alcohol consumption triggers immune responses that lead to cell damage, contributing to alcohol-associated liver disease (ALD). Despite its prevalence, no FDA-approved treatment for ALD currently exists. This study explores the cytoprotective effects of Gardenin A (GarA), a polymethoxylated flavone, for protection against alcohol-induced oxidative stress and inflammation in HepG2 and Caco2 cell lines. GarA was isolated, characterized and, tested in-vitro, showing maximum cell viability at 10 μg/ml using MTT assays. Further, lipid accumulation assay, reactive oxygen species (ROS) estimation and nuclear morphology visualization was carried out using different staining techniques. RT-qPCR was employed to examine the expression of various pro- and anti-inflammatory cytokines, along with Cytochrome P4502E1 (CYP2E1) and Sterol regulatory element binding protein-2 (SREBP2) and tight junction genes crucial for gut barrier integrity. Moreover, ELISA was carried out for key protein targets such as AMPK (phosphorylated and total), TNFα, C5aR1, HO-1 and Nrf2. GarA caused a marked decrease in lipid droplets, ROS levels, and expression of pro-inflammatory cytokines. It showed anti-inflammatory and anti-oxidant activity and helped maintain the gut barrier and nuclear integrity. In-silico studies showed the conserved amino acid interaction and affinity of GarA with C5aR1, and TNFα, compared to the interactions with known inhibitors/activators, further corroborating the results. This study is the first to explore the effects of GarA on ALD, underscoring its potential as an anti-inflammatory and anti-oxidant agent targeting the AMPK/Nrf2 signaling pathway, suggesting its future as a promising therapeutic candidate for mitigating alcohol-induced liver and gut damage.

Design, synthesis, and evaluation of 1,4-benzodioxane-hydrazone derivatives as potential therapeutics for skin cancer: In silico, in vitro, and in vivo studies

In the pursuit of novel chemotherapeutic agents for skin cancer, we synthesized a series of 1,4-benzodioxane-hydrazone derivatives (7a-l) using the Wolff-Kishner reaction. These compounds were initially screened against the NCI-60 oncological cell lines in a one-dose assay at 10 μM. Among them, compound 7e emerged as a potent inhibitor of cancer cell growth across 56 cell lines, with an average GI50 of 6.92 μM. Notably, it exhibited enhanced efficacy in melanoma cell lines, including MDA-MB-435, M14, SK-MEL-2, and UACC-62, with GI50 values of 0.20, 0.46, 0.57, and 0.27 μM, respectively. Apoptosis assay and cell cycle analysis studies revealed that compound 7e induced apoptosis and caused S-phase arrest in MDA-MB-435 cells. Furthermore, an in vitro enzyme inhibition assay against mTOR kinase yielded an IC50 of 5.47 μM, while molecular docking studies of compound 7e (docking score: -8.105 kcal/mol) supported its binding affinity. Compound 7e adhered to Lipinski's rule of five and displayed favourable ADMET properties. In vivo studies demonstrated its safety and efficacy in ameliorating skin cancer in a mice model when administered intraperitoneally at 20 mg/kg. Structure-activity relationships were established through in vitro, in vivo, molecular docking, and molecular dynamics analysis. Collectively, these findings highlight 1,4-benzodioxane-hydrazone derivatives as promising scaffold for the development of novel chemotherapeutic agents for skin cancer.

Biostability, in vivo antiviral activity against respiratory syncytial virus, and pharmacokinetic profiles of (-)-borneol esters

Respiratory syncytial virus (RSV) is a leading cause of severe lower respiratory tract infections, particularly in vulnerable populations such as infants and the elderly. In this study, we evaluated the metabolic stability, in vivo antiviral activity, and pharmacokinetic profiles of (-)-borneol esters, which were identified as potent RSV inhibitors through screening of a compound library. Two hit compounds, ST-2 and AS-645, caused a reduction in viral titers in RSV-infected mice. Intranasal administration of ST-2 proved more effective than oral one and showed enhanced antiviral activity and improved pharmacokinetic properties. Additionally, ST-2 manifested superior metabolic stability in human blood compared to murine and rat blood, suggesting that carboxylesterase activity is a key factor in the hydrolysis resistance. Given that carboxylesterase activity is higher in mouse blood than in human blood, this difference likely contributes to the observed stability of ST-2 in human blood. Molecular modeling confirmed the role of carboxylesterase in the hydrolysis of (-)-borneol esters. These findings suggest that ST-2 has potential for further development of drugs for RSV and other viral infections.

Unravelling soluble (pro)renin receptor-mediated endothelial dysfunction

BACKGROUND

Preeclampsia is characterized by maternal endothelial dysfunction and new-onset hypertension. Preeclamptic pregnancies have elevated levels of maternal soluble prorenin receptor (s(P)RR) and previous studies have shown that recombinant s(P)RR produces hypertension and vascular dysfunction. This study aimed to investigate the effects of PRO20, an s(P)RR antagonist, on s(P)RR-induced endothelial dysfunction and its interaction with the Angiotensin II Type 1 Receptor (AT1R).

METHODS

Human uterine microvascular endothelial cells (HUtMECs) were treated with 100 nM s(P)RR, with/without 10 nM PRO20, 10 μM Losartan (AT1R antagonist), or 10 μM Aliskerin (renin inhibitor). The ability of PRO20 to prevent endothelial dysfunction induced by patient serum from preeclamptic pregnancies was also assessed. Endothelial dysfunction markers were measured using immunoblot, qPCR, and ELISA. For AT1R mechanism studies, HUtMECs were treated with control or AT1R siRNA before s(P)RR exposure. AT1R and s(P)RR protein structures were predicted via AlphaFold-2 and docking examined using Schrödinger.

RESULTS

PRO20 mitigated s(P)RR-induced increases in the mRNA expression of endothelial dysfunction markers, endothelin-1, VCAM-1 and ICAM-1 and prevented s(P)RR and preeclamptic serum-induced increases in endothelin-1 and VCAM-1 protein. Aliskerin had no effect on s(P)RR-induced endothelial dysfunction. Losartan and an AT1R siRNA were able to prevent s(P)RR induced increases in VCAM-1 protein levels and ET-1 mRNA expression, respectively. Modelling suggested that PRO20 can impair s(P)RR-AT1R complex formation.

CONCLUSIONS

Elevated s(P)RR induces endothelial dysfunction at least partially through AT1R. PRO20 prevents s(P)RR-AT1R formation, suggesting it could be an effective therapeutic for preeclampsia and conditions requiring renin-angiotensin system suppression.

Structure-activity relationship study of navarixin analogues as dual CXCR2 and CCR7 antagonists

Despite the promise of the human chemokine receptor 7 (CCR7) as drug target for the treatment of cancer metastasis and autoimmune diseases, there are no potent and selective CCR7 antagonists known in literature. In this work, a 1,2,5-thiadiazole 1,1-dioxide with low μM activity as a CXCR2 and CCR7 antagonist was selected as starting point for a structure-activity relationship study. The replacement of the central thiadiazole dioxide motif with squaramide led to low nanomolar CCR7 antagonism. Additional systematic structural variations afforded various squaramide analogues that displayed potent CCR7 antagonism in a calcium mobilization assay with IC50 values in the low nM range. Unfortunately, the same compounds also displayed potent CXCR2 antagonistic activity and should therefore be considered as dual CCR7/CXCR2 antagonists.

Macleaya cordata protopine total alkaloids as potential treatment for diarrhoea: Mechanistic insights and target identification

Diarrhoea remains a major public health concern, particularly affecting young children and livestock. Macleaya cordata protopine total alkaloids (MPTA), a standardized extract approved in China for poultry diarrhoea, has demonstrated anti-inflammatory properties in intestinal disorders. The study aims to investigate the antidiarrheal mechanism of MPTA using castor oil- and E. coli-induced diarrhoea models in mice. We first tested MPTA for acute oral toxicity. Subsequently, the effect of MPTA on castor oil- and E. coli-induced diarrhoea in mice based on LD50 results. Network pharmacology analysis and target competition assays (inhibitors and antagonists) were integrated to identify targets for MPTA's antidiarrheal effects. Molecular docking was used to verify the binding ability of MPTA components to these receptors. The LD50 of MPTA was determined to be 426.1 mg/kg. The optimal MPTA activity was found at 8 mg/kg in both castor oil and in infectious models. Network pharmacology analysis revealed potential targets and pathways of MPTA against intestinal motility. The impact of MPTA on cholinergic, serotonin, dopaminergic, and adrenergic receptors was assessed using standard inhibitors and agonists to induce intestinal smooth muscle contractions or relaxations. Molecular docking confirmed the binding ability of MPTA components to these receptors. In conclusion, MPTA exhibits significant antidiarrheal effects in both castor oil and E. coli-induced diarrhoea models. Its mechanism may involve modulation of cholinergic, serotonin, dopaminergic, and adrenergic receptors, as well as inhibition of ion channels and anti-inflammatory actions. These findings highlight the potential of MPTA as a novel therapeutic agent for diarrhoea.

Activation of steroid hormone receptors by metabolism-disrupting chemicals

Exposure to metabolism-disrupting chemicals (MDCs), compounds largely belonging to the group of endocrine-disrupting chemicals (EDCs), is associated with metabolic dysfunctions such as dyslipidemia, insulin resistance and hepatic steatosis. Steroid hormone receptors (SHRs) are known targets for MDCs but their regulatory environment in the presence of environmental chemicals remains elusive. Here, we studied the activation and molecular interactions of SHRs exposed to 17 suspected MDCs including pesticides, plasticizers, pharmaceuticals, flame retardants, industrial chemicals and their metabolites by combining in vitro and in silico approaches. We first established and pre-validated reporter gene assays in HepG2 hepatoma cells to assess the activation of estrogen (ER), androgen (AR), glucocorticoid (GR) and progesterone (PR) receptors. Next, using RNA-seq and publicly available protein interaction data, we identified relevant SHR-interacting coregulators expressed in hepatic cells and measured their MDC-dependent interactions with SHRs using the Microarray Assay for Real-time Coregulator-Nuclear receptor Interaction (MARCoNI) technology. Finally, we examined MDC binding to ER and GR using molecular dynamics simulations. These combined approaches lead to identification of MDCs capable of SHR activation at picomolar-to-low micromolar concentrations and paralleled with their ability to induce recruitment of multiple coregulators. MDCs induced distinct SHR-coregulator binding patterns involving multiple coactivators, corepressors and other modulatory proteins. Our results have broadened the test battery to detect MDCs and indicate that the activation of SHRs by MDCs is driven by diverse molecular interactions.

Noscapine derivative 428 suppresses ferroptosis through targeting GPX4

Inhibiting ferroptosis represents a promising strategy to combat ferroptosis-related diseases. Here we show that 428, a selenide-containing noscapine derivative, effectively inhibits ferroptosis in various cell lines by enhancing the stability and activity of GPX4. TRIM41 was identified as a novel E3 ubiquitin ligase of GPX4 and 428 was demonstrated to bind to the selenocysteine residue Sec46 of GPX4 via the formation of a transient and reversible Se-Se bond, thereby blocking the interaction between GPX4 and TRIM41, stabilizing GPX4 and enhancing its activity. This unique dynamic covalent binding mode was preliminarily validated by structure-activity relationship analysis and molecular docking studies. Importantly, we demonstrated that 428 treatment alleviates bleomycin-induced pulmonary fibrosis in vivo by inhibiting ferroptosis. Overall, our studies identified a novel stabilizer and activator of GPX4, offering a potential therapeutic approach for the treatment of ferroptosis-related diseases and uncovering a new mechanism for regulating GPX4 degradation.

Design and synthesis of pyridopyrimidines targeting NEK6 kinase

We designed a series of pyrido[2,3-d]pyrimidine derivatives based on the structure of the NEK6 kinase inhibitor, compound 21 (2-amino-5-phenyl-5,11-dihydro-3H-indeno[2',1':5,6]pyrido[2,3-d]pyrimidine-4,6-dione), which share the same heterocyclic core. Chemical modifications, aimed at altering the molecular planarity of 21 to enhance water solubility, were guided by receptor-based ligand design and further supported by molecular docking, molecular dynamics simulations, and free energy perturbation calculations. Our results indicate that disrupting the planarity of 21 increases aqueous solubility - nearly doubling it in two cases- while reducing lipophilicity. Among the compounds tested, three showed both improved solubility and NEK6 inhibitory activity exceeding 50 % in single-dose assay.

Drosera rotundifolia L. as E. coli biofilm inhibitor: Insights into the mechanism of action using proteomics/metabolomics and toxicity studies

The successful sustainable cultivation of the well-known medicinal plant sundew on rewetted peatlands not only leads to the preservation of natural populations, but also provides a basis for the sustainable pharmaceutical use of the plant. The bioactive compounds of sundew, flavonoids and naphthoquinones, show biofilm-inhibiting properties against multidrug-resistant, ESBL-producing E. coli strains and open up new therapeutic possibilities. This study investigates the molecular mechanisms of these compounds in biofilm inhibition through proteomic analyses. Specific fractions of flavonoids and naphthoquinones, as well as individual substances like 7-methyljuglone and 2″-O-galloylhyperoside, are analyzed. Results show that naphthoquinones appear to act via central regulatory proteins such as OmpR and alter the stress response while flavonoids likely affect biofilm formation by creating an iron-poor environment through iron complexation and additionally influence polyamine balance, reducing intracellular spermidine levels. Further investigations including assays for iron complexation and analysis of polyamines confirmed the proteomic data. Safety evaluations through cytotoxicity tests in 3D cell cultures and the Galleria mellonella in vivo model confirm the safety of the extracts used. These findings highlight sundew as a promising candidate for new phytopharmaceuticals.

Computational discovery of novel PI3KC2α inhibitors using structure-based pharmacophore modeling, machine learning and molecular dynamic simulation

PI3KC2α is a lipid kinase associated with cancer metastasis and thrombosis. In this study, we present a novel computational workflow integrating structure-based pharmacophore modeling, machine learning (ML), and molecular dynamics (MD) simulations to discover new PI3KC2α inhibitors. Key innovations include the generation of diverse pharmacophores from both crystallographic and docking-derived complexes, coupled with data augmentation via ligand conformational sampling to enhance ML robustness. The optimal model, developed using XGBoost with genetic function algorithm (GFA) and Shapley additive explanations (SHAP), identified four critical pharmacophores and three descriptors governing bioactivity. Virtual screening of the NCI database using these pharmacophores yielded three hits, with H_1 (NCI: 725847) demonstrating MD-derived binding stability and affinity comparable to the potent inhibitor PITCOIN1 (IC50 = 95 nM). This study represents the first application of a conformation-augmented ML framework to PI3KC2α inhibition, offering a blueprint for targeting underexplored kinases with limited structural data.

HCK regulates NLRP12-mediated PANoptosis

NOD-like receptors (NLRs) are a highly conserved family of cytosolic pattern recognition receptors that drive innate immune responses against pathogens, pathogen-associated molecular patterns, damage-associated molecular patterns, and homeostatic disruptions. Within the NLR family, NLRP12 was recently identified as a key regulator of PANoptosis, which is an innate immune, lytic cell death pathway initiated by innate immune sensors and driven by caspases and RIPKs through PANoptosome complexes. While NLRP12 activation is critical for maintaining homeostasis, aberrant activation has been implicated in a broad range of disorders, including cancers and metabolic, infectious, autoinflammatory, and hemolytic diseases. However, the molecular mechanisms of NLRP12 activation remain poorly understood. Here, we identified hematopoietic cell kinase (HCK) as a regulator of NLRP12-mediated PANoptosis. HCK expression was significantly upregulated in response to NLRP12-PANoptosome triggers. Moreover, Hck knockdown inhibited NLRP12-mediated PANoptosis. Computational analyses identified residues in the putative interaction interface between NLRP12 and HCK, suggesting that HCK likely binds NLRP12 in the region between its NACHT domain and pyrin domain (PYD); removal of the NLRP12 PYD abrogated this interaction in vitro. Overall, our work identifies HCK as a regulator of NLRP12-mediated PANoptosis, suggesting that it may serve as a potential therapeutic target for mitigating inflammation and pathology.

Hydrophobicity-Controlled Self-Assembly of Supramolecular Peptide Nanotubes in Water

Polymer-conjugated peptides are attractive building blocks for the construction of new nanomaterials. However, the ability to control the self-assembly of these materials remains a major limitation to their wider utilization. Herein, we report a facile strategy to fine-tune the assembly of water-soluble hydrophilic polymer-conjugated cyclic peptides by incorporating a defined, short hydrocarbon linker between the polymer and peptide. This addition creates a well-defined hydrophobic "inner shell" that suppresses water from disrupting the organized peptide hydrogen bond network. Our approach is demonstrated using a series of cyclic peptide-linker-PDMA conjugates that were evaluated by asymmetric flow field flow fractionation, small angle neutron scattering and transmission electron microscopy. Molecular dynamics simulations were also used to show how the polymer and the peptide stacks interact and illustrate the impact of this hydrophobic inner shell approach. This strategy provides a modular approach to fine control the nanotube self-assembling behavior. We expect that this technique will improve the versatility of peptide nanotubes for the engineering of advanced nanomaterials.

Integrating Machine Learning-Based Pose Sampling with Established Scoring Functions for Virtual Screening

Physics-based docking methods have long been the cornerstone of structure-based virtual screening (VS). However, the emergence of machine learning (ML)-based docking approaches has opened new possibilities for enhancing VS technologies. In this study, we explore the integration of DiffDock-L, a leading ML-based pose sampling method, into VS workflows by combining it with the Vina, Gnina, and RTMScore scoring functions. We assess this integrated approach in terms of its VS effectiveness, pose sampling quality, and complementarity to traditional physics-based docking methods, such as AutoDock Vina. Our findings from the DUDE-Z benchmark dataset show that DiffDock-L performs competitively in both VS performance and pose sampling in cross-docking settings. In most cases, it generates physically plausible and biologically relevant poses, establishing itself as a viable alternative to physics-based docking algorithms. Additionally, we found that the choice of scoring function significantly influences VS success.

An mRNA-display derived cyclic peptide scaffold reveals the substrate binding interactions of an N-terminal cysteine oxidase

N-terminal cysteine oxidases (NCOs) act as enzymatic oxygen (O2) sensors, coordinating cellular changes to hypoxia in animals and plants. They regulate the O2-dependent stability of proteins bearing an N-terminal cysteine residue through the N-degron pathway. Despite their important role in hypoxic adaptation, which renders them potential therapeutic and agrichemical targets, structural information on NCO substrate binding remains elusive. To overcome this challenge, we employed a unique strategy by which a cyclic peptide inhibitor of the mammalian NCO, 2-aminoethanethiol dioxygenase (ADO), was identified by mRNA display and used as a scaffold to graft substrate moieties. This allowed the determination of two substrate analogue-bound crystal structures of ADO. Key binding interactions were revealed, including bidentate coordination of the N-terminal residue at the metal cofactor. Subsequent structure guided mutagenesis identified aspartate-206 as an essential catalytic residue, playing a role in reactive oxygen intermediate orientation or stabilisation. These findings provide fundamental information on ADO substrate interactions, which can elucidate enzyme mechanism and act as a platform for chemical discovery.

Ursane hybrids with 5-amino-1,2,3,4-thiatriazole, 1-tetrazole-5-thione, and 1-tetrazole-5-amines and study of their inhibition of main SARS-CoV-2 protease

A series of new heterocyclic ursane and 28-norursane hybrids - derivatives of 5-amino-1,2,3,4-thiatriazole, 1-tetrazole-5-thione, and 1-tetrazole-5-amines were prepared. Reacting triterpenoids holding NCS groups at different distances from the pentacyclic backbone with hydrazine hydrate resulted in ursane-derived hydrazinecarbothioamides. Subsequent nitrosation afforded terpenoid derivatives of 5-amino-1,2,3,4-thiatriazole. Heterocyclization of amino-thioureas with 3β-acetoxyurs-12-en-28-yl substituent under the action of Hg(OAc)2-NaN3 led to hybrids of 1-tetrazole-5-amines. 1-Tetrazole-5-thiones with different positions of heterocycle relative to the triterpene skeleton were prepared by coupling sodium azide with triterpene isothiocyanates. The activity of the new heterocyclic derivatives as inhibitors of 3CLpro of SARS-CoV-2 was investigated. Remarkable inhibition was observed for the 1-tetrazole-5-thione hybrids of triterpenoids. The highest activity among the studied compounds was provided by the combination of a 1-tetrazole-5-thione moiety at the C(28)H2 group of the ursane frame having a free OH group at the 3-position. Molecular docking assumed the covalent binding of 3CLpro via the formation of a disulfide bond between the thiol groups of the catalytic Cys145 and the tetrazole heterocycle of the new hybrid compounds. The triterpenoid backbone provided multiple external hydrophobic contacts essential for the stability of the complex. The results demonstrate the potential of heterocyclic thione hybrids as non-peptidomimetic covalent inhibitors targeting 3CLpro protease (3-Chymotrypsin-like Protease).

Biochemical investigation of pathogenic missense mutations of human 4-amino butyrate aminotransferase towards the understanding of the molecular pathogenesis of GABA transaminase deficiency

Gamma-amino butyrate aminotransferase (GABA-AT or ABAT) is a pyridoxal 5'-phosphate (PLP)-dependent enzyme that catalyzes the conversion of GABA and α-ketoglutarate into succinic semialdehyde and L-glutamate. In humans, the primary physiological role of GABA-AT is to control the level of GABA in neuronal tissues. Mutations on ABAT gene are associated to GABA-AT deficiency, an ultra-rare autosomal recessive disorder characterized by accelerated linear growth, severe psychomotor retardation, seizures, hypotonia, and hyperreflexia. So far, several missense pathogenic mutations of GABA-AT have been identified; however, their molecular effects at protein level have been poorly investigated. In this work a biochemical characterization of 10 pathogenic variants of human GABA-AT was carried out by expressing the protein in HEK-293 cells. Moreover, in-silico analyses of the variants were performed to corroborate the experimental findings. Altogether, the data obtained on protein expression level, GABA transaminase activity, and the predicted structural impact allowed us to classify the variants into three distinct groups, such as: (i) variants with strong structural and catalytic defects (p.P152S, p.L211F, and p.L478P); (ii) variants characterized mainly by a strong catalytic defect (p.R220K, p.Q296H, and p.R377W); (iii) variants exhibiting moderate structural and catalytic defects maintaining substantial transaminase activity (p.R92Q, p.F213C, p.G465D, and p.G465R). Based on these results, we provide a picture of the molecular defects of different GABA-AT pathogenic variants with the aim of gaining insights into the enzymatic phenotypes in GABA-AT deficiency.

Structure-Binding Relationship of 2-Amino-1,8-Naphthyridine Dimers: Role of Linkage Positions on DNA and RNA Recognition

The study explores the synthesis, structural analysis, and binding properties of eight analogs of 2-amino-1,8-naphthyridine dimers (ANPxys) targeting DNA and RNA. These dimers, derived from ANP77, are connected at varying positions to investigate how positional alterations influence molecular conformations and their interactions with nucleic acids. The primary focus lies on evaluating the effects of these structural variations on DNA and RNA binding through fluorescence quenching and thermal denaturation assays. Absorption and fluorescence measurements revealed distinct electronic states for ANPxys, with emission maxima between 389.5 and 398.5 nm. Conformational analysis indicated that most ANPxys adopt unstacked conformations in aqueous solutions, though some, like ANP47 and ANP67, showed higher probabilities of stacked conformations. Thermal denaturation studies demonstrated ANPxys bind and stabilize cytosine-rich DNA motifs with varying affinities, with ANP77 showing the strongest effects. RNA binding studies targeting U/CC motifs across 256 sequences revealed unique fluorescence quenching patterns for each ANPxy, reflecting sequence specificity. Hierarchical clustering grouped ANPxys into parallel-stacked and twisted-stacked clusters, correlating their conformations with binding preferences. This work highlights the critical role of connection positions in determining ANPxy binding specificity and conformational behavior. The findings provide a basis for designing small molecules with tunable structures and enhanced RNA-binding capabilities, paving the way for the development of RNA-targeted therapeutics.

Functional enzyme delivery via surface-modified mesoporous silica nanoparticles in 3D printed nanocomposite hydrogels

Three-dimensional (3D) printed hydrogel-based scaffolds have emerged as promising for the delivery of biologicals. Recently, we developed a printable plant-based nanocomposite hydrogel, composed of anionic cellulose nanofibers (T-CNF) and methacrylated galactoglucomannan (GGMMA), reinforced with mesoporous silica nanoparticles (MSNs) of different surface charges. However, ensuring the biological activity of the delivered biomolecules requires further investigation to validate the functionality of the developed biomaterial. To investigate this, in this study, horseradish peroxidase (HRP) and lysozyme were selected as distinct model proteins, assessing their immobilization stability and biological activity after MSN immobilization and 3D printing. The interactions between the enzymes and differently surface-modified MSNs were explored using multi-parametric surface plasmon resonance (MP-SPR) and molecular dynamics (MD) simulations. We observed that MSN surface charge is key to the extent of enzyme adsorption and activity control. Positively charged MSNs showed the highest HRP immobilization but caused significant activity loss in both enzymes. In contrast, near-neutral and negatively charged MSNs provided improved stability and activity retention for HRP and lysozyme, respectively. Except for lysozyme/hydrogel, HRP/hydrogel and enzyme-loaded nanocomposite hydrogels (HRP-loaded near-neutral and lysozyme-loaded negatively charged MSNs) were successfully 3D printed using different UV post-curing times. While enzyme-laden nanocomposite scaffolds showed promising immobilization stability, the presence of the photoinitiator caused significant inactivation for both enzymes. Irrespective of the crosslinking approach, this matrix demonstrates significant potential as a delivery carrier for various biomolecules, with promising applications in tissue engineering and wound healing.

Identification of naturally occurring drug-resistant mutations of SARS-CoV-2 papain-like protease

The SARS-CoV-2 papain-like protease (PLpro) is a cysteine protease that cleaves viral polyproteins and antagonizes the host immune response during viral replication. Jun12682 and PF-07957472 are the first-in-class PLpro inhibitors showing potent in vivo antiviral efficacy in mouse models. In this study, we characterize naturally occurring mutations at residues located at the drug-binding site of Jun12682. The results reveal several PLpro mutants showing significant drug resistance while maintaining comparable enzymatic activity as the wild-type PLpro. The physiological relevance of the identified drug-resistant mutants, including E167G and Q269H, is validated through independent serial viral passage experiments. Molecular dynamics simulations and perturbative free energy calculations show that drug-resistant PLpro mutants weaken hydrogen bonding and π-π stacking interactions. Collectively, this study identifies E167, Y268, and Q269 as drug-resistant hotspots for PLpro inhibitors that bind to the BL2 loop and groove region, which are valuable in informing the design of the next-generation PLpro inhibitors.

Therapeutic potential of allosteric HECT E3 ligase inhibition

Targeting ubiquitin E3 ligases is therapeutically attractive; however, the absence of an active-site pocket impedes computational approaches for identifying inhibitors. In a large, unbiased biochemical screen, we discover inhibitors that bind a cryptic cavity distant from the catalytic cysteine of the homologous to E6-associated protein C terminus domain (HECT) E3 ligase, SMAD ubiquitin regulatory factor 1 (SMURF1). Structural and biochemical analyses and engineered escape mutants revealed that these inhibitors restrict an essential catalytic motion by extending an α helix over a conserved glycine hinge. SMURF1 levels are increased in pulmonary arterial hypertension (PAH), a disease caused by mutation of bone morphogenetic protein receptor-2 (BMPR2). We demonstrated that SMURF1 inhibition prevented BMPR2 ubiquitylation, normalized bone morphogenetic protein (BMP) signaling, restored pulmonary vascular cell homeostasis, and reversed pathology in established experimental PAH. Leveraging this deep mechanistic understanding, we undertook an in silico machine-learning-based screen to identify inhibitors of the prototypic HECT E6AP and confirmed glycine-hinge-dependent allosteric activity in vitro. Inhibiting HECTs and other glycine-hinge proteins opens a new druggable space.

Physicochemical Characterization of Kynurenine Pathway Metabolites

The kynurenine pathway is a significant metabolic route involved in the catabolism of tryptophan, producing various bioactive metabolites with crucial roles as antioxidants in immune regulation and neurobiology. This study investigates the acid-base properties of picolinic acid, kynurenic acid, kynurenine, and 3-hydroxykynurenine, utilizing computational simulations and experimental techniques, including potentiometric and nuclear magnetic resonance titrations. The results reveal distinct pKa values, with kynurenic acid exhibiting a single dissociation step around 2.4, while kynurenine displays three dissociation steps governed by interactions between its functional groups. Additionally, 3-hydroxykynurenine shows overlapping dissociations in two separate pH regions, suggesting nuanced behavior influenced by its molecular structure. The analysis of intramolecular hydrogen bonding in protonation microspecies across varying pH highlights the relevance of the charge state and hydrogen transfer potential of these metabolites in the context of their radical scavenging ability. At physiological pH, most kynurenine and 3-hydroxykynurenine entities exist in zwitterionic form, with hydrogen bonding stabilizing the aromatic amino group, which may significantly influence their interactions with proteins and reactive oxygen species. This study provides critical insights into the acid-base equilibria of kynurenine pathway metabolites.

Organic Cage Rotaxanes

Organic cages are a robust class of molecular hosts with a myriad of applications in materials science. Despite this, there has been a paucity of explorations into the modification of their properties via external functionalization. In this work, [n]rotaxanes featuring unoccupied organic cages as stopper components and a small 2,2'-bipyridine macrocycle were constructed using the active metal template (AMT) approach. By exploiting a scrambling methodology, it was possible to synthesize cages with a defined number of interlocked components (n = 2-4). The gas uptake, solubility, and thermal properties of the interlocked systems were compared against those of their constituent, non-interlocked components. In this manner, we were able to demonstrate the potential of exploiting the mechanical bond for modulating the physiochemical properties of these molecular materials.

Design, optimization, and ADMET evaluation of S11a-0000168202: A promising LIMK1 inhibitor for gastric cancer treatment

This study focuses on the development and optimization of S11a-0000168202, a novel LIMK1 inhibitor with potential therapeutic applications in gastric cancer. Through scaffold hopping and structural modification of HIT100844099, S11a-0000168202 demonstrated enhanced binding stability and stronger interactions with key LIMK1 residues, including GLU-414, ILE-416, and HIS-464. Molecular dynamics simulations and MMGBSA analyses confirmed the compound's stability, while ADMET evaluation revealed favorable properties such as moderate lipophilicity, good human intestinal absorption, and low P-glycoprotein inhibition. Despite the promising computational results, the lack of experimental validation remains a limitation. Future studies should focus on in vitro and in vivo testing to confirm S11a-0000168202's efficacy, pharmacokinetics, and safety. This compound holds significant potential as a therapeutic agent for LIMK1-targeted gastric cancer treatment.

Comprehensive immunoinformatics and bioinformatics strategies for designing a multi-epitope based vaccine targeting structural proteins of Nipah virus

Background

Nipah virus (NiV) is characterized by recurring outbreaks and causes severe neurological impact, leading to increased mortality rates. Despite the severity of the disease, there is no proven post-exposure treatment available, emphasizing the critical need for the development of an effective vaccine.

Objective

This study was aimed at designing a multi-epitope based vaccine candidate based on an in-silico approach.

Methods

NiV's Structural proteins were screened for B and T-cell epitopes, assessing characteristics like antigenicity, immunogenicity, allergenicity, and toxicity. Two vaccine constructs (NiV_1 & 2) were designed using different adjuvants (Cholera toxin and Beta-defensin 3) and linkers and their predicted 3D structures were evaluated for interaction with Toll-Like Receptor TLR-3 using docking and molecular dynamics (MD) simulation studies. Finally, The potential expression of the vaccine construct in Escherichia coli (E. coli.) was verified by cloning it into the PET28a (+) vector and immune simulations were undertaken.

Results

The study identified 30 conserved, antigenic, immunogenic, non-allergenic, and non-toxic epitopes with a broad population coverage. Based on the stability of vaccine construct in MD simulations results, NiV_1 was considered for further analysis. In-silico immune simulations of NiV_1 indicated a substantial immunogenic response. Moreover, codon optimization and in-silico cloning validated the expressions of designed vaccine construct NiV_1 in E. coli.

Conclusion

The findings indicate that the NiV_1 vaccine construct has the potential to elicit both cellular and humoral immune responses. Additional in vitro and in vivo investigations are required to validate the computational observations.

Identification of druggable binding sites and small molecules as modulators of TMC1

Our ability to hear and maintain balance relies on the proper functioning of inner ear sensory hair cells, which translate mechanical stimuli into electrical signals via mechano-electrical transducer (MET) channels, composed of TMC1/2 proteins. However, the therapeutic use of ototoxic drugs, such as aminoglycosides and cisplatin, which can enter hair cells through MET channels, often leads to profound auditory and vestibular dysfunction. To date, our understanding of how small-molecule modulators interact with TMCs remains limited, hampering the discovery of novel drugs. Here, we propose a structure-based drug screening approach, integrating 3D-pharmacophore modeling, molecular dynamics simulations of the TMC1 + CIB2 + TMIE complex, and experimental validation. Our pipeline successfully identified three potential drug-binding sites within the TMC1 pore, phospholipids, and key amino acids involved in the binding of several compounds, as well as FDA-approved drugs that reduced dye uptake in cultured cochlear explants. Our pipeline offers a broad application for discovering modulators for mechanosensitive ion channels.

Synthesis and characterization of folate functionalized core-shell pluronic/chitosan nanoparticles against rheumatoid arthritis

Significant advances in novel drug delivery systems have led to the development of ligand-conjugated nanoparticles, enabling targeted delivery of therapeutic agents to disease-specific sites. A widely adopted approach for treating rheumatoid arthritis involves targeting folate receptors, which are overexpressed in inflamed tissues. This study focused on formulating methotrexate-loaded, folate-conjugated core-shell polymeric nanoparticles (PF/CS). These nanoparticles were synthesized using self-micellization and ionic gelation techniques, resulting in particles with an average size of 185.0 ± 2.08 nm, a PDI of <0.5, and a zeta potential of 19.9 ± 2.23 mV indicating excellent stability and uniformity. Ligand conjugation was confirmed using 1H Nuclear Magnetic Resonance Spectroscopy and Fourier Transformed Infrared Spectroscopy. Further physicochemical characterization, including Differential Scanning Calorimetry, Thermo-Gravimetric Analysis, and X-ray Diffraction analysis, demonstrated good compatibility and thermal stability. In vitro studies showed sustained drug release for up to 72 h and higher cytotoxicity against RAW 264.7 macrophage cells with folate-conjugated PF/CS nanoparticles compared to non-conjugated ones. Ex-vivo hemocompatibility testing confirmed their non-hemolytic nature. Acute toxicity studies indicated biocompatibility and safety. In vivo assessments in rats showed enhanced therapeutic effects with folate-conjugated nanoparticles. In silico modeling supported experimental findings. It is concluded that folate-conjugated PF/CS nanoparticles offer a promising platform for sustained methotrexate delivery in rheumatoid arthritis treatment.

A deep learning and molecular modeling approach to repurposing Cangrelor as a potential inhibitor of Nipah virus

Deforestation, urbanization, and climate change have significantly increased the risk of zoonotic diseases. Nipah virus (NiV) of Paramyxoviridae family and Henipavirus genus is transmitted by Pteropus bats. Climate-induced changes in bat migration patterns and food availability enhances the virus's adaptability, in turn increasing the potential for transmission and outbreak risk. NiV infection has high human fatality rate. With no antiviral drugs or vaccines available, exploring the complex machinery involved in viral RNA synthesis presents a promising target for therapy. Drug repurposing provides a fast-track approach by identifying existing drugs with potential to target NiV RNA-dependent RNA polymerase (L), bypassing the time-consuming process of developing novel compounds. To facilitate this, we developed an attention-based deep learning model that utilizes pharmacophore properties of the active sites and their binding efficacy with NiV L protein. Around 500 FDA-approved drugs were filtered and assessed for their ability to bind NiV L protein. Compared to the control Remdesivir, we identified Cangrelor, an antiplatelet drug for cardiovascular diseases, with stronger binding affinity to NiV L (glide score of -12.30 kcal/mol). Molecular dynamics simulations further revealed stable binding (RMSD of 3.54 Å) and a post-MD binding energy of -181.84 kcal/mol. The strong binding of Cangrelor is illustrated through trajectory analysis, principal component analysis, and solvent accessible surface area, further confirming the stable interaction with the active site of NiV RdRp. Cangrelor can interact with NiV L protein and may potentially interfere with its replication. These findings suggest that Cangrelor will be a potential drug candidate that can effectively interact with the NiV L protein and potentially disrupt the viral replication. Further in vivo studies are warranted to explore its potential as a repurposable antiviral drug.

Identification of Bacterial Oligopeptidase B Inhibitors from Microbial Natural Products: Molecular Insights, Docking Studies, MD Simulations, and ADMET Predictions

Background/Objectives: The increasing threat of antibiotic resistance and the declining efficiency of traditional drug discovery pipelines highlight the urgent need for novel drug targets and effective enzyme inhibitors against infectious diseases. Oligopeptidase B (OPB), a serine protease with trypsin-like specificity that processes low-molecular-weight peptides and oligopeptides, is present in bacteria and certain parasites but absent in mammals. This unique distribution makes OPB an attractive and selective target for antimicrobial drug development. Methods: Three-dimensional models of OPB from Serratia marcescens and Stenotrophomonas maltophilia, previously identified by our research group, were constructed via homology modeling using the best available OPB template from the RCSB Protein Data Bank. The S. marcescens OPB model was subjected to high-throughput virtual screening (HTVS) against the Natural Products Atlas (npatlas) database. Top-ranking compounds were further evaluated using Glide standard precision (SP) and extra precision (XP) docking protocols. Binding affinities were refined using molecular mechanics with generalized born and surface area (MM-GBSA) calculations. Molecular dynamics (MD) simulations assessed binding stability, while absorption distribution metabolism excretion and toxicity (ADMET) profiling evaluated drug-likeness and pharmacokinetic properties. Results: Ten natural product compounds demonstrated stronger binding affinities than antipain, a well-known oligopeptide-based protease inhibitor, as indicated by their more favorable MM-GBSA scores of -60.90 kcal/mol (S. marcescens) and -27.07 kcal/mol (S. maltophilia). Among these, dichrysobactin and validamycin E consistently exhibited favorable binding profiles across both OPB models. MD simulations confirmed the stability of their interactions with OPB active sites, maintaining favorable binding conformations throughout the simulation period. ADMET analysis suggested that while both compounds show promise, lead optimization is required to enhance their drug-like characteristics. Conclusions: This study identifies dichrysobactin and validamycin E as promising OPB inhibitors with potential antimicrobial activity. These findings support their further development as selective and potent agents against bacterial pathogens, including resistant strains, and underscore the need for experimental validation to confirm their efficacy and safety.

Comparative anti-oxidant and anti-inflammatory study of diverse honey types of Kashmir valley through In Vitro, analytical chemistry and computational approach

Diverse factors including geographical and floral origin have marked impact on honey parameters. These factors in the long run influence the different activities exerted by honey. Herein, we performed the novel comparative study of five different honey types of Kashmir valley differing in floral origin apart from latitude, longitude and altitude. Following the rigorous comparison of their antioxidant and anti-inflammatory activity through In vitro study, the most promising honey was screened for various molecules using high-resolution liquid chromatography mass spectrometry (HR-LCMS) approach. Moreover, the identified molecules were docked against the inflammation implicated molecular targets namely histone deacetylase (HDAC)-3 and cyclooxygenase-2 (COX-2). Eventually, the binding free energy assessment was performed using conventional and thermal molecular mechanics with generalized Born surface area (MM-GBSA). The maximum binding affinity demonstrating molecule was evaluated for stability and compatibility with COX-2 by making the use of extended molecular dynamics simulation method. This study proved Robinia pseudoacacia honey has the maximum potential for alleviating the free radicals and inflammation. Further, the luteolin and genistein confirmed through HR-LCMS evinced the highest propensity of binding towards COX-2 and HDAC3 respectively.

Efficient Small-Molecule Reversal Agents for Anticoagulant Fondaparinux

Fondaparinux is a highly anionic synthetic heparinoid pentasaccharide used as an anticoagulant for specific clinical conditions and surgeries. As a non-natural small-molecule drug, it presents pharmacokinetic and pharmacodynamic advantages, as well as high stability and low immunogenicity, when compared with different forms of heparin. However, its broader usage is hampered by different factors like price, existence of alternative anticoagulants, or, specifically in this case, the lack of an effective antidote that is highly recommendable for avoiding uncontrolled bleeding. In this work, we describe two synthetic small molecules derived from spermine (3AC and 3FF) that efficiently revert the anticoagulant activity of fondaparinux. In an in vitro enzymatic assay related to blood coagulation, the spermine derivatives show potent activity as fondaparinux antidotes, with higher activity than ciraparantag (a small molecule in the clinical phase as an anticoagulant antidote) and much higher activity than protamine, the only approved antidote for unfractioned heparin but inefficient against fondaparinux. Remarkably, naked-eye ex vivo tests demonstrated their efficacy in freshly extracted mice blood. Mechanistic studies show that both small molecules strongly bind fondaparinux in buffered water, as detected by fluorescence and NMR spectroscopy and confirmed by molecular dynamics simulations. Thus, these spermine derivatives are promising reversal agents against heparinoid anticoagulants with a wide range of molecular weights, overcoming the drawbacks of those antidotes based on biomacromolecules.

Discovery and Evaluation of Active Site-Directed, Potent, and Selective Sulfophenyl Acetic Amide-Based Inhibitors for the Laforin Phosphatase

Lafora disease is a rare and fatal progressive myoclonus epilepsy characterized by the accumulation of insoluble glycogen deposits in the brain and peripheral tissues. Mutations in the gene encoding the glycogen phosphatase laforin result in Lafora disease. Currently, there are no laforin-specific chemical probes, limiting our understanding of the roles of laforin in glycogen metabolism and other cellular processes. Here, we identified sulfophenyl acetic amide (SPAA), as a novel nonhydrolyzable phosphotyrosine mimetic for laforin inhibition. Using fragment-based and scaffold-hopping strategies, we discovered several highly potent and selective active site-directed laforin inhibitors. Among them, compound 9c displayed a Ki value of 1.9 ± 0.2 nM and more than 8300-fold preference for laforin. Moreover, these inhibitors efficiently block laforin-mediated glucan dephosphorylation inside the cell and possess favorable pharmacokinetic properties in mice. These chemical probes will enable further investigation of the roles of laforin in normal physiological processes and in diseases.

Dissecting oxidative folding of conotoxins using 3D structures of cysteine mutants predicted by AlphaFold 3: A case study of α-conotoxin RgIA, χ-conotoxin CMrVIA and ω-conotoxin MVIIA-Gly

The ability of AlphaFold 3 to accurately predict the 3D structure of polypeptides has been explored to investigate the oxidative folding steps of conotoxins. The peptides α-conotoxin RgIA (α-RgIA) and χ-conotoxin CMrVIA (χ-CMrVIA) share a similar cysteine pattern but differ in their native disulfide connectivity. These short peptides, containing two intramolecular disulfides, may undergo sequential steps of disulfide formation during the oxidative folding process. The current report computed all six possible single disulfide alanine mutants of the peptides and predicted their 3D structures using the AlphaFold 3 server. The potential energy of the conformers derived from the five predicted model structures of the peptides was calculated using the OPLS4 force field in Schrödinger's MacroModel software. The relative potential energy of the single disulfide mutant peptides was computed using the Boltzmann-weighted average energy of the conformers of the corresponding peptides. [C2A,C8A]α-RgIA and [C2A,C11A]χ-CMrVIA are the most stable forms, corresponding to the native single disulfide intermediate analogues. Accordingly, the folding events for α-RgIA are C3-C12 followed by C2-C8, while for χ-CMrVIA, they are C3-C8 followed by C2-C11 connectivity. The current report also explored the native folding steps of an Inhibitory Cystine Knot (ICK) motif peptide ω-conotoxin-MVIIA-Gly using one/two cysteine disulfide alanine mutants. The computation of relative potential energy of the mutant peptides indicates the formation of C15-C25 followed by C8-C20 and C1-C16 disulfide bonds. The newly proposed technique that combines AlphaFold 3 with MacroModel conformational sampling tool is allowing to identify the oxidative folding steps of disulfide-rich peptides.

Protective function of the voltage-gated potassium channel Kv11.3 in a mouse model of cardiac ischemia/reperfusion injury

Voltage-gated potassium (Kv) channels contribute to repolarization in excitable tissues such as nerves and cardiac muscle; consequently, they control the firing frequency and duration of action potential. Their dysfunction can thus cause neurological disorders and cardiac disorders with arrhythmias. The dysfunction of Kv11.3 is associated with bipolar disorder, but no reports have linked it to heart disease. Kv11.3-knocked out (KO) mice exhibit behavioral abnormalities, but they do not have cardiac abnormalities. Ischemia-reperfusion (I/R) experiments were performed on the hearts of Kv11.3 KO mice to determine whether they would differ from wild-type mice when exposed to stimuli that could induce sudden cardiac death. The mortality rates and infarct size of the Kv11.3 KO mice increased after cardiac I/R. The corrected QT interval was shortened in the wild-type mice after cardiac I/R, but it remained nearly unchanged in Kv11.3 KO mice with alterations in heart rate variability. These phenotypes could be reproduced by administering high-dose NS-1643, a Kv11.3 channel antagonist, after cardiac I/R. The infarct size had no significant difference in the ex vivo cardiac I/R experiment in contrast to the in vivo cardiac I/R experiment. Our study indicated that Kv11.3 protects the myocardium from I/R injury through neural pathways.

Strong protection by bazedoxifene against chemically-induced ferroptotic neuronal death in vitro and in vivo

Ferroptosis, a form of regulated cell death associated with glutathione depletion and excess lipid peroxidation, can be induced in cultured cells by chemicals (e.g., erastin and RSL3). It has been shown that protein disulfide isomerase (PDI) is a mediator of chemically-induced ferroptosis and also a crucial target for ferroptosis protection. The present study reports that bazedoxifene (BAZ), a selective estrogen receptor modulator, is an inhibitor of PDI and can strongly rescue neuronal cells from chemically-induced oxidative ferroptosis. We find that BAZ can directly bind to PDI and inhibit its catalytic activity. Computational modeling analysis reveals that BAZ forms a hydrogen bond with PDI's His256 residue. Inhibition of PDI by BAZ markedly reduces iNOS and nNOS dimerization (i.e., catalytic activation) and NO accumulation, and these effects of BAZ are associated with reductions in cellular ROS and lipid-ROS and protection against chemically-induced ferroptosis. In addition, the direct antioxidant activity of BAZ may also partially contribute to its protection against chemically-induced ferroptosis. In vivo animal experiments show that mice treated with BAZ are strongly protected against kainic acid-induced oxidative hippocampal neuronal injury and memory deficits. Together, these results reveal that BAZ is a potent inhibitor of PDI and can strongly protect against chemically-induced ferroptosis in hippocampal neurons both in vitro and in vivo. This work provides evidence for an estrogen receptor-independent, PDI-mediated novel mechanism of neuroprotection by BAZ.

Empagliflozin Repurposing for Lafora Disease: A Pilot Clinical Trial and Preclinical Investigation of Novel Therapeutic Targets

BACKGROUND

Lafora disease (LD) is an ultra-rare and fatal neurodegenerative disorder with limited therapeutic options. Current treatments primarily address symptoms, with modest efficacy in halting disease progression, thus highlighting the urgent need for novel therapeutic approaches. Gene therapy, antisense oligonucleotides, and recombinant enzymes have recently been, and still are, under investigation. Drug repurposing may offer a promising approach to identify new, possibly effective, therapies.

METHODS

This study aims to investigate the conditions for repurposing empagliflozin, an SGLT2 (sodium/glucose cotransporter-2) inhibitor, as a potential treatment for LD and to establish a clinical protocol. Clinical phase: This 12-month prospective observational study will assess the safety and clinical efficacy of empagliflozin in two patients with early to intermediate LD stage. The primary endpoints will include changes in the severity of epilepsy and cognitive function, while the secondary endpoints will assess motor function, global function, and autonomy. Multiple clinical and instrumental evaluations (including MRI and PET with 18F-fluorodeoxyglucose) will be performed before and during treatment. Safety monitoring will include regular clinical assessments and reports of adverse events. Preclinical phase: In silico studies (using both molecular docking calculations and reverse ligand-based screening) and in vitro cell-based assays will allow us to investigate the effects of empagliflozin (and other gliflozins) on some key targets likely implicated in LD pathogenesis, such as GLUT1, GLUT3, glycogen synthase (hGYS), and glycogen phosphorylase (GP), as suggested in the literature and digital platforms for in silico target fishing.

RESULTS

The expected outcome of this study is twofold, i.e., (i) assessing the safety and tolerability of empagliflozin in LD patients and (ii) gathering preliminary data on its potential efficacy in improving clinical and neurologic features. Additionally, the in silico and in vitro studies may provide new insights into the mechanisms through which empagliflozin may exert its therapeutic effects in LD.

CONCLUSION

The findings of this study are expected to provide evidence in support of the repurposing of empagliflozin for the treatment of LD.

Sarcoendoplasmic reticulum calcium ATPase is an essential and druggable lipid-dependent ion pump in Toxoplasma gondii

Toxoplasma gondii is a common intracellular pathogenic protist causing acute and chronic infections in many warm-blooded organisms. Calcium homeostasis is pivotal for its asexual reproduction in mammalian host cells, and sarcoendoplasmic reticulum calcium-ATPase (SERCA) is considered vital for maintaining ion homeostasis within the parasite. This work studied the physiological relevance, structure-function relationship, mechanism, and therapeutic value of SERCA in the acutely-infectious tachyzoite stage of T. gondii. A conditional depletion of SERCA, located in the endoplasmic reticulum, by auxin-inducible degradation is lethal for the parasite due to severe defects in its replication, gliding motility, and invasion. The observed phenotypes are caused by dysregulated calcium ion homeostasis and microneme secretion in the absence of TgSERCA. Furthermore, ectopic expression of TgSERCA restored the lytic cycle of a phosphatidylthreonine-null and phosphatidylserine-enriched mutant with perturbed calcium homeostasis, motility and invasion. These lipids are expressed in the parasite ER, co-localizing with TgSERCA. Last but not least, the structure-function modeling and ligand docking of TgSERCA with a library comprising >5000 chemicals identified two compounds (RB-15, NR-301) that inhibited the lytic cycle by affecting the tachyzoite locomotion, invasion, microneme discharge, and calcium levels. In conclusion, we demonstrate TgSERCA as an indispensable lipid-assisted calcium pump in T. gondii and report small molecules with therapeutic potential against toxoplasmosis.

Deciphering the mechanism of baicalein in cervical cancer via bioinformatics, machine learning and computational simulations: PIM1 and CDK2 are key target proteins

Cervical cancer is one of the leading causes of death among women worldwide. Current treatments are limited by chemoresistance and chemotherapeutic agents' adverse effects, prompting the search for better therapeutic alternatives. Baicalein, a natural compound with potent antitumor activity and low toxicity, has drawn significant attention. However, the precise mechanisms of baicalein against cervical cancer remain to be fully elucidated. In this study, bioinformatics and machine learning algorithms predicted six potential core targets of baicalein against cervical cancer. Molecular docking and molecular dynamics simulations were employed to further validate these targets, with a focus on assessing their binding affinity and stability. The molecular docking results demonstrated that five of the core targets exhibited significant binding affinity with baicalein. Notably, PIM1 and CDK2 showed stable binding conformations in molecular dynamics simulations. GO and KEGG enrichment analyses indicated baicalein might regulate cell cycle progression via histone kinase - mediated phosphorylation modifications. Thus, baicalein likely suppresses cervical cancer cells' abnormal proliferation by inhibiting PIM1 and CDK2 activity, inducing cell cycle arrest.

A new potent and selective peroxisome proliferator-activated receptor alpha partial agonist displays anti-steatotic effects In vitro and behaves as a safe hypolipidemic and hypoglycemic agent in a diabetic mouse model

A rational drug design approach led to the synthesis of three pairs of enantiomers derived from the peroxisome proliferator-activated receptor (PPAR) pan agonist AL29-26, identifying (S)-2 as a potent and selective PPARα partial agonist. Molecular docking and molecular dynamics simulations elucidated the binding modes of (S)-2 within the ligand-binding domains of PPARα and PPARγ. In vitro, (S)-2 demonstrated significant anti-steatotic effects, upregulating key PPARα target genes involved in lipid metabolism. In vivo, (S)-2 exhibited hypolipidemic and antihyperglycemic activity in a diabetic mouse model, outperforming fenofibrate in lowering blood glucose and lipid levels, while showing no toxicity in major organs (artery, kidney, liver, pancreas). The therapeutic effects of ((S)-2 were attributed to its PPARα selectivity, reduced activation of PPARγ, and mild protein tyrosine phosphatase 1B (PTP1B) inhibition. These findings highlight (S)-2 as a promising lead compound for the development of safer and more effective treatments for dyslipidemic type 2 diabetes.

HMCN1 variants aggravate epidermolysis bullosa simplex phenotype

Epidermolysis bullosa simplex (EBS) refers to a heterogeneous group of inherited skin disorders characterized by blister formation within the basal cell layer. The disease is characterized by marked variations in phenotype severity, suggesting co-inheritance of genetic modifiers. We identified three deleterious variants in HMCN1 that co-segregated with a more severe phenotype in a group of 20 individuals with EBS caused by mutations in KRT14, encoding keratin 14 (K14). HMCN1 codes for hemicentin-1. Protein modeling, molecular dynamics simulations, and functional experiments showed that all three HMCN1 variants disrupt protein stability. Hemicentin-1 was found to be expressed in human skin above the BMZ. Using yeast-2-hybrid, co-immunoprecipitation, and proximity ligation assays, we found that hemicentin-1 binds K14. Three-dimensional skin equivalents grown from hemicentin-1-deficient cells were found to spontaneously develop subepidermal blisters, and HMCN1 downregulation was found to reduce keratin intermediate filament formation. In conclusion, hemicentin-1 binds K14 and contributes to BMZ stability, which explains the fact that deleterious HMCN1 variants co-segregate with a more severe phenotype in KRT14-associated EBS.