A hierarchical approach to all-atom protein loop prediction

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.

Molecular docking and MD simulations reveal protease inhibitors block the catalytic residues in Prp8 intein of Aspergillus fumigatus: a potential target for antimycotics

Resistance to azoles and amphotericin B especially in Aspergillus fumigatus is a growing concern towards the treatment of invasive fungal infection. At this critical juncture, intein splicing would be a productive, and innovative target to establish therapies against resistant strains. Intein splicing is the central event for the activation of host protein, essential for the growth and survival of various microorganisms including A. fumigatus. The splicing process is a four-step protease-like nucleophilic cascade. Thus, we hypothesise that protease inhibitors would successfully halt intein splicing and potentially restrict the growth of the aforementioned pathogen. Using Rosetta Fold and molecular dynamics simulations, we modelled Prp8 intein structure; resembling classic intein fold with horse shoe shaped splicing domain. To fully comprehend the active site of Afu Prp8 intein, C1, T62, H65, H818, N819 from intein sequences and S820, the first C-extein residue are selected. Molecular docking shows that two FDA-approved drugs, i.e. Lufotrelvir and Remdesivir triphosphate efficiently interact with Prp8 intein from the assortment of 212 protease inhibitors. MD simulation portrayed that Prp8 undergoes conformational change upon ligand binding, and inferred the molecular recognition and stability of the docked complexes. Per-residue decomposition analysis confirms the importance of F: block R802, V803, and Q807 binding pocket in intein splicing domain towards recognition of inhibitors, along with active site residues through strong hydrogen bonds and hydrophobic contacts. However, in vitro and in vivo assays are required to confirm the inhibitory action on Prp8 intein splicing; which may pave the way for the development of new antifungals for A. fumigatus.

Molecular docking, molecular dynamics simulation, and MM/PBSA analysis of ginger phytocompounds as a potential inhibitor of AcrB for treating multidrug-resistant Klebsiella pneumoniae infections

The emergence of Multidrug resistance (MDR) in human pathogens has defected the existing antibiotics and compelled us to understand more about the basic science behind alternate anti-infective drug discovery. Soon, proteome analysis identified AcrB efflux pump protein as a promising drug target using plant-driven phytocompounds used in traditional medicine systems with lesser side effects. Thus, the present study aims to explore the novel, less toxic, and natural inhibitors of Klebsiella pneumoniae AcrB pump protein from 69 Zingiber officinale phyto-molecules available in the SpiceRx database through computational-biology approaches. AcrB protein's homology-modelling was carried out to get a 3D structure. The multistep-docking (HTVS, SP, and XP) were employed to eliminate less-suitable compounds in each step based on the docking score. The chosen hit-compounds underwent induced-fit docking (IFD). Based on the XP GScore, the top three compounds, epicatechin (-10.78), 6-gingerol (-9.71), and quercetin (-9.09) kcal/mol, were selected for further calculation of binding free energy (MM/GBSA). Furthermore, the short-listed compounds were assessed for their drug-like properties based on in silico ADMET properties and Pa, Pi values. In addition, the molecular dynamics simulation (MDS) studies for 250 ns elucidated the binding mechanism of epicatechin, 6-gingerol, and quercetin to AcrB. From the dynamic binding free energy calculations using MM/PBSA, 6-gingerol exhibited a strong binding affinity towards AcrB. Further, the 6-gingerol complex's energy fluctuation was observed from the free energy landscape. In conclusion, 6-gingerol has a promising inhibiting potential against the AcrB efflux pump and thus necessitates further validation through in vitro and in vivo experiments.

Unraveling the Binding Mode of TSC2-Rheb through Protein Docking and Simulations

Proteasome inhibitors (PIs) constitute the first line of therapy for multiple myeloma (MM). Despite the impressive clinical efficacy, MM remains fatal due to the development of drug resistance over time. During MM progression, stress responses to hypoxia and PIs suppress mammalian target of rapamycin complex 1 (mTORC1) activity by releasing tuberous sclerosis complex 2 (TSC2), which deactivates Ras homologue enriched in brain (Rheb), a crucial regulator of mTORC1. The efficacy of PIs targeting MM is enhanced when mTORC1 is hyperactivated. We thus propose that the inhibition of TSC2 will improve the efficacy of PIs targeting MM. To the best of our knowledge, no cocrystallized structure of the TSC2-Rheb complex has been reported. We therefore developed a representative model using the individual structures of TSC2 (PDB: 7DL2) and Rheb (PDB: 1XTS). Computational modeling involving an extensive protein-protein docking consensus approach was performed to determine the putative binding mode of TSC2-Rheb. The proposed docking poses were refined, clustered, and evaluated by MD simulations to explore the conformational dynamics and protein mobility, particularly at the drug-binding interface of TSC2-Rheb. Our results agree with the suggested binding mode of TSC2-Rheb previously reported in the literature. The results reported herein establish a basis for the development of new inhibitors blocking the binding of TSC2 and Rheb, aiming to reinstate mTORC1 activation and facilitate improved efficacy of PIs against multiple myeloma.

Computational insights into the targeted inhibition of lipoxygenase in Pseudomonas aeruginosa: hints for drug design

Pseudomonas aeruginosa is regarded as the most opportunistic pathogen. It can induce ferroptosis in humans. It secretes a unique lipoxygenase (LOX) isoform, pLoxA that can oxidize polyenoic fatty acids. Unlike other lipoxygenases, pLoxA can oxygenate membrane phospholipids like phosphatidylethanolamine, leading to hemolysis of red blood cells (RBC). This functional overlap with human 15-LOX that uses the same substrate has provided a bottleneck to the discovery of pLoxA-specific inhibitors and there is an immediate need to find pLoxA specific drugs. The active site of pLoxA is much larger than LOX enzymes, reflecting its ability to accommodate bulky substrates, such as phospholipids. The molecular docking of two experimentally established inhibitors and the further molecular dynamics simulations provided possible key residues in the active site of pLoxA. Our study found that this region is essentially hydrophobic including His 377 and His 382 that are placed to the non-heme iron atom and help to stabilize the inhibitors in the binding site along with hydrophobic residues contribute well toward ligand interactions that involve Phe 415, Ile 416 and Leu 424. MD simulations showed that interactions with those residues were dynamic in nature. Main contribution to binding stability arose via π-π stacking, π-cation, and alkyl interactions.

Mechanistic insights into novel cyano-pyrimidine pendant chalcone derivatives as LSD1 inhibitors by docking, ADMET, MM/GBSA, and molecular dynamics simulation

Cancer presents a formidable and complex foe, standing as one of the foremost contributors to disease-related fatalities across the globe. According to data from the Global Cancer Observatory (GLOBOCAN), projections indicate a staggering 28.4 million cases of cancer, encompassing both new diagnoses and deaths, by 2040. Therefore, developing effective and comprehensive treatment approaches for cancer patients is essential and the conventional approved treatments for cancers are associated with various harmful side effects. Our study aims to address the critical and widespread need for alternative therapies that can effectively combat cancer with minimal side effects. The present contribution outlines a targeted approach using Lysine Specific Demethylase 1 (LSD1) to evaluate novel cyano-pyrimidine pendant chalcone derivatives as potential antiproliferative agents. Two sets of novel cyano-pyrimidine pendant chalcone derivatives were produced, and molecular docking was performed on the LSD1 protein. The ligands A1 and B1 belonging to series A and B, respectively, were found to have the highest docking scores of -11.095 and -10.773 kcal/mol, in that order. The ADME and toxicity studies of the ligands showed promising responses with respect to various pharmacokinetic and physicochemical parameters. The Molecular dynamics (MD) simulation results indicated effective diffusion of both complexes inside the protein cavity, facilitated by prominent interactions with various amino acids. Additionally, the complexes displayed high relative binding free energy. The computational screening of ligands indicates that ligands A1 and B1 exhibit potential for further exploration using various in vitro and in vivo techniques. These ligands may then serve as promising leads in the discovery of cancer drugs. The in-silico screening of the novel library of cyano-pyrimidine pendant chalcone derivatives was performed with a combination of molecular docking, MM-GBSA, ADME, toxicity and MD simulation. Molecular docking and MM-GBSA were conducted using the Glide and Prime tools, respectively, of the Schrödinger suite 12.8. The ligands were analysed for ADME using the Swiss ADME, while toxicity risks were evaluated using Osiris Property Explorer. Additionally, a 400ns MD simulation of LIGA1 and LIGB1 against the protein LSD1 was performed using the Desmond tool of Schrödinger suite 12.8 to validate the docking results and analyse the behaviour and stability of the complexes.

3D-QSAR-based pharmacophore modelling of quinazoline derivatives for the identification of acetylcholinesterase inhibitors through virtual screening, molecular docking, molecular dynamics and DFT studies

Alzheimer's disease (AD) is a progressive neurological disorder responsible for the cognitive dysfunction and cognitive impairment in the patients. Acetylcholinesterase inhibitors (AChEIs) are used to treat AD however, these only provided symptomatic relief and more efficient drug molecules are desired for the effective treatment of the disease. In this article, ligand-based drug-designing strategy was used to develop and validate a field-based 3D-QSAR pharmacophore model on quinazoline-based AChEIs reported in the literature. The validated pharmacophore model (AAAHR_1) was used as a prefilter to screen an ASINEX database via virtual screening workflow (VSW). The hits generated were subjected to MM-GBSA to identify potential AChEIs and top three scoring molecules (BAS 05264565, LEG 12727144 and SYN 22339886) were evaluated for thermodynamic stability at the target site using molecular dynamic simulations. Additionally, DFT study was performed to predict the reactivity of lead molecules towards acetylcholinesterase (AChE). Thus, by utilising various computational tools, three molecules were identified as potent AChEIs that can be developed as potential drug candidates for the treatment of AD.

CDK8 inhibitor KY-065 rescues skeletal abnormalities in achondroplasia model mice

Cyclin-dependent kinase 8 (CDK8) is a transcription-related CDK family member implicated in the regulation of bone homeostasis, and we recently demonstrated that our internally developed CDK8 inhibitor KY-065 can prevent postmenopausal osteoporosis in a mouse model. Achondroplasia (ACH), the most common form of genetic dwarfism in humans, is caused by a gain-of-function mutation in fibroblast growth factor receptor 3 (FGFR3), a receptor tyrosine kinase that activates downstream mitogen-activated protein kinase (MAPK) and signal transducer and activator of transcription (STAT) signaling pathways. The first precision drug approved for the treatment of ACH in children, the C-type natriuretic peptide analog vosoritide, antagonizes the MAPK pathway, while there are currently no effective and safe medications targeting the STAT1 pathway. Here, we demonstrate that KY-065 rescues impaired chondrogenesis and stunted long bone growth in the Fgfr3Ach mouse model of ACH. KY-065 inhibited CDK8 with high affinity in vitro by competing with ATP. The CDK8 expression and STAT1Ser727 phosphorylation were upregulated in chondrocytes isolated from ACH model mice, and KY-065 repressed its phosphorylation and restored normal chondrogenic differentiation without affecting MAPK activation. Moreover, daily administration of 10 mg/kg KY-065 to Fgfr3Ach mice (yielding a peak concentration of 22.0 ± 1.47 μM in plasma) resulted in significant elongation of long bone and improved growth plate cytoarchitecture. Collectively, these findings identify the CDK8 in chondrocytes as a potential therapeutic target for ACH and KY-065 as a promising candidate drug treatment for this debilitating skeletal disease.

Inhibition of respiratory syncytial virus by Daclatasvir and its derivatives: synthesis of computational derivatives as a new drug development

The most common cause of respiratory tract illness in newborns and young children is the respiratory syncytial virus (RSV). There is no approved vaccination or specific antiviral medication for RSV infections. Here, an attempt has been made to explore the potential of currently marketed drugs as well as their probable derivatives to improve the possibility of developing stronger medications against RSV. From the 100 synthetic drug compounds library, the best drug molecule was identified through drug-likeness properties, toxicity, molecular docking and molecular dynamics simulations. Molecular Mechanics Generalized Born Surface Area (MM-GBSA) was also a method that was applied in this study. Daclatasvir showed the highest binding energy and appeared as the best drug to inhibit matrix protein and a fusion protein of RSV. Based on Daclatasvir, 40 computational derivatives were made. D28, D34 and D40 showed far better results than the actual drug. Changes in lipophilicity character increase the binding energy of derivatives. Molecular dynamic simulations showed their non-deviated, non-fluctuated and stable complex formation with target proteins. The high number of amino acid contacts throughout the trajectory increases the stability and effectiveness of derivatives. The key to producing a novel medicine to eradicate RSV is provided by derivatives. Daclatasvir will be employed as a potential RSV inhibitor up until that point.

Insights into interactions between taxanes and P-glycoprotein using biophysical and in silico methods

Multidrug resistance mediated by P-glycoprotein (Pgp) is a significant obstacle to cancer chemotherapy. Taxane drugs, including paclitaxel, docetaxel, and cabazitaxel, are used to treat multiple types of cancer. All taxane drugs are Pgp substrates, but cabazitaxel is also a Pgp inhibitor, indicating potential differential interactions between Pgp and different taxanes. Here, we showed for the first time that cabazitaxel had a partial inhibitory effect on the ATPase activity at concentrations higher than 10 µM. We found the KD of paclitaxel, docetaxel, and cabazitaxel to Pgp are 0.85 µM, 40.59 µM, and 13.53 µM, respectively. Based on acrylamide quenching, paclitaxel induced Pgp into a wide inward-facing open conformation at a high concentration but a slightly occluded conformation at lower concentrations. Both docetaxel and cabazitaxel shifted Pgp towards occluded states, each drug resulting in a unique degree of occlusion. Furthermore, molecular docking and energy calculations revealed that cabazitaxel binds with the "access tunnel" and blocks the subsequent nucleotide-binding domain dimerization. Our results indicate that the preference of taxanes for different binding sites on Pgp leads to distinct transport mechanisms. These results provide valuable insight into the interaction between taxanes and Pgp, which will enhance future drug development.

Unveiling nucleosome dynamics: A comparative study using all-atom and coarse-grained simulations enhanced by principal component analysis

The conformational dynamics of the DNA in the nucleosome may play a role in governing gene regulation and accessibility and impact higher-order chromatin structure. This study investigates nucleosome dynamics using both all-atom and coarse-grained (CG) molecular dynamics simulations, focusing on the SIRAH force field. Simulations are performed for two nucleosomal DNA sequences-alpha satellite palindromic and Widom-601-over 6 μs at physiological salt concentrations. A comparative analysis of structural parameters, such as groove widths and base pair geometries, reveals good agreement between atomistic and CG models, although CG simulations exhibit broader conformational sampling and greater breathing motion of DNA ends. Principal component analysis is applied to DNA structural parameters, revealing multiple free energy minima, especially in CG simulations. These findings highlight the potential of the SIRAH CG force field for studying large-scale nucleosome dynamics, offering insights into DNA repositioning and sequence-dependent behavior.

Ranolazine attenuates mouse detrusor contractility: Evidence for the involvement of calcium-related mechanisms

Ranolazine (RNZ) is a multifaceted ion channel modulator approved for the treatment of angina. Although various pleiotropic effects on the cardiovascular system have been demonstrated, its efficacy in the urinary system remains not fully understood. Here, we aimed to investigate the effect of RNZ on mouse detrusor smooth muscle (DSM) contractility and the mechanism(s) of its action by using isolated tissue bath technique. RNZ significantly decreased carbachol (CCh)-, KCl- and electrical field stimulation-induced contractility and induced relaxation in DSM concentration-dependently. Furthermore, RNZ-induced relaxation of KCl-precontracted DSM strips was not altered in the presence of 4-aminopyridine, BaCl2, glibenclamide, TEA, propranolol, L-NAME or methylene blue, indicating that K+ channels, nitric oxide/cGMP pathway or β-adrenoreceptors are not involved in the relaxant effect of RNZ. Also, RNZ significantly inhibited the contractile response induced by CaCl2, CCh, and Bay K8644 under Ca++-free conditions. Regarding the molecular docking and cytosolic Ca++ mobilization assays, RNZ showed affinity for the antagonist binding site of L-type Ca++ channels and significantly decreased cytosolic Ca++ level in A7r5 cells. These findings suggest the inhibition of Ca++ influx and release may contribute to RNZ-induced DSM relaxation. Hence, our results provide strong evidence that RNZ has a notable relaxant effect on mouse DSM by inhibiting Ca++ influx and release of Ca++ from intracellular stores and it has the potential to be a therapeutic candidate for LUTS.

Targeting Plasmodium falciparum Schizont Egress Antigen-1 in Infected Red Blood Cells: Docking-Based Fingerprinting, Density Functional Theory, Molecular Dynamics Simulations, and Binding Free Energy Analysis

Background: Malaria remains a global health crisis, with the World Health Organization (WHO) reporting 241 million cases and 627,000 deaths worldwide in 2020, predominantly affecting Sub-Saharan Africa. The region accounted for 95% of cases and 96% of deaths, reflecting the immense challenges in malaria prevention and treatment. Plasmodium falciparum Schizont Egress Antigen-1 (PfSEA-1) is crucial in facilitating immune evasion and promoting the sequestration of infected red blood cells (RBCs), contributing to severe malaria symptoms, including cerebral malaria, and necessitates the urgent identification of novel or repurposed drugs targeting PfSEA1. Methods: The protein structure of PfSEA-1 (UniProt ID: A0A143ZXM2) was modelled in three dimensions, prepared, and subjected to a 50 ns molecular dynamics (MD) simulation to achieve a stable structure. The equilibrated structure was minimised for molecular docking against the DrugBank compound library. Docking analysis identified potential inhibitors, including Alparabinos, Dihycid, Ambenzyne, Amiflupipquamine, Ametchomine, and Chlobenethyzenol, with docking scores ranging from -8.107 to -4.481 kcal/mol. Advanced analyses such as interaction fingerprints, density functional theory (DFT), and pharmacokinetics evaluations were conducted. Finally, a 100 ns MD simulation in the NPT ensemble was performed to assess the stability of protein-ligand complexes, with binding free energy and total energy calculations derived from the simulation trajectories. Results and Discussion: The identified compounds exhibited satisfactory pharmacokinetic profiles and binding interactions with PfSEA-1. The MD simulations demonstrated overall stability, with minor fluctuations in some instances. Key intermolecular interactions were observed, supporting the binding stability of the identified compounds. Binding free energy calculations confirmed favourable interactions, underscoring their potential as therapeutic agents against Plasmodium falciparum. While the in silico results are promising, experimental validation is essential to confirm their efficacy and safety for clinical use. Conclusion: These findings highlight PfSEA-1 as a promising antimalarial target and identify potential inhibitors with strong binding affinities and favourable pharmacokinetics. While the computational results are encouraging, further in vitro and in vivo validation is necessary to confirm their therapeutic potential and facilitate future drug development.

Discovery of novel acetylcholinesterase inhibitors through AI-powered structure prediction and high-performance computing-enhanced virtual screening

Virtual screening (VS) methodologies have become key in the drug discovery process but are also applicable to other fields including catalysis, material design, and, more recently, insecticide solutions. Indeed, the search for effective pest control agents is a critical industrial objective, driven by the need to meet stringent regulations and address public health concerns. Cockroaches, known vectors of numerous diseases, represent a major challenge due to the toxicity of existing control measures to humans. In this article, we leverage an Artificial Intelligence (AI)-based screening of the Drug Bank (DB) database to identify novel acetylcholinesterase (AChE) inhibitors, a previously uncharacterized target in the American cockroach (Periplaneta americana). Our AI-based VS pipeline starts with the deep-learning-based AlphaFold to predict the previously unknown 3D structure of AChE based on its amino acid sequence. This first step enables the subsequent ligand-receptor VS of potential inhibitors, the development of which is performed using a consensus VS protocol based on two different tools: Glide, an industry-leading solution, and METADOCK 2, a metaheuristic-based tool that takes advantage of GPU acceleration. The proposed VS pipeline is further refined through rescoring to pinpoint the most promising biocide compounds against cockroaches. We show the search space explored by different metaheuristics generated by METADOCK 2 and how this search is more exhaustive, but complementary, than the one offered by Glide. Finally, we applied Molecular Mechanics Generalized Born Surface Area (MMGBSA) to list the most promising compounds to inhibit the AChE enzyme.

Determination of the Negative Allosteric Binding Site of Cannabidiol at the CB1 Receptor: A Combined Computational and Site-Directed Mutagenesis Study

Cannabinoid receptor 1 (CB1R) has been extensively studied as a potential therapeutic target for various conditions, including pain management, obesity, emesis, and metabolic syndrome. Unlike orthosteric agonists such as Δ9-tetrahydrocannabinol (THC), cannabidiol (CBD) has been identified as a negative allosteric modulator (NAM) of CB1R, among its other pharmacological targets. Previous computational and structural studies have proposed various binding sites for CB1R NAMs. An X-ray crystal structure revealed a binding site for the NAM, ORG27569, at an extrahelical location within the inner leaflet of the membrane. In contrast, multiple computational studies have previously proposed several potential allosteric binding sites for CBD within the CB1R structure. Given that a prior structural study suggested CBD might occupy the same site as ORG27569, we conducted a comprehensive investigation of potential CBD binding sites using molecular docking, molecular dynamics (MD) simulations, metadynamics (MTD) simulations, binding free-energy calculations, and in vitro mutagenesis experiments. Molecular docking, MD, and MTD simulations results, along with binding free-energy calculations, suggest that CBD may potentially bind to either the same extrahelical site as ORG27569 or a previously unidentified intracellular site located near TMHs 2, 6, and 7 and helix 8. This intracellular site is consistent with allosteric binding sites observed in other G protein-coupled receptors (GPCRs). To establish the most favorable allosteric site for CBD, we conducted site-directed mutagenesis of key residues at each site. Mutations at S4018.47ΔA and D4038.49ΔA augmented the binding of [3H]-SR141716A, suggesting these residues play critical roles in CBD binding. As a result, the combined computational and mutagenesis results identified a binding site for CBD between TMHs 2, 6, and 7 and helix 8, involving residues Y1532.40, I1562.43, M3376.29, L3416.33, S4018.47, and D4038.49. These findings provide valuable insights into how CBD binds to CB1R, thereby informing the rational design of new, selective, and potent NAMs. Moreover, the elucidation of this previously unexplored allosteric site might explain the polypharmacology of CBD due to structural conservation among Class A GPCRs.

Synthesis and mechanistic studies of 4-aminoquinoline-Isatin molecular hybrids and Schiff's bases as promising antimicrobial agents

In this investigation, to determine their potential as specific antibacterial agents, Schiff's bases (LT-SB1-23 and SB1-SB12) and novel quinoline-isatin hybrids were subjected to microbiological testing. The in-vitro screening against bacterial strains (Escherichia coli, Enterococcus faecalis, Bacillus subtilis, Staphylococcus aureus, Pseudomonas aeruginosa, and Salmonella typhi) exhibited their antibacterial potential with many of the compounds showing inhibition range of 90-100 % at 200 μg/mL, against most of the tested strains. The MIC values of some of the compounds showed good antibacterial efficacy with values ranging from 32 to 128 μg/mL. Their bacterial growth inhibitory potential was further supported by disk diffusion and growth curve assays. Interestingly, one of the Schiff's bases (LT-SB7) displayed strong synergistic activity against E. coli and S. typhi with 16-64 folds reduction in MIC values. Additionally, it exhibited up to 85 % suppression of biofilm at ½MIC against AA209 environmental bacterial isolate and reduced the development of multidrug-resistant bacterial isolates. Promising compound LT-SB7 underwent 100 ns molecular dynamics simulations with biofilm-causing protein (PDB ID: 7C7U) to assess conformational changes and complex stability. Overall, this study identified compounds as effective antibacterial alternatives for the future.

Computational and in vitro evaluation of sumac-derived ©Rutan compounds towards Sars-CoV-2 Mpro inhibition

The emergence of the SARS-CoV-2 virus caused the COVID-19 outbreak leading to a global pandemic. Natural substances started being screened for their antiviral activity by computational and in-vitro techniques. Here, we evaluated the anti-SARS-CoV-2 main protease (Mpro) efficacy of ©Rutan, which contains five polyphenols (R5, R6, R7, R7', and R8) extracted from sumac Rhus coriaria L. We obtained three fractions after large-scale purification: fraction 1 held R5, fraction 2 consisted of R6, R7 and R7', and fraction 3 held R8. In vitro results showed their anti-Mpro potential: IC50 values of R5 and R8 made 42.52 µM and 5.48 µM, respectively. Further, we studied Mpro-polyphenol interactions by in silico analysis to understand mechanistic extrapolation of Rutan binding nature with Mpro. We extensively incorporated a series of in silico techniques. Initially, for the docking protocol validation, redocking of the co-crystal ligand GC-376* to the binding pocket of Mpro was carried out. The representative docked complexes were subjected to long-range 500 ns molecular dynamics simulations. The binding free energy (BFE in kcal/mol) of components were calculated as follows: R8 (-104.636) > R6 (-93.754) > R7' (-92.113) > R5 (-81.115) > R7 (-67.243). In silico results of R5 and R8 correspond with their in vitro outcomes. Furthermore, the per-residue decomposition analysis showed C145, E166, and Q189 residues as the hotspot residues for components contributing to maximum BFE energies. All five components effectively interact with the catalytic pocket of Mpro and form stable complexes that allow the estimation of their inhibitory activity. Assay kit analyses revealed that Rutan and its components have effective anti-SARS-CoV-2 Mpro inhibitory activity.

Rational Identification of Ritonavir as IL-20 Receptor A Ligand Endowed with Antiproliferative Properties in Breast Cancer Cells

Targeting the tumor microenvironment (TME) is an attractive strategy for developing new drugs with anticancer activity against triple-negative breast cancer (TNBC). Interleukins (ILs) are key players in the TME cytokine network promoting cancer progression. Recent studies have highlighted the involvement of IL-20 receptor subunit alpha (IL-20RA) signalling in several cancers, including BC, in which IL-20RA is highly expressed, correlating with poor prognosis and influencing tumoral characteristics such as proliferation, cell death, invasiveness, and TME activity. Therefore, elucidating the role of the IL-20RA signalling pathway could form the basis for developing new therapeutic strategies. This study aimed to identify selective bioactive ligands able to affect IL-20RA activity. Virtual screening of over 310,000 compounds from both the DrugBank and ZINC15 databases identified four potential hit compounds tested for their anticancer activity against TNBC in vitro cell lines. Notably, Ritonavir, a well-known Human Immunodeficiency Virus Type 1 (HIV-1) protease inhibitor, significantly inhibited cell proliferation (about 40% at 50 µM, p < 0.001). IL-20 preincubation counteracted Ritonavir's cytostatic effect while IL-20RA knockdown restored proliferation in Ritonavir-treated TNBC cells. In conclusion, these findings demonstrated that Ritonavir reduced TNBC cell proliferation through IL-20RA activity modulation, suggesting its potential repurposing as a therapeutic agent for TNBC management.

Investigating the multitargeted anti-diabetic potential of cucurbitane-type triterpenoid from Momordica charantia: an LC-MS, docking-based MM\GBSA and MD simulation study

Type 2 diabetes accounts for the largest percentage of all diabetic cases worldwide. Cucurbitane-type triterpenes are mainly found in Momordica charantia and possess excellent pharmacological activities. This study was designed to identify cucurbitane-type triterpene from Momordica charantia using Liquid Chromatography-Mass Spectrometry (LC-MS) analysis, examine its anti-diabetic property with molecular docking against diabetes enzymes (alpha-amylase, alpha-glucosidase, dipeptidyl dipeptidase IV and peroxisome proliferator-activated receptor gamma). The stability and interactions of the docked complexes were investigated using molecular dynamics simulation, while the pharmacokinetic and toxicity profile of the ligand was examined using an ADMET server. (23E)-Cucurbita-5,23,25-triene-3,7-dione (CUB) was identified from the LC-MS profiling of the methanolic extract of M. charantia. The molecular docking studies showed that the identified phytochemical elicited good binding energy against all the target receptors. The RMSD and RMSF plots obtained from the 100 ns molecular dynamics simulation showed that the ligand was stable and established substantial interactions with the amino acid residues of the diabetes enzymes which were confirmed by the MM\GBSA computations. The pharmacokinetic and toxicity properties of the ligand showed it was safer as an anti-diabetic drug candidate. Extensive isolation, in vitro and in vivo studies of the ligand against the diabetic enzymes is recommended.Communicated by Ramaswamy H. Sarma.

Rational design of thiazolidine-4-one-gallic acid hybrid derivatives as selective partial PPARγ modulators: an in-silico approach for type 2 diabetes treatment

Type 2 diabetes mellitus is a bipolar metabolic disorder characterized by abnormalities in insulin production from β-cells and insulin resistance. Thiazolidinediones are potent anti-diabetic agents that act through the modulation of the peroxisome proliferator-activated receptor γ (PPARγ), a nuclear receptor. However, their full agonistic activity leads to severe side effects by stabilizing Helix12 through strong hydrogen bonding with the TYR473 residue. Partial and selective PPARγ modulators (GW0072, GQ16, VSP-51, MRL-20, MBX-213, INT131) have demonstrated superior results compared to full agonists without causing adverse effects, as reported in existing data. To address this uncertainty and advance therapeutic options, we identified and designed a novel class of compounds (A1-A23) based on a hybrid structure combining phenolic and Thiazolidine-4-one's moieties. Our rational drug design strategy incorporated structural-activity relationship principle, and validated the docking studies through calculated the root mean square deviation. Additionally, we conducted molecular docking, binding energy, molecular dynamics simulations, and post-molecular dynamics calculations to evaluate the dynamics behavior between the ligands and protein. The selected ligands demonstrated highly favorable docking scores and binding energies, comparable to the co-crystal (rosiglitazone) such as A12 (-13.9 kcal/mol and -86.2 kcal/mol), A1 (-11.1 kcal/mol and -79.5 kcal/mol), A13 (-11.3 kcal/mol and -91.4 kcal/mol), and the co-crystal itself (-9.8 kcal/mol and -76 kcal/mol), respectively. Finally, the MD revealed that, the selected ligands were equally contributed for stabilization of Helix12 and β-sheets. It was concluded, the designed ligands (A12, A1, and A13) exhibited weaker hydrogen-bond interactions with specific residue TYR473 which partially modulated the PPARγ protein.Communicated by Ramaswamy H. Sarma.

Insights into Molecular Interactions and Biological Effect of Natural Stilbenoids at the TRPA1 Ion Channel

Natural stilbenoids, polyphenolic compounds notably found in Scots pine and Norway spruce, have been shown to exhibit analgesic and anti-inflammatory effects through the TRPA1 channel, making them promising hits for the development of novel agents to treat inflammatory diseases and pain. In this study, we computationally investigated the putative binding sites of natural stilbenoids at the TRPA1 channel. Specifically, we employed molecular docking and MD simulation approaches to explore three known ligand binding sites at TRPA1. Furthermore, the biological effect of the studied compounds on TRPA1 was assessed in vitro using a fluorescent imaging plate reader (FLIPR™) calcium assay. Our modeling results suggest the stilbenoids exhibit higher affinity to the two agonist binding sites than the antagonistic site. Consistent with this, the in vitro results showed that the stilbenoids act as moderate TRPA1 channel agonists and likely inhibit the channel through a desensitization mechanism rather than act as pure TRPA1 antagonists. Additionally, our bias-force pulling simulations proposed an additional binding pocket for the natural stilbenoids that is distinct from the known ligand binding sites at TRPA1. The results of the study give useful insights into structure-based design and development of novel therapeutic TRPA1 modulators.

Discovery of potential RSK1 inhibitors for cancer therapy using virtual screening, molecular docking, molecular dynamics simulation, and MM/GBSA calculations

The p90 ribosomal protein S6 Kinase (RSK) family belongs to Ser/Thr protein kinases that includes four isoform RSK1-4 in mammals. The ribosomal protein S6 Kinase 1 (RSK1) is also known as ribosomal protein S6 kinase alpha-1 (RPS6KA1) is a special protein due to their two catalytic regions that is associated with abundantly various cancers and it is proposed as a drug target. Several RSK1 isoform inhibitors have been reported but none of them are used in clinical studies. Thus, we aimed to perform ligand pharmacophore mapping with the known inhibitor and structure-based virtual screening studies to determine potential candidates against RSK1-terminal kinase domains CTKD and NTKD. The studied compounds from the databases (ApexBio, ChEMBL, ChemDiv). The molecular docking study was performed with the resulted candidates by using CDOCKER and Glide/SP methods. The four candidates with the highest docking scores were used for further 100-ns molecular dynamics (MD) simulations and Molecular Mechanics Generalised Born and Surface Area (MM/GBSA) calculations. The root mean square deviation (RMSD) for protein complexes were found between 2 Å and 4 Å. Solvent accessible surface area (SASA), radius of gyration (Rg), and polar surface area (PSA) values were calculated for compounds. The binding free energies were calculated between -72.22 kcal/mol and -82.44 kcal/mol. The interaction diagrams showed that hydrogen bond, alkyl, and π-alkyl interactions were observed with specific residues such as Leu144, Lys94, Asp142 for RSK1-NTKD, and Cys532, Cys556, Lys447, Asn540 for RSK1-CTKD. The identified compounds may be potential inhibitor candidates of RSK1 following the preclinical studies.Communicated by Ramaswamy H. Sarma.

Novel inhibitors of the (VIBVN) NAT protein identified through pharmacophore modeling

Arylamine N-acetyltransferases (NATs, E.C. 2.3.1.5) constitute a family of phase II drug metabolizing enzymes. These enzymes catalyze the transfer of acetyl groups from acetyl-CoA to a variety of substrates including arylamines, arylhydrazines, and N-hydroxyarylamines. By facilitating these reactions, NATs play a pivotal role in the detoxification and metabolic processing of a wide range of drugs and carcinogens. NAT in marine V. vulnificus plays a role in the metabolism of drugs, leading to the development of drug resistance in marine V. vulnificus. However, inhibitors targeted marine V. vulnificus NAT [(VIBVN)NAT] remain unclear. Therefore, our research aimed to identify potential hit compounds that target (VIBVN)NAT. We integrated multiple computational approaches to screen for effective inhibitors. From this process, we identified two hit compounds, AK-968-11563024 and AG-205-36710025, with IC50 values of 18.86 µM and 33.27 µM, respectively. Molecular dynamics simulations further elucidated the binding mechanism between (VIBVN)NAT and AK-968-11563024. Our study revealed that AK-968-11563024 forms stable interactions with PHE124, HIS167, and TRP230, which may contribute to its biological activity. Our findings provide a valuable foundation for the future development of drugs targeted therapeutics against (VIBVN)NAT.

Microbial-based natural products as potential inhibitors targeting DNA gyrase B of Mycobacterium tuberculosis: an in silico study

Introduction

Since the emergence of Mycobacterium tuberculosis (MBT) strains resistant to most currently used anti-tubercular drugs, there has been an urgent need to develop efficient drugs capable of modulating new therapeutic targets. Mycobacterial DNA gyrase is an enzyme that plays a crucial role in the replication and transcription of DNA in MBT. Consequently, targeting this enzyme is of particular interest in developing new drugs for the treatment of drug-resistant tuberculosis, including multidrug-resistant tuberculosis (MDR-TB) and extensively drug-resistant tuberculosis (XDR-TB).

Methods

In the present study, multiple computational tools were adopted to screen a microbial-based natural products database (NPAtlas) for potential inhibitors of the ATPase activity of MBT DNA gyrase.

Results and discussion

Twelve hits were initially identified as the top candidates based on their docking scores (ranging from -9.491 to -10.77 kcal/mol) and binding free energies (-60.37 to -73.21 kcal/mol). Following this, computational filters, including ADME-T profiling and pharmacophore modeling, were applied to further refine the selection. As a result, three compounds 1-Hydroxy-D-788-7, Erythrin, and Pyrindolol K2 emerged as the most promising, exhibiting favorable drug-like properties. Notably, 1-Hydroxy-D-788-7, an anthracycline derivative, demonstrated superior binding affinity in molecular dynamics simulations. The RMSD values, ranging from 1.7 to 2.5 Å, alongside RMSF analysis and a detailed evaluation of the established interaction forces, revealed that 1-Hydroxy-D-788-7 was the strongest binder to Mycobacterial DNA Gyrase B. The stable binding and favorable interaction profile highlighted 1-Hydroxy-D-788-7 as a top hit. These comprehensive computational findings strongly support the potential of 1-Hydroxy-D-788-7 as an effective anti-TB lead compound, warranting further experimental validation to confirm its therapeutic efficacy.

Examining Prenylated Xanthones as Potential Inhibitors Against Ketohexokinase C Isoform for the Treatment of Fructose-Driven Metabolic Disorders: An Integrated Computational Approach

Background/Objectives: Fructose-driven metabolic disorders, such as obesity, non-alcoholic fatty liver disease (NAFLD), dyslipidemia, and type 2 diabetes, are significant global health challenges. Ketohexokinase C (KHK-C), a key enzyme in fructose metabolism, is a promising therapeutic target. α-Mangostin, a naturally occurring prenylated xanthone, has been identified as an effective KHK-C inhibitor, prompting exploration of its analogs for enhanced efficacy. This study aimed to identify α-Mangostin analogs with improved inhibitory properties against KHK-C to address these disorders. Methods: A library of 1383 analogs was compiled from chemical databases and the literature. Molecular docking, binding free energy calculations, pharmacokinetic assessments, molecular dynamics simulations, and quantum mechani-cal analyses were used to screen and evaluate the compounds. α-Mangostin's binding affinity (37.34 kcal/mol) served as the benchmark. Results: Sixteen analogs demonstrated binding affinities superior to α-Mangostin (from -45.51 to -61.3 kcal/mol), LY-3522348 (-45.36 kcal/mol), and reported marine-derived inhibitors (from -22.74 to -51.83 kcal/mol). Hits 7, 8, 9, 13, and 15 not only surpassed these benchmarks in binding affinity, but also exhibited superior pharmacokinetic properties compared to α-Mangostin, LY-3522348, and marine-derived inhibitors, indicating strong in vivo potential. Among these, hit 8 emerged as the best performer, achieving a binding free energy of -61.30 kcal/mol, 100% predicted oral absorption, enhanced metabolic stability, and stable molecular dynamics. Conclusions: Hit 8 emerged as the most promising candidate due to its superior binding affinity, favorable pharmacokinetics, and stable interactions with KHK-C. These findings highlight its potential for treating fructose-driven metabolic disorders, warranting further experimental validation.

Identification of potential inhibitors for MAP4K4 in glaucoma using meta-dynamics-based dissociation free energy calculation

Glaucoma, a prevalent eye ailment causing irreversible vision loss, affects over 295 million individuals globally, necessitating the exploration of novel therapeutic avenues. Despite extensive research on targets like the phosphodiesterase enzyme and rho kinase, the potential of MAP4K4 in glaucoma remains untapped. This study aims to identify potent MAP4K4 inhibitors to counteract retinal cell apoptosis and oxidative stress associated with glaucoma. Using HTVS and XP docking, 911,059 compounds were screened. The MMGBSA calculation and pharmacokinetics analysis were used to shortlist the compounds. After performing 75 molecular dynamics simulations, further meta-dynamics were employed to calculate dissociation-free energy and find potential MAP4K4 inhibitors. Findings indicated that ZINC06717217 and ZINC38836256 exhibited remarkable promise, with docking scores of -9.57 and -11.12 and MMGBSA binding energies of -91.07 kcal/mol and -87.52 kcal/mol, respectively. Comparative analysis with the reference compound Q27453723 underscored their superior stability, requiring dissociation-free energies of -15.11 kcal/mol and -12.46 kcal/mol to disengage from the docked complex. This underscored their robust binding affinity. ZINC06717217 and ZINC38836256 show promising stability and strong binding to the MAP4K4 protein. Hence, these findings are promising in inhibiting MAP4K4 for glaucoma treatment, potentially leading to more effective treatment and curing blindness. KEY MESSAGES: First to incorporate the dissociation-free energy for identifying compounds for glaucoma treatment. In-silico analysis showed that ZINC06717217 and ZINC38836256 are promising compounds for targeting MAP4K4.

Design and Synthesis of Topoisomerases-Histone Deacetylase Dual Targeted Quinoline-Bridged Hydroxamates as Anticancer Agents

The multifactorial nature of cancer requires treatment that involves simultaneous targeting of associated overexpressed proteins and cell signaling pathways, possibly leading to synergistic effects. Herein, we present a systematic study that involves the simultaneous inhibition of human topoisomerases (hTopos) and histone deacetylases (HDACs) by multitargeted quinoline-bridged hydroxamic acid derivatives. These compounds were rationally designed considering pharmacophoric features and catalytic sites of the cross-talk proteins, synthesized, and assessed for their anticancer potential. Our findings revealed that the compound 5c significantly produced anticancer effects in vitro and in vivo by reducing the tumor growth and its size in the A549 cell-induced lung cancer xenograft model through multiple mechanisms, primarily by multi-inhibition of hTopoI/II and HDACs, especially HDAC1 via atypical binding. The present paper discusses detailed mechanistic biological investigations, structure-activity effects supported by computational docking studies, and DMPK studies and provides future scope for lead optimization and modification.

Lucidin from Rubia cordifolia Outperforms FDA-Approved Lapatinib as a Potential Multitargeted Candidate for Breast Cancer Signalling Proteins

Background: Breast cancer remains a significant global health concern, with approximately 2.3 million diagnosed cases and 670,000 deaths annually. Current targeted therapies face challenges such as resistance and adverse side effects. This study aimed to explore natural compounds as potential multitargeted breast cancer therapeutics, focusing on Lucidin, an anthraquinone derived from Rubia cordifolia, and comparing its efficacy with Lapatinib, an FDA-approved drug. Methods: We performed multitargeted molecular docking studies on key breast cancer proteins using a natural compound library from ZINC. Comparative analyses of Lucidin and Lapatinib included molecular interaction fingerprints, pharmacokinetics, WaterMap computations (5 ns) to assess water thermodynamics and binding interactions, and Molecular Dynamics Simulations (100 ns) in water to evaluate complex stability and dynamic behaviour. Results: Lucidin demonstrated significant binding affinity and interaction potential with multiple breast cancer targets, outperforming Lapatinib in stability and binding interactions. WaterMap analysis revealed favourable hydration site energetics for Lucidin, enhancing its efficacy. The multitargeted profile of Lucidin suggests a broader therapeutic approach with potential to overcome resistance and side effects associated with Lapatinib. Conclusions: Lucidin shows promise as a novel, multitargeted anti-breast cancer agent with improved efficacy over Lapatinib. These findings provide a foundation for further in vitro and in vivo validation to develop Lucidin as a potential therapeutic option for breast cancer treatment.

Impact of Intracellular Proteins on μ-Opioid Receptor Structure and Ligand Binding

Chronic pain is a prevalent problem affecting approximately one out of every five adults in the U.S. The most effective way to treat chronic pain is with opioids, but they cause dangerous side effects such as tolerance, addiction, and respiratory depression, which makes them quite deadly. Opioids, such as fentanyl, target the μ-opioid receptor (MOR), which can then bind to the intracellular Gi protein or the β-arrestin protein. The Gi pathway is primarily responsible for pain relief and potential side effects, but the β-arrestin pathway is chiefly responsible for the unwanted side effects. Ideally, an effective pain medication without side effects would bind to MOR, which would bias signaling solely through the Gi pathway. We used the Bio3D library to conduct principal component analysis to compare the cryo-electron microscopy MOR structure in complex with the Gi versus an X-ray crystallography MOR structure with a nanobody acting as a Gi mimic. Our results agree with a previous study by Munro, which concluded that nanobody-bound MOR is structurally different than Gi-bound MOR. Furthermore, we investigated the structural diversity of opioids that can bind to MOR. Quantum mechanical calculations show that the low energy solution structures of fentanyl differ from the one bound to MOR in the experimental structure, and pKa calculations reveal that fentanyl is protonated in aqueous solution. Glide docking studies show that higher energy structures of fentanyl in solution form favorable docking complexes with MOR. Our calculations show the relative abundance of each fentanyl conformation in solution as well as the energetic barriers that need to be overcome to bind to MOR. Docking studies confirm that multiple fentanyl conformations can bind to the receptor. Perhaps a variety of conformations of fentanyl can stabilize multiple conformations of the MOR, which can explain why fentanyl can induce different intracellular signaling and multiple physiological effects.

Exploring Inhibition Mechanisms in Wildtype and T315I BCR-ABL1: An In Silico Approach Integrating Virtual Screening, MD Simulations, and MM-GBSA Analysis

The BCR-ABL tyrosine kinase which is responsible for the pathogenesis of chronic myeloid leukemia (CML), has emerged as a promising therapeutic target. To address this issue, we employed a comprehensive computational approach integrating virtual screening, molecular dynamics (MD) simulations, and MM-GBSA (Molecular Mechanics/Generalized Born Surface Area) analysis to identify potential inhibitors and elucidate their binding mechanisms. Initially, virtual screening was conducted on 994 compounds from the ZINC database and, these compounds were docked against wildtype and T315I mutant ABL1 for the Type I and Type II ABL1 kinase inhibition mechanisms. In our molecular docking analysis for Type I inhibition, compound 911 demonstrated notable affinity towards the wildtype ABL1, with a binding energy of -14.91 kcal/mol, while compound 972 showed significant binding affinity towards the mutant ABL1, with a binding energy of -14.27 kcal/mol. In the Type II inhibition mechanism, the compounds with the highest binding affinity were compound 261 in wildtype ABL1 with -17.05 kcal/mol binding energy and compound 966 to the mutant ABL1 with a binding energy of -16.29 kcal/mol. Furthermore, analyses of MD simulations and MM/GBSA binding free energy (ΔG) were performed for target proteins with compounds, that exhibited the most favorable binding affinities with target proteins. The selected hit compounds showed ΔG scores ranging from -118.09 to -74.85 kJ/mol in both wildtype and mutant ABL1. Considering all in silico studies performed, it can be inferred that the identified molecules hold promise as potential candidates for drug design aimed at targeting CML.

ADP-ribosyltransferase-based biocatalysis of nonhydrolyzable NAD+ analogs

Enzyme promiscuity is the ability of an enzyme to catalyze an unexpected side reaction in addition to its main reaction. Here, we describe a biocatalytic process to produce nonhydrolyzable NAD+ analogs based on the ADP-ribosyltransferase activity of pertussis toxin PtxS1 subunit. First, in identical manner to normal catalysis, PtxS1 activates NAD+ to form the reactive oxocarbenium cation. Subsequently, the electrophilic ribose 1' carbon of the oxocarbenium cation is subject of an attack by the nitrogen atom of an amino group coupled to nicotinamide mimicking compounds. The nitrogen atom acts as the nucleophile instead of the natural sulfur atom substrate of the human Gαi protein. The invention builds on structural data indicating the presence of an NAD+ analog, benzamide amino adenine dinucleotide, at the NAD+ binding site of PtxS1. This was witnessed upon cocrystallization of PtxS1 with NAD+ and 3-aminobenzamide (3-AB). A pharmacophore-based screening on 3-AB followed by quantum mechanical simulations identified analogs of 3-AB with capacity to react with the oxocarbenium cation. Based on HPLC and mass spectrometry, we confirmed the formation of benzamide amino adenine dinucleotide by PtxS1, and also identified two new chemical entities. We name the new entities as isoindolone amine adenine dinucleotide, and isoquinolinone amine adenine dinucleotide, the latter being a highly fluorescent compound. The new NAD+ analogs emerge as valuable tools to study the structural biology and enzymology of NAD+ binding and consuming enzymes, such as human poly(ADP-ribose) polymerases and bacterial ADP-ribosyltransferase exotoxins, and to advance the ongoing drug development efforts.

A Computational Study of Phenothiazine Derivatives as Acetylcholinesterase Inhibitors Targeting Alzheimer's Disease

BACKGROUND

Alzheimer's disease is a neurodegenerative disorder that affects learning, memory and behavioral turbulence in elderly patients. Acetylcholinesterase (AChE) inhibitors act as anti-Alzheimer's agents. Phenothiazine derivatives are considered momentous anti-Alzheimer's agents because of their AChE inhibitory activity. The elevated levels and increased expression of this protein have been associated with Alzheimer's disease. Coumarin-fused phenothiazines have emerged as significant anti-Alzheimer's agents due to their notable receptor inhibitory activity.

OBJECTIVE

Some unique phenothiazine analogs were designed, and computational studies were conducted to explore their inhibitory activity against the AChE enzyme (PDB id: 4EY7) by using the Schrodinger suite-2019-4.

METHODS

Docking studies were conducted by using the Glide module; binding free energies were calculated by means of the Prime MM-GBSA module, and Molecular dynamics (MD) simulation was performed by using the Desmond module of the Schrodinger suite. Glide scores were used to find out the binding affinity of the ligands with the target 4EY7.

RESULTS

The compounds exhibited enhanced hydrophobic interactions and formed hydrogen bonds, effectively impeding Acetylcholinesterase. The Glide scores for the compounds ranged from -13.4237 to -8.43439, surpassing the standard (Donepezil) with a score of -16.9898. Interestingly, a positive value was obtained for the MM-GBSA binding of the potent inhibitor. To gain insights into the dynamic behavior of the protein A8, molecular dynamics (MD) simulations were employed.

CONCLUSION

Based on the results, the study concludes that phenothiazine derivatives show promise as acetylcholinesterase inhibitors. Compounds with notable Glide scores are poised to exhibit significant anti-Alzheimer's activity, suggesting their potential therapeutic efficacy. Further in vitro and in vivo investigations are warranted to validate and explore the therapeutic potentials of these compounds.

Network pharmacology analysis of Plumbago zeylanica to identify the therapeutic targets and molecular mechanisms involved in ameliorating hemorrhoids

Plumbago zeylanica is an important plant used in the Ayurvedic system of medicine for the treatment of hemorrhoids or piles. Despite its clinical uses, its molecular mechanism, for ameliorating hemorrhoids is not yet explored. Hence, the present study evaluated the plausible molecular mechanisms of P. zeylanica in the treatment of hemorrhoids using network pharmacology and other in silico analysis. Network pharmacology was carried out by protein, GO, and KEGG enrichment analysis. Further ADME/T, molecular docking and dynamics studies of the resultant bioactive compounds of P. zeylanica with the regulated proteins were evaluated. Results of the network pharmacology analysis revealed that the key pathways and plausible molecular mechanisms involved in the treatment effects of P. zeylanica on hemorrhoids are cell migration, proliferation, motility, and apoptosis which are synchronized by cancer, focal adhesion, and by signalling relaxin, Rap1, and calcium pathways which indicates the involvement of angiogenesis and vasodilation which are the characteristic features of hemorrhoids. Further, the molecular docking and dynamics studies revealed that the bio active ingredients of P. zeylanica strongly bind with the key target proteins in the ambiance of hemorrhoids. Hence, the study revealed the mechanism of P. zeylanica in ameliorating hemorrhoids.Communicated by Ramaswamy H. Sarma.

Repurposing FDA-Approved Drugs for Eumycetoma Treatment: Homology Modeling and Computational Screening of CYP51 Inhibitors

Eumycetoma, a chronic fungal infection caused by Madurella mycetomatis, is a neglected tropical disease characterized by tumor-like growths that can lead to permanent disability and deformities if untreated. Predominantly affecting regions in Africa, South America, and Asia, it imposes significant physical, social, and economic burdens. Current treatments, including antifungal drugs like itraconazole, often show variable efficacy, with severe cases necessitating surgical intervention or amputation. Drug discovery for eumycetoma faces challenges due to limited understanding of the disease's molecular mechanisms and the lack of 3D structures for key targets such as Madurella mycetomatis CYP51, a well-known target for azoles' antifungal agents. To address these challenges, this study employed computational approaches, including homology modeling, virtual screening, free energy calculations, and molecular dynamics simulations, to repurpose FDA-approved drugs as potential treatments for eumycetoma targeting Madurella mycetomatis CYP51. To this end, a library of 2619 FDA-approved drugs was screened, identifying three promising candidates: montelukast, vilanterol, and lidoflazine. These compounds demonstrated favorable binding affinities, strong interactions with critical residues of the homology model of Madurella mycetomatis CYP51, and stability in molecular dynamics simulations, offering potential for further investigation as effective therapeutic options for eumycetoma.

Hemagglutinin 3 and 8 can be the most efficient influenza subtypes for human host invasion; a comparative in silico approach

The severity of the influenza virus infection is largely determined by its ability to invade the human host receptor. This critical step is conducted by utilizing hemagglutinin (HA) due to its binding with sialic acid 2,6 (SA). Though 18 subtypes (H1-H18) of HA have been identified, the most efficient one for conducting the host entry has not yet been resolved. This study aims to assess the severity of infections for HA variants by conducting a comparative docking of H1-H18 with the human SA receptor. Eighteen viral 3D structures were retrieved, minimized, and optimized for docking with human SA. In all retrieved structures, five conserved amino acid residues were selected for docking with human SA. Special protein grids were prepared by locating these five residues in the 18 selected subtypes. Results showed that H3 and H8 exerted the highest standard precision and extra precision docking scores, and the highest binding affinities with the human SA, respectively. Phylogenetic analyses confirmed the actual positioning of the selected 3D structures and showed these docked structures belonged to their usual classes due to the extremely close distances found in each docked subtype compared with its corresponding non-docked structures. H8-SA showed slightly better RMSD and SASA values than H3-SA, while H3-SIA showed more favourable radius of gyration scores than H8-SIA in the majority of the simulation period. Due to the highest affinity of binding of H3 and H8 with the human receptor, special caution should be exercised regarding any possible outbreak mediated by these subtypes in human populations. However, it is important to acknowledge a limitation inherent to the computational approach; it may hold relative rather than absolute significance. Further research is needed to deepen our understanding of the intricate interplay between HA variants and the host receptor, taking into account the broader context of viral infection dynamics.Communicated by Ramaswamy H. Sarma.

Evolution of SARS-CoV-2 spike trimers towards optimized heparan sulfate cross-linking and inter-chain mobility

The heparan sulfate (HS)-rich extracellular matrix (ECM) serves as an initial interaction site for the homotrimeric spike (S) protein of SARS-CoV-2 to facilitate subsequent docking to angiotensin-converting enzyme 2 (ACE2) receptors and cellular infection. More recent variants, notably Omicron, have evolved by swapping several amino acids to positively charged residues to enhance the interaction of the S-protein trimer with the negatively charged HS. However, these enhanced interactions may reduce Omicron's ability to move through the HS-rich ECM to effectively find ACE2 receptors and infect cells, raising the question of how to mechanistically explain HS-associated viral movement. In this work, we show that Omicron S proteins have evolved to balance HS interaction stability and dynamics, resulting in enhanced mobility on an HS-functionalized artificial matrix. This property is achieved by the ability of Omicron S-proteins to cross-link at least two HS chains, allowing direct S-protein switching between chains as a prerequisite for cell surface mobility. Optimized HS interactions can be targeted pharmaceutically, as an HS mimetic significantly suppressed surface binding and cellular infection specifically of the Omicron variant. These findings suggest a robust way to interfere with SARS-CoV-2 Omicron infection and potentially future variants.

A Combined Approach for Rapid Dereplication of Herb-Drug Interaction Causative Agents in Botanical Extracts-A Molecular Networking Strategy To Identify Potential Pregnane X Receptor (PXR) Modulators in Yohimbe

Despite promising preliminary biology, natural products isolation efforts may be confounded when the active compound is not isolated during bioassay-guided purification or classical pharmacognostic research investigations. A more rational isolation procedure connecting the polypharmacology of an herb to its individual constituents must be applied to better detect bioactive molecules before tedious analytical steps are considered. While Pausinystalia johimbe (yohimbe) has been traditionally used in herbal medicine as a general tonic, an aphrodisiac, a performance enhancer, and an integral part of various dietary supplements, the hydroethanolic extract of yohimbe was identified to possess at least 3-4-fold induction of the pregnane X receptor (PXR) at 30 μg/mL, a key nuclear receptor implicated in adverse interactions, viz., herb-drug interactions (HDIs). For rapid dereplication of potential HDI agents within yohimbe, a novel MS/MS-based molecular networking analysis was integrated with in vitro data and in silico analysis of activity at PXR. Analysis of the molecular network of biologically active fractions resulted in the dereplication of three oxindole alkaloids, 14 indole alkaloids, and eight N-oxide alkaloids as the primary causative agents for PXR induction. The findings of this study indicate that this strategy could effectively guide the rapid dereplication of bioactive causative agents within complex botanical extracts. Additionally, it serves as a proof-of-concept for using integrated MS/MS-based molecular networking analysis to assess the safety profile of botanical supplements.

Evaluation of the Anti-Amyloid and Anti-Inflammatory Properties of a Novel Vanadium(IV)-Curcumin Complex in Lipopolysaccharides-Stimulated Primary Rat Neuron-Microglia Mixed Cultures

Lipopolysaccharides (LPS) are bacterial mediators of neuroinflammation that have been detected in close association with pathological protein aggregations of Alzheimer's disease. LPS induce the release of cytokines by microglia and mediate the upregulation of inducible nitric oxide synthase (iNOS)-a mechanism also associated with amyloidosis. Curcumin is a recognized natural medicine but has extremely low bioavailability. V-Cur, a novel hemocompatible Vanadium(IV)-curcumin complex with higher solubility and bioactivity than curcumin, is studied here. Co-cultures consisting of rat primary neurons and microglia were treated with LPS and/or curcumin or V-Cur. V-Cur disrupted LPS-induced overexpression of amyloid precursor protein (APP) and the in vitro aggregation of human insulin (HI), more effectively than curcumin. Cell stimulation with LPS also increased full-length, inactive, and total iNOS levels, and the inflammation markers IL-1β and TNF-α. Both curcumin and V-Cur alleviated these effects, with V-Cur reducing iNOS levels more than curcumin. Complementary insights into possible bioactivity mechanisms of both curcumin and V-Cur were provided by In silico molecular docking calculations on Aβ1-42, APP, Aβ fibrils, HI, and iNOS. This study renders curcumin-based compounds a promising anti-inflammatory intervention that may be proven a strong tool in the effort to mitigate neurodegenerative disease pathology and neuroinflammatory conditions.

Structure- and Ligand-Based Virtual Screening for Identification of Novel TRPV4 Antagonists

Transient receptor potential vanilloid (TRPV) 4 is involved in signaling pathways specifically mediating pain and inflammation, making it a promising target for the treatment of various painful and inflammatory conditions. However, only one drug candidate targeting TRPV4 has entered the clinical trials. To identify potential TRPV4 inhibitors for drug development, we screened a library of ion channel-modulating compounds using both structure- and ligand-based virtual screening approaches. Since a high-resolution experimental structure of the human TRPV4 (hTRPV4) was not available during this study, we used a comparative model of hTRPV4 for the structure-based screening by molecular docking. The ligand-based virtual screening was performed using the pharmacophoric features of two known TRPV4 antagonists. Five potential hits were selected based on either the binding stability or the pharmacophore match, and their effect on hTRPV4 was tested using a FLIPRtetra assay. All tested compounds inhibited hTRPV4 at 30 µM, with compound Z1213735368 showing an IC50 of 8 µM at a concentration of 10 µM. Furthermore, natural stilbenoids, known to modulate other TRP channels, were evaluated for their hTRPV4 binding and inhibitory potential. The findings provide insight into the structural determinants of hTRPV4 modulation and may facilitate further efforts in developing therapeutic hTRPV4 ligands.

The Diverse Binding Modes Explain the Nanomolar Levels of Inhibitory Activities Against 1-Deoxy-d-Xylulose 5-Phosphate Reductoisomerase from Plasmodium falciparum Exhibited by Reverse Hydroxamate Analogs of Fosmidomycin with Varying N-Substituents

It is established that reverse hydroxamate analogs of fosmidomycin inhibit the growth of Plasmodium falciparum by inhibiting 1-deoxy-d-xylulose 5-phosphate reductoisomerase (DXR), the second enzyme of the non-mevalonate pathway, which is absent in humans. Recent biochemical studies have demonstrated that novel reverse fosmidomycin analogs with phenylalkyl substituents at the hydroxamate nitrogen exhibit inhibitory activities against PfDXR at the nanomolar level. Moreover, crystallographic analyses have revealed that the phenyl moiety of the N-phenylpropyl substituent is accommodated in a previously unidentified subpocket within the active site of PfDXR. In this study, the crystal structures of PfDXR in complex with a series of reverse N-phenylalkyl derivatives of fosmidomycin were determined to ascertain whether the high inhibitory activities of the derivatives are consistently attributable to the utilization of the subpocket of PfDXR. While all reverse fosmidomycin derivatives with an N-substituted phenylalkyl group exhibit potent inhibitory activity against PfDXR, the present crystal structure analyses revealed that their binding modes to the PfDXR are not uniform. In these compounds, the nanomolar inhibitory activities appear to be driven by binding modes distinct from that observed for the inhibitor containing the N-phenylpropyl group. The structural information obtained in this study will provide a basis for further design of fosmidomycin derivatives.

Neuroprotective Potential of Indole-Based Compounds: A Biochemical Study on Antioxidant Properties and Amyloid Disaggregation in Neuroblastoma Cells

Based on the established neuroprotective properties of indole-based compounds and their significant potential as multi-targeted therapeutic agents, a series of synthetic indole-phenolic compounds was evaluated as multifunctional neuroprotectors. Each compound demonstrated metal-chelating properties, particularly in sequestering copper ions, with quantitative analysis revealing approximately 40% chelating activity across all the compounds. In cellular models, these hybrid compounds exhibited strong antioxidant and cytoprotective effects, countering reactive oxygen species (ROS) generated by the Aβ(25-35) peptide and its oxidative byproduct, hydrogen peroxide, as demonstrated by quantitative analysis showing on average a 25% increase in cell viability and a reduction in ROS levels to basal states. Further analysis using thioflavin T fluorescence assays, circular dichroism, and computational studies indicated that the synthesized derivatives effectively promoted the self-disaggregation of the Aβ(25-35) fragment. Taken together, these findings suggest a unique profile of neuroprotective actions for indole-phenolic derivatives, combining chelating, antioxidant, and anti-aggregation properties, which position them as promising compounds for the development of multifunctional agents in Alzheimer's disease therapy. The methods used provide reliable in vitro data, although further in vivo validation and assessment of blood-brain barrier penetration are needed to confirm therapeutic efficacy and safety.

Novel Tripeptides as Tyrosinase Inhibitors: In Silico and In Vitro Approaches

Tyrosinase is a key enzyme responsible for the formation of melanin (a natural skin pigment with ultraviolet-protection properties). However, some people experience melanin overproduction, so new, safe, and biocompatible enzyme inhibitors are sought. New tripeptide tyrosinase inhibitors were developed using molecular modeling. A combinatorial library of tripeptides was prepared and docked to the mushroom tyrosinase crystal structure and investigated with molecular dynamics. Based on the results of calculations and expert knowledge, the three potentially most active peptides (CSF, CSN, CVL) were selected. Their in vitro properties were examined, and they achieved half-maximal inhibitory concentration (IC50) values of 136.04, 177.74, and 261.79 µM, respectively. These compounds attach to the binding pocket of tyrosinase mainly through hydrogen bonds and salt bridges. Molecular dynamics simulations demonstrated the stability of the peptid-tyrosinase complexes and highlighted the persistence of key interactions throughout the simulation period. The ability of these peptides to complex copper ions was also confirmed. The CSF peptide showed the highest chelating activity with copper. The 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay confirmed that none of the test tripeptides showed cytotoxicity toward the reconstructed human epidermis. Our results indicated that the developed tripeptides were non-toxic and effective tyrosinase inhibitors. They could be applied as raw materials in skin-brightening or anti-aging cosmetic products.

Reversal of insulin resistance to combat type 2 diabetes mellitus by newer thiazolidinedione's in fructose induced insulin resistant rats

In our pursuit of discovering new antidiabetic agents to manage type 2 diabetes mellitus (T2DM), our approach aimed to identify the bioactive feature/pharmacophore responsible for PPAR-γ expression, as it is accountable for the glucose homeostasis and lipid metabolism. This was achieved by pharmacophore model generation, screening of rationally designed newer thiazolidinedione's library, identifying synthesizing and characterizing the top ten molecules (5a-5j) for their (Invitro & invivo) antidiabetic activity. Preliminary screening of all the ligands by Invitro glucose uptake assay in L6 myotubes (skeletal muscle cell line of rats) revealed compound 5b and 5f stimulated the glucose uptake with 79.29 ± 1.02 % and 74.58 ± 1.02 % respectively compared to pioglitazone with 82.36 ± 0.98 %. This was validated by PPAR-γ TF expression assay, which highlighted a dose dependent increase in transactivation of PPAR-γ. These compounds 5b and 5f were evaluated in fructose induced insulin resistance rat model. Where the treatment with 5b and 5f markedly increased the exogenous clearance of glucose and exogenous insulin via OGTT and ITT respectively, also improved the glucose utilization by significantly increasing content of glycogen and uptake of glucose in rat hemidiaphragm and reversed insulin resistance. Likewise a significant decreased in the VLDL and triglyceride levels was seen in 5b and 5f treated groups compared to insulin resistant (IR) group. It improved glycogenesis by catabolism of glucose and maintained glycaemic control. Similarly it had marked action on enzymatic oxidative biomarkers. Compound 5b displayed better, improved T1/2 (half-life) of 4.21 h and Kel (elimination constant) of 0.381 was noticed in comparison to compound 5f indicating the pharmacokinetic profile. Insilico studies like DFT calculations refined the geometry of 5b and 5f ligands, docking and molecular simulation provided the insights in binding affinity, dynamic behaviour and stability of ligands in PPAR-γ ligand binding domain. MM/GBSA provided the energetics of 5b and 5f in binding pocket. Finally network pharmacology identified ADIPOQ (adiponectin), NR1C3 (PPAR-γ), SLC2A4 (GLUT4), and LEP (leptin) proteins associate with compound 5b and 5f and enriched in Adipocytokine pathway, and PPAR-γ signaling pathway.

Novel apocynin regulates TRPV1 activity in the trigeminal system and controls pain in a temporomandibular joint neurogenic model

OBJECTIVE

Herein, we investigate the potential analgesic effect of a newly synthesized chalcone-derived apocynin in a neurogenic pain model.

METHODS

Molecular docking was used to foretell the apocynin binding features and dynamics with the TRPV1 channel, and the activity was tested in vitro, using transfected HEK 293T cells with the rat TRPV1 receptor. The analgesic effect of apocynin was investigated using a capsaicin-induced pain model. The expression of TRPV1, TRPA1, TRPM8, and MAPKs was assessed by electrophoresis, and immunosorbent assays were performed to quantify the neurotransmitters Substance P, Glutamate, and CGRP. A survival assay using Galleria mellonella was carried out to determine the toxicity.

RESULTS

We observed that apocynin exhibits greater thermodynamic stability. Upon apocynin ligand binding, it changes the electrostatic potential for a predominantly electronegative state in the interior and neutral in its external vanilloid pocket. Treatment of apocynin induces antinociceptive effects against the noxious challenge of capsaicin. Histologically, apocynin decreased the number of TRPV1+ immunopositive cells. Electrophoresis showed reduced phosphorylation of p44/42 (ERK1/2) and decreased protein levels of substance P, and CGRP. In the survival assay, apocynin showed low toxicity.

CONCLUSIONS

In conclusion, we provide proof-of-principles that the newly synthesized apocynin compound effectively prevented nociception in a neurogenic model of orofacial pain.

Structure Characterization of Zinc Finger Motif 1 and 2 of GLI1 DNA Binding Region

As a transcription factor, GLI1 plays an important role in cell cycle regulation, DNA replication, and DNA damage responses. The aberrant activation of GLI1 has been associated with cancers such as glioma, osteosarcoma, and rhabdomyosarcoma. The binding of GLI1 to a specific DNA sequence was achieved by five tandem zinc finger motifs (Zif motifs) on the N-terminal part of the molecule. Here, we reported a novel homodimeric crystal structure of Zif1-2. These two Zif motifs are linearized. Namely, Zif2 does not bend and interact with Zif1 of the same molecule. Instead, Zif1 from one molecule interacts with Zif2 from another molecule. The dimer interface of Zif1-2 is unique and different from the conformation of Zif1-2 from the GLI1-DNA co-crystal structure. The dimeric conformation of Zif motifs could represent the native conformation of apo form GLI1 Zif motifs in the cell. The molecular dynamics simulation result of the homodimer, the in silico mutagenesis, and the predicted protease stability of these mutants using a large language model are also presented.

Regulatory interactions between APOBEC3B N- and C-terminal domains

APOBEC3B (A3B) is implicated in DNA mutations that facilitate tumor evolution. Although structures of its individual N- and C-terminal domains (NTD and CTD) have been resolved through X-ray crystallography, the full-length A3B (fl-A3B) structure remains elusive, limiting understanding of its dynamics and mechanisms. In particular, the APOBEC3B C-terminal domain (A3Bctd) active site is frequently closed in models and structures. In this study, we built several new models of fl-A3B using integrative structural biology methods and selected a top model for further dynamical investigation. We compared dynamics of the truncated (A3Bctd) to the fl-A3B via conventional and Gaussian accelerated molecular dynamics (MD) simulations. Subsequently, we employed weighted ensemble methods to explore the fl-A3B active site opening mechanism, finding that interactions at the NTD-CTD interface enhance the opening frequency of the fl-A3B active site. Our findings shed light on the structural dynamics of fl-A3B, which may offer new avenues for therapeutic intervention in cancer.

An evaluation of the precision of computational methods used in drug development initiatives

Computational approaches are commonly employed to expedite and provide decision-making for the drug development process. Drug development programs that involve targets without known crystal structures can be quite challenging. In many cases, a viable approach is to generate reliable homology models using the amino acid sequence of the target. This is followed by a series of validation steps, druggable pocket detection, and then moving forward with lead identification and validation. This study commenced by conducting an initial benchmark exercise using a series of computationally designed sequences for steroid-binding proteins. By conducting an unbiased comparison with the released X-ray crystal structures, the homology models that were generated demonstrated reliable outcomes. The aligned homology models showed a root mean square deviation (RMSD) of less than 0.6 Å when compared to the corresponding X-ray structures. Three different methods were used to detect the druggable cavities for comparison, and the identified pockets closely resembled those of the crystal structures. The achievement of near-native pose prediction was made possible by utilizing the comprehensive binding energy function that characterizes the interaction between each pose and the neighboring residues. In order to address the issue of limited correlation between entropy and internal energy in docking, an alternative was devised by incorporating entropy as a post-docking optimization step to enhance the accuracy of ligand binding affinity predictions and improve the overall quality of the results.

Input Pose is Key to Performance of Free Energy Perturbation: Benchmarking with Monoacylglycerol Lipase

Free energy perturbation (FEP) methodologies have become commonplace methods for modeling potency in hit-to-lead and lead optimization stages of drug discovery. The conformational states of the initial poses of compounds for FEP+ calculations are often set up by alignment to a cocrystal structure ligand, but it is not clear if this method provides the best result for all proteins or all ligands. Not only are ligand conformational states potential variables in modeling compound potency in FEP but also the selection of crystallographic water molecules for inclusion in the FEP input structures can impact FEP models. Here, we report the results of FEP calculations using FEP+ from Schrödinger and starting from maximum common substructure alignment and docked poses generated with an array of docking methodologies. As a benchmark data set, we use monoacylglycerol lipase (MAGL), an important clinical drug target in cancer malignancy, neurological diseases, and metabolic disorders, and a set of 17 MAGL inhibitors. We found a large variation among FEP+ correlations to experimental IC50 values depending on the method used to generate the input pose and that the inclusion of ligand-based information in the docking process, with some methods, increases the correlation between FEP+ free energies and IC50 values. Upon analysis of the initial poses, we found that the differences in FEP+ correlations stemmed from rotation around a tertiary amide bond as well as translation of the compound toward the more hydrophobic side of the MAGL pocket. FEP+ estimation improved across all pose modeling methods when hydrogen bond constraint information was added. However, simple maximum common substructure alignment in the presence of all crystallographic water molecules outperformed all other methods in correlation between estimated and experimental IC50 values. Taken together, these findings suggest that pose selection and crystallographic water inclusion greatly impact how well FEP+ estimated IC50 values align with experimental IC50 values and that modelers should benchmark a few different pose generation methodologies and different water inclusion strategies for their hit-to-lead and lead optimization drug discovery projects.

Discovery of CHF-6523, an Inhaled Selective PI3Kδ Inhibitor for the Treatment of Chronic Obstructive Pulmonary Disease

The design of inhaled selective phosphatidylinositol 3-kinase delta (PI3Kδ) inhibitors for the treatment of inflammatory lung diseases was pursued. Knowledge-based design of a novel isocoumarin scaffold that was able to adopt a propeller-shape topology ensured the desired PI3Kδ selectivity. Achievement of low nanomolar cellular potencies through hinge binder group optimization, reduction of intrinsic permeability through head group optimization to extend lung retention, and screening of crystalline forms suitable for administration as dry powders culminated in the identification of compound 18. This novel inhaled selective PI3Kδ inhibitor displayed durable anti-inflammatory activity in a disease-relevant rat model of Th-2-driven acute lung inflammation and safe in vitro and in vivo preclinical profiles. Therefore, compound 18 showed the appropriate discovery profile and was progressed to clinical trials in healthy volunteers and chronic obstructive pulmonary disease (COPD) patients as CHF-6523.

Bioisosteric replacement of the carboxylic acid group in Hepatitis-C virus NS5B thumb site II inhibitors: phenylalanine derivatives

Hepatitis C virus (HCV) is a global health concern and the NS5B RNA-dependent RNA polymerase (RdRp) of HCV is an attractive target for drug discovery due to its role in viral replication. This study focuses on NS5B thumb site II inhibitors, specifically phenylalanine derivatives, and explores bioisosteric replacement and prodrug strategies to overcome limitations associated with carboxylic acid functionality. The synthesized compounds demonstrated antiviral activity, with compound 6d showing the most potent activity with an EC50 value of 3.717 μM. The hydroxamidine derivatives 7a-d showed EC50 values ranging from 3.9 μM to 11.3 μM. However, the acidic heterocyclic derivatives containing the oxadiazolone (8a-d) and oxadiazolethione (9a-d) rings did not exhibit measurable activity. A methylated heterocycle 10b showed a hint of activity at 8.09 μM. The pivaloyloxymethyl derivatives 11a and 11b did not show antiviral activity. Further studies are warranted to fully understand the effects of these modifications and to explore additional strategies for developing novel therapeutic options for HCV.