End-Point Binding Free Energy Calculation with MM/PBSA and MM/GBSA: Strategies and Applications in Drug Design

Discovery of Flavonol derivatives as porcine reproductive and respiratory syndrome virus inhibitors

Porcine reproductive and respiratory syndrome virus (PRRSV) causes serious threat to the global pig industry, and there was still no efficient treatment for porcine reproductive and respiratory syndrome (PRRS). Flavonol compounds were reported to show antiviral activity against a series of different virus. In this study, we designed a series of flavonol derivatives as promising lead structure for PRRSV inhibitors. A flavonol derivative database with diverse structures was first generated, and their anti-PRRSV activity were test. Among these compounds, compound 4s showed promising anti-PRRSV activity with EC50 values of 0.45 μM. In addition, it exhibited low cytotoxicity with CC50 higher than 100 μM. We also found that compound 4s inhibited PRRSV might be by repressing the activity of nsp4 protease. Molecular modeling study revealed that compound 4s binding to nsp4 mainly relies on a salt bridge and hydrophobic interaction. Our results might provide a new way for the development of PRRSV inhibitors.

Virtual screening, in silico pharmacokinetic and toxicity profiling of colchicine-based inhibitors of estrogen receptor of breast cancer

The declining efficacies of existing drugs against estrogen receptor positive (ER+) breast cancer due to multidrug resistance, acute toxicities, and poor pharmacokinetic properties has necessitated the discovery of newer ones. In this study, colchicine analogues with proven in vitro activities against breast cancer cells were screened against estrogen receptor alpha (ERα) via molecular docking simulations to identify some promising drug candidates. The identified ligands were further subjected to MM/GBSA calculations to ascertain their solvation-dependent Gibb's free energy of binding (∆GB). Three most promising ligands (MPLs); 12, 16, and 21 with ∆GB values of - 40.37, - 40.31, and - 40.26 kcal/mol, respectively, were identified. When compared with tamoxifen (standard drug) whose ∆GB value is - 38.66 kcal/mol, the MPLs appear more potent. The kinetic stabilities of 12, 16, and 21 were confirmed by DFT (B3LYP/6-31G*) calculations and the time-dependent thermodynamic stabilities of their complexes with ERα were established by molecular dynamic simulations. In addition, the MPLs display positive pharmacokinetic and toxicity profiles and could be excellent sources of potent and non-toxic drug candidates against ER+ breast carcinoma.

Identification of small covalent inhibitors targeting DsbA using virtual screening, covalent docking, and molecular dynamics simulations

Antimicrobial resistance (AMR) is a growing global health threat, highlighting the urgent need for new therapeutic strategies. The development of bacterial antivirulence agents and antibiotic adjuvants offers two promising strategies for combating bacterial infections. The DsbA protein is crucial for bacterial virulence and resistance, catalyzing the formation of disulfide bonds in bacterial proteins, making it an attractive target for novel antibiotics. In this study, we employed virtual screening, covalent docking, and molecular dynamics simulations to screen a library of 69,579 compounds for inhibitors targeting Cys30, a key nucleophilic residue in the CXXC catalytic motif of DsbA. We identified four small molecule covalent inhibitors that form covalent bonds with DsbA. The MM/PBSA results indicate that three covalent compounds (Cov28322, Cov16876, and Cov64052) have lower binding energies than the positive control. However, covalent binding typically offers superior target specificity and durability. These inhibitors primarily interact with key regions of DsbA, including the CXXC motif and L2 loop, suggesting their potential to disrupt DsbA's catalytic activity. This study provides a theoretical basis for designing DsbA covalent inhibitors as antibiotic adjuvants, presenting a promising strategy to combat bacterial infections and AMR.

Potential P-glycoprotein (P-gp) inhibitors from SuperDRUG2 database toward reversing multidrug resistance in cancer treatment: Database mining, molecular dynamics, and binding energy estimations

P-glycoprotein (P-gp) transporter is included in the failure of various carcinoma chemotherapeutics because of the multidrug resistance (MDR) phenomenon, in which the chemotherapeutic drugs are eliminated from target cells. Consequently, inhibiting P-gp transporter function is a prospective strategy for cancer treatment. In the current study, the SuperDRUG2 database containing >4600 pharmaceutical compounds was virtually screened toward the P-gp transporter utilizing the docking predictions. For inhibitors with a docking score lower than -10.5 kcal/mol, molecular dynamics (MD) simulations were performed, accompanied by binding energy evaluations using the MM-GBSA approach. In accordance with the MM-GBSA//100 ns MD, angiotensin amide (SD003508), terlipressin (SD002603), argipressin (SD002535), and lanreotide (SD001365) exhibited potential binding affinities against the P-gp transporter with ΔGbinding < -120.0 kcal/mol. The outstanding consistency of the investigated inhibitors inside the P-gp binding pocket was shown by the post-dynamics analyses. Additionally, MD simulations of the inhibitor-P-gp complexes in a POPC membrane environment were conducted to mimic the physiological conditions. These results demonstrated that angiotensin amide, terlipressin, argipressin, and lanreotide are promising P-gp inhibitors and deserve additional in-vitro/in-vivo studies.

Role of in situ surfactant modification of lignin structure and surface properties during glycerol pretreatment in modulating cellulase-lignin binding affinities

Surfactants are effective agents for enhancing lignocellulosic pretreatment, synergistically modifying lignin with polyols to improve substrate hydrolyzability while achieving comparable delignification. However, the mechanisms underlying the multiple modifications from dual in situ surfactant/polyols grafting that passivate lignin-cellulase interactions and their core affecting factors remain unclear. Following the previously developed polyethylene glycol (PEG) and Triton-assisted pretreatment, the intrinsic correlation among lignin structures, physical barriers, and cellulase interactions was analyzed in this study. The surfactant grafting onto lignin can significantly decrease non-productive cellulase adsorption by 5-59 % compared to the initial glycerol-modified lignin. Structurally, the changes in lignin aliphatic -OH (r > 0.93), H-OH (r > 0.98), and G-OH (r > 0.74) showed strong correlations with cellulase adsorption; the -COOH and C=O were not well-valiadted for assessing the non-productive interaction. Physically, surfactant modification also induced changes in lignin surface structure, with variations in specific surface area, pore size, and pore volume showing positive correlations (r > 0.71). The structurally modified lignin had a relatively strong affinity for exo-glucanase and β-glucosidase in enzyme cocktails, while it reduced the irreversible adsorption of lignin onto cellulases (up to 97 % of total adsorbed protein). The secondary structure of desorbed cellulases underwent obvious changes independent of lignin structural modifications, with lowering β-sheet content and increasing random coil content. Based on molecular forces, surfactant modification lowered the binding free energy of cellulases by 60.3-86.5 %, and the reduction in H-bonding interaction was predominant. This study provides mechanistic insights for constructing lignin-modified pretreatments to enhance the substrate hydrolyzability.

Targeting GPR52 for potential agonists for schizophrenia therapy: A computational drug discovery study

G Protein-Coupled Receptors (GPCRs) are one of the most attractive therapeutic targets due to their active role in different systems and disease types. The increasing three-dimensional structure information of GPCRs has made them interesting for Structure-Based Drug Design (SBDD) studies. There are various orphan GPCRs whose endogenous molecules have not yet been identified, although their structural information is known. The recent discovery of the three-dimensional structure of GPR52, an orphan GPCR involved in central nervous system diseases, made it stand out as a drug target. In this study, it is aimed to find a lead drug molecule candidate for GPR52 by using structure-based drug design techniques. The study comprises a set of SBDD methods, including preparation of a small molecule library, pharmacophore modeling, molecular docking, consensus scoring, molecular dynamics simulations, calculation of binding free energy, and in silico pharmacokinetic studies for GPR52. It is expected that the molecules obtained as a result of the study may be strong candidates for in vitro and in vivo experiments or could be used as lead drug molecules in new drug discovery and development studies.

Synergistic insights into positive allosteric modulator and agonist using Gaussian accelerated and tau random acceleration simulations in the metabotropic glutamate receptor 2

Schizophrenia is a severe brain disorder that usually produces a lifetime of disability. Related research shows activating metabotropic glutamate receptors holds therapeutic potential. Agonist-positive allosteric modulations (ago-PAMs) not only activate metabotropic glutamate receptors but also enhance glutamate-induced responses, offering a promising treatment strategy. However, the molecular mechanisms by which ago-PAM enhances glutamate-induced responses remain unclear, as does the potential influence of glutamate on ago-PAM. In this study, Gaussian accelerated molecular dynamics and tau random acceleration molecular dynamics simulations were employed to investigate the molecular mechanism between ago-PAM and glutamate in full-length mGlu2. Results suggest that the ago-PAM JNJ-46281222 enhances the binding affinity and residence time of glutamates in the Venus flytrap (VFT) domains by initiating a variant reverse communication from the heptahelical transmembrane (7TM) domains to VFTs via the cysteine-rich domains. Meanwhile, glutamate facilitates the interaction between Trp676 and Glu701 to further induce the relaxation of TM5, promoting the opening of the PAM-binding pocket. Glutamate can also promote the upward rotation of the cyclopropylmethyl group of the JNJ-46281222 to bring the TM6-TM6 distance closer. Nevertheless, it remains uncertain how the binding between mGlu2 and G protein differs when induced by small molecules binding in allosteric sites, orthosteric sites, or both. In conclusion, this study shed new light on the positive coordination relationship between ago-PAM and glutamate in the full-length mGlu2 receptor, which could help develop novel and more effective ago-PAM to treat schizophrenia.

Monophasic coamorphous sulpiride: a leap in physicochemical attributes and dual inhibition of GlyT1 and P-glycoprotein, supported by experimental and computational insights

Study aimed to design and development of a supramolecular formulation of sulpiride (SUL) to enhance its solubility, dissolution and permeability by targeting a novel GlyT1 inhibition mechanism. SUL is commonly used to treat gastric and duodenal ulcers, migraine, anti-emetic, anti-depressive and anti-dyspeptic conditions. Additionally, Naringin (NARI) was incorporated as a co-former to enhance the drug's intestinal permeability by targeting P-glycoprotein (P-gp) efflux inhibition. NARI, a flavonoid has diverse biological activities, including anti-apoptotic, anti-oxidant, and anti-inflammatory properties. This study aims to design and develop a supramolecular formulation of SUL with NARI to enhance its solubility, dissolution, and permeability by targeting a novel GlyT1 inhibition mechanism, extensive experimental characterization was performed using solid-state experimental techniques in conjunction with a computational approach. This approach included quantum mechanics-based molecular dynamics (MD) simulation and density functional theory (DFT) studies to investigate intermolecular interactions, phase transformation and various electronic structure-based properties. The findings of the miscibility study, radial distribution function (RDF) analysis, quantitative simulations of hydrogen/π-π bond interactions and geometry optimization aided in comprehending the coamorphization aspects of SUL-NARI Supramolecular systems. Molecular docking and MD simulation were performed for detailed binding affinity assessment and target validation. The solubility, dissolution and ex-vivo permeability studies demonstrated significant improvements with 31.88-fold, 9.13-fold and 1.83-fold increments, respectively. Furthermore, biological assessments revealed superior neuroprotective effects in the SUL-NARI coamorphous system compared to pure SUL. In conclusion, this study highlights the advantages of a drug-nutraceutical supramolecular formulation for improving the solubility and permeability of SUL, targeting novel schizophrenia treatment approaches through combined computational and experimental analyses.

Assessing the potential of Psidium guajava derived phytoconstituents as anticholinesterase inhibitor to combat Alzheimer's disease: an in-silico and in-vitro approach

Acetylcholinesterase (AChE) inhibitors play a crucial role in the treatment of Alzheimer's disease. These drugs increase acetylcholine levels by inhibiting the enzyme responsible for its degradation, which is a vital neurotransmitter involved in memory and cognition. This intervention intermittently improves cognitive symptoms and augments neurotransmission. This study investigates the potential of Psidium guajava fruit extract as an acetylcholinesterase (AChE) inhibitor for Alzheimer's disease treatment. Molecular characteristics and drug-likeness were analyzed after HR-LCMS revealed phytocompounds in an ethanolic extract of Psidium guajava fruit. Selected phytocompounds were subjected to molecular docking against AChE, with the best-docked compound then undergoing MD simulation, MMGBSA, DCCM, FEL, and PCA investigations to evaluate the complex stability. The hit compound's potential toxicity and further pharmacokinetic features were also predicted. Anticholinesterase activity was also studied using in vitro assay. The HR-LCMS uncovered 68 compounds. Based on computational analysis, Fluspirilene was determined to have the highest potential to inhibit AChE. It was discovered that the Fluspirilene-AChE complex is stable and that Fluspirilene has a high binding affinity for AChE. Extract of Psidium guajava fruit significantly inhibits AChE (88.37% at 200 μg/ml). It is comparable to the standard AChE inhibitor Galantamine. Fluspirilene exhibited remarkable binding to AChE. Psidium guajava fruit extract demonstrated substantial AChE inhibitory activity, indicating its potential for Alzheimer's treatment. The study underscores natural sources' significance in drug discovery.

In silico approaches for predicting natural compounds with therapeutic potential and vaccine candidates against Streptococcus equi

Equine strangles is a prevalent disease that affects the upper respiratory in horses and is caused by the Gram-positive bacterium Streptococcus equi. In addition to strangles, other clinical conditions are caused by the two S. equi subspecies, equi and zooepidemicus, which present relevant zoonotic potential. Treatment of infections caused by S. equi has become challenging due to the worldwide spreading of infected horses and the unavailability of effective therapeutics and vaccines. Penicillin treatment is often recommended, but multidrug resistance issues arised. We explored the whole genome sequence of 18 S. equi isolates to identify candidate proteins to be targeted by natural drug-like compounds or explored as immunogens. We considered only proteins shared among the sequenced strains of subspecies equi and zooepidemicus, absent in the equine host and predicted to be essential and involved in virulence. Of these, 4 proteins with cytoplasmic subcellular location were selected for molecular docking with a library of 5008 compounds, while 6 proteins were proposed as prominent immunogens against S. equi due to their probabilities of behaving as adhesins. The molecular docking analyses revealed the best ten ligands for each of the 4 drug target candidates, and they were ranked according to their binding affinities and the number of hydrogen bonds for complex stability. Finally, the natural 5-ring compound C25H20F3N5O3 excelled in molecular dynamics simulations for the increased stability in the interaction with UDP-N-acetylenolpyruvoylglucosamine reductase (MurB). This research paves the way to developing new therapeutics to minimize the impacts caused by S. equi infections.

Main methods and tools for peptide development based on protein-protein interactions (PPIs)

Protein-protein interactions (PPIs) regulate essential physiological and pathological processes. Due to their large and shallow binding surfaces, PPIs are often considered challenging drug targets for small molecules. Peptides offer a viable alternative, as they can bind these targets, acting as regulators or mimicking interaction partners. This review focuses on competitive peptides, a class of orthosteric modulators that disrupt PPI formation. We provide a concise yet comprehensive overview of recent advancements in in-silico peptide design, highlighting computational strategies that have improved the efficiency and accuracy of PPI-targeting peptides. Additionally, we examine cutting-edge experimental methods for evaluating PPI-based peptides. By exploring the interplay between computational design and experimental validation, this review presents a structured framework for developing effective peptide therapeutics targeting PPIs in various diseases.

In silico screening of natural products as uPAR inhibitors via multiple structure-based docking and molecular dynamics simulations

Cancer remains one of the most pressing challenges to global healthcare, exerting a significant impact on patient life expectancy. Cancer metastasis is a critical determinant of the lethality and treatment resistance of cancer. The urokinase-type plasminogen activator receptor (uPAR) shows great potential as a target for anticancer and antimetastatic therapies. In this work, we aimed to identify potential uPAR inhibitors by structural dynamics-based virtual screenings against a natural product library on four representative apo-uPAR structural models recently derived from long-timescale molecular dynamics (MD) simulations. Fifteen potential inhibitors (NP1-NP15) were initially identified through molecular docking, consensus scoring, and visual inspection. Subsequently, we employed MD-based molecular mechanics-generalized Born surface area (MM-GBSA) calculations to evaluate their binding affinities to uPAR. Structural dynamics analyses further indicated that all of the top 6 compounds exhibited stable binding to uPAR and interacted with the critical residues in the binding interface between uPAR and its endogenous ligand uPA, suggesting their potential as uPAR inhibitors by interrupting the uPAR-uPA interaction. We finally predicted the ADMET properties of these compounds. The natural products NP5, NP12, and NP14 with better binding affinities to uPAR than the uPAR inhibitors previously discovered by us were proven to be potentially orally active in humans. This work offers potential uPAR inhibitors that may contribute to the development of novel effective anticancer and antimetastatic therapeutics.

Screening of phytochemicals from Clerodendrum inerme (L.) Gaertn as potential anti-breast cancer compounds targeting EGFR: an in-silico approach

Breast cancer (BC) is the most prevalent malignancy among women around the world. The epidermal growth factor receptor (EGFR) is a tyrosine kinase receptor (RTK) of the ErbB/HER family. It is essential for triggering the cellular signaling cascades that control cell growth and survival. However, perturbations in EGFR signaling lead to cancer development and progression. Hence, EGFR is regarded as a prominent therapeutic target for breast cancer. Therefore, in the current investigation, EGFR was targeted with phytochemicals from Clerodendrum inerme (L.) Gaertn (C. inerme). A total of 121 phytochemicals identified by gas chromatography-mass spectrometry (GC-MS) analysis were screened against EGFR through molecular docking, ADMET analyses (Absorption, Distribution, Metabolism, Excretion, and Toxicity), PASS predictions, and molecular dynamics simulation, which revealed three potential hit compounds with CIDs 10586 [i.e. alpha-bisabolol (-6.4 kcal/mol)], 550281 [i.e. 2,(4,4-Trimethyl-3-hydroxymethyl-5a-(3-methyl-but-2-enyl)-cyclohexene) (-6.5 kcal/mol)], and 161271 [i.e. salvigenin (-7.4 kcal/mol)]. The FDA-approved drug gefitinib was used to compare the inhibitory effects of the phytochemicals. The top selected compounds exhibited good ADMET properties and obeyed Lipinski's rule of five (ROF). The molecular docking analysis showed that salvigenin was the best among the three compounds and formed bonds with the key residue Met 793. Furthermore, the molecular mechanics generalized born surface area (MMGBSA) calculations, molecular dynamics simulation, and normal mode analysis validated the binding affinity of the compounds and also revealed the strong stability and compactness of phytochemicals at the docked site. Additionally, DFT and DOS analyses were done to study the reactivity of the compounds and to further validate the selected phytochemicals. These results suggest that the identified phytochemicals possess high inhibitory potential against the target EGFR and can treat breast cancer. However, further in vitro and in vivo investigations are warranted towards the development of these constituents into novel anti-cancer drugs.

Molecular dynamics simulations show how antibodies may rescue HIV-1 mutants incapable of infecting host cells

High mutation and replication rates of HIV-1 result in the continuous generation of variants, allowing it to adapt to changing host environments. Mutations often have deleterious effects, but variants carrying them are rapidly purged. Surprisingly, a particular variant incapable of entering host cells was found to be rescued by host antibodies targeting HIV-1. Understanding the molecular mechanism of this rescue is important to develop and improve antibody-based therapies. To unravel the underlying mechanisms, we performed fully atomistic molecular dynamics simulations of the HIV-1 gp41 trimer responsible for viral entry into host cells, its entry-deficient variant, and its complex with the rescuing antibody. We find that the Q563R mutation, which the entry-deficient variant carries, prevents the native conformation of the gp41 6-helix bundle required for entry and stabilizes an alternative conformation instead. This is the consequence of substantial changes in the secondary structure and interactions between the domains of gp41. Binding of the antibody F240 to gp41 reverses these changes and re-establishes the native conformation, resulting in rescue. To test the generality of this mechanism, we performed simulations with the entry-deficient L565A variant and antibody 3D6. We find that 3D6 binding was able to reverse structural and interaction changes introduced by the mutation and restore the native gp41 conformation. Viral variants may not only escape antibodies but be aided by them in their survival, potentially compromising antibody-based therapies, including vaccination and passive immunization. Our simulation framework could serve as a tool to assess the likelihood of such resistance against specific antibodies.

Stereo-selectivity of enantiomeric inhibitors to ubiquitin-specific protease 7 (USP7) dissected by molecular docking, molecular dynamics simulations, and binding free energy calculations

The ubiquitin-specific protease 7 (USP7), as a member of deubiquitination enzymes, represents an attractive therapeutic target for various cancers, including prostate cancer and liver cancer. The change of the inhibitor stereocenter from the S to R stereochemistry (S-ALM → R-ALM34) markedly improved USP7 inhibitory activity. However, the molecular mechanism for the stereo-selectivity of enantiomeric inhibitors to USP7 is still unclear. In this work, molecular docking, molecular dynamics (MD) simulations, molecular mechanics/Generalized-Born surface area (MM/GBSA) calculations, and free energy landscapes were performed to address this mystery. MD simulations revealed that S-ALM34 showed a high degree of conformational flexibility compared to the R-ALM34 counterpart, and S-ALM34 binding led to the enhanced intradomain motions of USP7, especially the BL1 and BL2 loops and the two helices α4 and α5. MM/GBSA calculations showed that the binding strength of R-ALM34 to USP7 was stronger than that of S-ALM34 by - 4.99 kcal/mol, a similar trend observed by experimental data. MM/GBSA free energy decomposition was further performed to differentiate the ligand-residue spectrum. These analyses not only identified the hotspot residues interacting with R-ALM34, but also revealed that the hydrophobic interactions from F409, K420, H456, and Y514 play the major determinants in the binding of R-ALM34 to USP7. This result is anticipated to shed light on energetic basis and conformational dynamics information to aid in the design of more potent and selective inhibitors targeting USP7.

In silico identification and characterization of small molecule binding to the CD1d immunoreceptor

CD1 immunoreceptors are a non-classical major histocompatibility complex (MHC) that present antigens to T cells to elucidate immune responses against disease. The antigen repertoire of CD1 has been composed primarily of lipids until recently when CD1d-restricted T cells were shown to be activated by non-lipidic small molecules, such as phenyl pentamethyl dihydrobenzofuran sulfonate (PPBF) and related benzofuran sulfonates. To date structural insights into PPBF/CD1d interactions are lacking, so it is unknown whether small molecule and lipid antigens are presented and recognized through similar mechanisms. Furthermore, it is unknown whether CD1d can bind to and present a broader range of small molecule metabolites to T cells, acting out functions analogous to the MHC class I related protein MR1. Here, we perform in silico docking and molecular dynamics simulations to structurally characterize small molecule interactions with CD1d. PPBF was supported to be presented to T cell receptors through the CD1d F' pocket. Virtual screening of CD1d against more than 17,000 small molecules with diverse geometry and chemistry identified several novel scaffolds, including phytosterols, cholesterols, triterpenes, and carbazole alkaloids, that serve as candidate CD1d antigens. Protein-ligand interaction profiling revealed conserved residues in the CD1d F' pocket that similarly anchor small molecules and lipids. Our results suggest that CD1d could have the intrinsic ability to bind and present a broad range of small molecule metabolites to T cells to carry out its function beyond lipid antigen presentation.

Allosteric site engagement and cooperativity mechanism by PHI1 for BRAFV600E kinase inhibition

With the ability to reveal allosteric sites, Ponatinib and Ponatinib Hybrid Inhibitor 1 (PHI1) are novel inhibitors of BRAF, a potent oncogene that activates the MAPK pathway. PHI1 also exhibits unique positive cooperativity, with enhanced inhibition on the other monomer when one monomer of the BRAFV600E dimer bound to an inhibitor. The abovementioned properties lack rigorous theoretical verification, so this study compared the interaction mechanisms of four inhibitor types and explored the source of the cooperativity of PHI1 via various computational methods. Results revealed that residues on the αC-helix formed hydrogen bonds with inhibitors, shifting the position of the αC-helix. PHI1 induced binding pocket contraction through contact with allosteric sites. Entropy contributions were considerably weakened when both BRAFV600E monomers were occupied, thereby increasing the binding ability of PHI1, indicating that entropy contributions were the main source of PHI1 cooperativity. The change in overall motion intensity tightened the binding pocket, increasing the binding abilities of hotspot residues, including Arg575 and Leu567. Moreover, three key hydrogen bonds formed between PHI1 and BRAFV600E in the dimer system were conducive to the binding. The insights derived from this study are expected to advance the development of inhibitors targeting BRAFV600E kinase.

High-throughput virtual screening and empirical validation of probable inhibitors of Plasmodium falciparum and vivax glutathione transferase using bromosulfophthalein as the benchmark ligand

Plasmodium falciparum Glutathione S-Transferase (PfGST) and Plasmodium vivax Glutathione S-Transferase (PvGST) play vital roles in detoxification and parasite survival, making them key targets for antimalarial drug development. These enzymes offer potential for creating therapies with improved efficacy, reduced resistance, and minimal toxicity. Natural compounds like flavonoids, known for their antiplasmodial properties, are promising scaffolds for new drug designs. This study computationally screened baicalin (BA) and 5,7,3'-Trihydroxy-6,4',5'-trimethoxyflavone (TTMF), synthesizable and affordable flavonoids from the MedChemExpress database, as potential inhibitors of PfGST and PvGST, outperforming BSP. Molecular dynamics simulations revealed that BA and TTMF stabilize enzyme interactions through hydrogen bonds and van der Waals forces, altering protein compactness and dynamics, suggesting non-competitive, allosteric inhibition. Empirical validation showed complete enzymatic inhibition by BA and TTMF with IC50 values of 1.69 and 1.71 μM, respectively, while minimizing human GST inhibition. Using 1-chloro-2,4-dinitrobenzene and reduced glutathione (GSH) as substrates, BA and TTMF demonstrated tight binding near the hydrophobic substrate-binding sites of PfGST and PvGST. Spectroscopic analysis using 8-anilino-1-naphthalenesulfonate (ANS) confirmed their ligandin effects and binding at the dimer interface. These findings highlight BA and TTMF as promising candidates for developing effective antimalarial therapies.

Design of Mimetic Antibodies Targeting the SARS-CoV-2 Spike Glycoprotein Based on the GB1 Domain: A Molecular Simulation and Experimental Study

In the context of fast and significant technological transformations, it is natural for innovative artificial intelligence (AI) methods to emerge for the design of bioactive molecules. In this study, we demonstrated that the design of mimetic antibodies (MA) can be achieved using a combination of software and algorithms traditionally employed in molecular simulation. This combination, organized as a genetic algorithm (GA), has the potential to address one of the main challenges in the design of bioactive molecules: GA convergence occurs rapidly due to the careful selection of initial populations based on intermolecular interactions at antigenic surfaces. Experimental immunoenzymatic tests prove that the GA successfully optimized the molecular recognition capacity of one of the MA. One of the significant results of this study is the discovery of new structural motifs, which can be designed in an original and innovative way based on the MA structure itself, eliminating the need for preexisting databases. Through the GA developed in this study, we demonstrated the application of a new protocol capable of guiding experimental methods in the development of new bioactive molecules.

Computational drug design for neurosyphilis disease by targeting Phosphoglycerate Kinase in Treponema pallidum with enhanced binding affinity and reduced toxicity

Neurosyphilis, a severe neurological complication of syphilitic infection caused by the gram-negative spirochete Treponema pallidum poses significant challenges in treatment due to its irregular physiology and lack of efficacy in present therapeutic strategies. Here, we report a new approach to developing drug treatment that targets the enzyme phosphoglycerate kinase (PGK), an essential component of the T. pallidum glycolytic pathway. Therefore, a ligand was designed involving common neuroprotectant elements reported from literature by a computational drug design method, to increase their binding energy with lower toxicity. The calculated binding affinity of the designed ligand with PGK was analyzed by molecular docking to be - 116.68 kcal/mol. Also, interaction analysis predicted that there are 5 hydrophobic bonds and 3 hydrogen bonds present between the docked complex. Afterward, in-silico ADMET studies were conducted for the designed ligand that determined a strong pharmacological profile with good absorption, zero violation of Lipinski's rule, and non-toxic properties. DFT analysis further optimized the ligand with a HOMO/LOMO gap value of 0.01421 kcal/mol indicating higher reactivity and enhanced electronic interactions, improving ligand efficiency. Moreover, pharmacophore modeling confirmed the reactive nature of the ligand. Furthermore, MD simulations showed stability in the overall structure. The output shows that our optimized ligand has statistically better binding affinity than the currently used drug penicillin, with improved pharmacokinetic profiles. This work demonstrates the importance of ligand design for the discovery of new drugs to treat neurosyphilis.

Multisite λ-Dynamics for Protein-DNA Binding Affinity Prediction

Transcription factors (TFs) regulate gene expression by binding to specific DNA sequences, playing critical roles in cellular processes and disease pathways. Computational methods, particularly λ-Dynamics, offer a promising approach for predicting TF relative binding affinities. This study evaluates the effectiveness of different λ-Dynamics perturbation schemes in determining binding free energy changes (ΔΔGb) of the WRKY transcription factor upon mutating its W-box binding site (GGTCAA) to a nonspecific sequence (GATAAA). Among the schemes tested, the single λ per base pair protocol demonstrated the fastest convergence and highest precision. Extending this protocol to additional mutants (GGTCCG and GGACAA) yielded ΔΔGb values that successfully ranked binding affinities, showcasing its strong potential for high-throughput screening of DNA binding sites.

Pan-cancer analysis of CDC7 in human tumors: Integrative multi-omics insights and discovery of novel marine-based inhibitors through machine learning and computational approaches

Cancer remains a significant global health challenge, with the Cell Division Cycle 7 (CDC7) protein emerging as a potential therapeutic target due to its critical role in tumor proliferation, survival, and resistance. However, a comprehensive analysis of CDC7 across multiple cancers is lacking, and existing therapeutic options have come with limited clinical success. The aim of this is to integrate a comprehensive pan-cancer analysis of CDC7 with the identification of novel marine-derived inhibitors, bridging the understanding of CDC7's role as a prognostic biomarker and therapeutic target across diverse cancer types. In this study, we conducted a pan-cancer analysis of CDC7 across 33 tumor types using publicly available datasets to evaluate its expression, genetic alterations, immune interactions, survival, and prognostic significance. Additionally, a marine-derived compound library of 31,492 molecules was screened to identify potential CDC7 inhibitors using chemoinformatics and machine learning. The top candidates underwent rigorous evaluations, including molecular docking, pharmacokinetics, toxicity, Density Functional Theory (DFT) calculations, and Molecular Dynamics (MD) simulations. The findings revealed that CDC7 is overexpressed in several cancers and is associated with poor survival outcomes and unfavorable prognosis. Enrichment analysis linked CDC7 to critical DNA replication pathways, while its role in modulating tumor-immune interactions highlighted its potential as a target for immunotherapy. Among all tested compounds, Tetrahydroaltersolanol D (CMNPD21999) exhibited the strongest binding affinity and stability, along with better drug-likeness and zero toxicity. These attributes highlight its potential as a promising drug candidate for CDC7 inhibition and future cancer treatment development. Furthermore, additional in vitro and in vivo studies are required to confirm the effectiveness of this drug candidate against the CDC7 protein.

Exploration of small molecules as inhibitors of potential BACE1 protein to treat amyloid cerebrovascular disease by employing molecular modeling and simulation approaches

Amyloid cerebrovascular disease, primarily driven by the accumulation of amyloid-beta (Aβ) peptides, is intricately linked to neurodegenerative disorders like Alzheimer's disease. BACE1 (beta-site amyloid precursor protein cleaving enzyme 1) plays a critical role in the production of Aβ, making it a key therapeutic target. In the current work, a CNS library of ChemDiv database containing 44085 compounds was screened against the BACE1 protein. Initially, a structure-based pharmacophore hypothesis was constructed, followed by virtual screening, with the screened hits docked to the BACE1 protein to determine the optimal binding modes. The docking results were examined using the glide gscore and chemical interactions of the docked molecules. The cutoff value of -5 kcal/mol was used to select hits with high binding affinities. A total of seven hits were chosen based on the glide g score. Furthermore, the possible binding mechanisms of the docked ligands were investigated, and it was discovered that all seven selected ligands occupied the same site in the predicted binding pocket of protein. The bioactivity scores of the compounds demonstrated that the chosen compounds possess the features of lead compounds. The toxicity risks and ADMET features of the selected hits were anticipated, and four compounds, J032-0080, SC13-0774, V030-0915, and V006-5608 were chosen for stability analysis. The selected hits were extremely stable and strongly bound to the BACE1 pocket, and conformational changes caused by RMSD, RMSF, and protein-ligand interactions were assessed using MD modeling. Similarly, principal component analysis revealed a large static number of hydrogen bonds. The MM/GBSA binding free energies maps revealed a significant energy contribution in the binding of selected hits to BACE1. The binding free energy landscapes indicated that the hits were bound with a high binding affinity. Thus, the hits could serve as lead compounds in biophysical investigations to limit the biological activity of the BACE1 protein.

Molecular mechanism of ZER1-mediated recognition of N-terminal glycine in protein degradation

The N-terminal glycine (Gly/N-degron) serves as a degradation signal recognized by specific E3 ligases, playing a crucial role in protein quality control and maintaining intracellular protein homeostasis. Zinc finger E3 ubiquitin protein ligase 1 (ZER1), a substrate receptor of the Cullin 2-RING E3 ubiquitin ligase, recognizes N-terminal glycine and other small N-terminal residues (such as serine, alanine, and cysteine), mediating protein degradation through the Gly/N-degron pathway. In this study, we employed all-atom molecular dynamics (MD) simulations and binding free energy calculations to study the binding mode of ZER1 with N-terminal glycine and the effects of key residue mutations on this recognition process. The results show that the binding of glycine-containing peptides and key residue mutations have minimal impact on ZER1 structural stability. During ZER1-peptide binding, van der Waals and electrostatic interactions are the primary driving forces. Residues W552, N553, D556, N597, I678, N579, R681, and K716 play significant roles in the recognition process, with mutations in these residues affecting the electrostatic distribution and hydrophobic properties of the ZER1 binding site, thereby influencing peptide binding. Additionally, ZER1 forms a complex hydrogen-bond network with the peptide, which stabilizes the peptide like an anchor. D556A and N597A disrupt the hydrogen bond between the N-terminal residue (G1) and ZER1. These findings provide a molecular-level understanding of the N-terminal degron pathway and lay a foundation for future related research.

In silico maturation of DNA aptamer against the prostate-specific antigen (PSA) and kinetic analysis

The detection of the prostate-specific antigen (PSA) serves as a critical marker for the diagnosis and follow-up of prostate cancer. DNA aptamers targeting PSA have been successfully screened using the systematic evolution of ligands by exponential enrichment (SELEX) technique, complemented by in silico maturation processes. In this study, we aim to optimize a truncated aptamer, denoted as TA87, through computational methods and to analyze potential aptamer candidates in the aptamer-PSA interactions. The PSA antibody, aptamer ΔPSap4#5, and an identified but unpublished aptamer, PSAG221, were evaluated in quartz crystal microbalance (QCM) experiments alongside aptamers derived from TA87. The Tanimoto similarity score and the ZDOCK program, coupled with the ZRANK scoring function, were adopted to assess the secondary structure of single-point mutants of TA87 and their binding interactions with PSA, respectively. Detailed analyses of the aptamer-protein complexes were conducted using molecular dynamics (MD) simulations. Mutations TA87M24 and TA87M49, along with PSAG221 and TA87, showed superior ZDOCK scores compared to ΔPSap4#5. MD simulations further suggested that PSAG221 aptamer might offer enhanced binding to PSA over ΔPSap4#5. The affinity constant (KD) values for the antibody, ΔPSap4#5, PSAG221, TA87, TA87M24, and TA87M49 with PSA were determined through QCM measurements to be 0.35, 0.33, 0.35, 0.56, 0.45, and 0.51 μM-1, respectively. The experimental results showed that the truncated aptamers, TA87, and the two mutations, TA87M24 and TA87M49, did not demonstrate superior PSA binding affinity. Aptamer PSAG221 demonstrated performance comparable to that of the antibody, although slightly inferior to ΔPSap4#5. The aptamer PSAG221 reported in this study could be an alternative probe for developing future PSA aptasensor platforms.

Characterization of physicochemical properties of different epigallocatechin-3-gallate nanoparticles and their effect on bioavailability

Epigallocatechin-3-gallate (EGCG), a major catechin in green tea, exhibits potent antioxidant and disease-preventive properties, but its application is limited by poor stability and bioavailability. This study aimed to address these challenges by preparing and characterizing three EGCG-loaded nanoparticles: chitosan-EGCG-tripolyphosphate nanoparticles (CE-NPs), β-cyclodextrin-EGCG (BE-NPs), and EGCG-nanostructured lipid carriers (NE-NPs). BE-NPs exhibited the highest loading performance and retention rate under thermal environment (89.78 % after 10 h at 80 °C). NE-NPs had the highest EGCG stability in alkaline condition (45 % after 4 h at pH 7.4). Compared to free EGCG, all NPs significantly improved in vitro bioaccessibility following incubation in simulated gastrointestinal digestion for 4 h; BE-NPs enhanced oral bioavailability by 1.71 times in vivo. Additionally, CE-NPs and NE-NPs increased the relative abundance of Faecalibaculum, Erysipelotrichaceae, and Bifidobacterium in the colons of Sprague-Dawley rats. These findings suggest that BE-NPs are a promising nano-delivery system for enhancing EGCG stability and bioavailability in healthy organisms.

Molecular docking and molecular dynamics simulations revealed interaction mechanism of acetylcholinesterase with organophosphorus pesticides and their alternatives

Organophosphate pesticides (OPs) are widely used in agricultural fields and can inhibit the activity of human acetylcholinesterase (hAChE) by covalently binding to serine at the enzyme's active site. However, the molecular recognition mechanisms beyond their covalent binding remain unclear. This study employed molecular docking along with molecular dynamics simulations (MD) to investigate four representative OPs, Phosphamidon, Monocrotophos, Dichlorvos, and Trichlorfon, as well as two potential alternatives Magnolol (MAG) and Honokiol (HON), to understand the conformational change of hAChE and its molecular recognition mechanism. The results indicate that, in addition to these OPs, the selected substitutes also induce various changes in the internal structure of hAChE, especially interactions with key residues around Trp86, Tyr124, Tyr337, and His447. Energy calculations utilizing MM-GBSA and SIE methods further reveal the critical role of van der Waals interactions in hAChE's interaction with these OPs and their substitutes. It is worth noting that two potential pesticide alternatives MAG and HON differ in structure from OPs at the benzene ring and hydroxyl positions, resulting in their weaker binding energy with hAChE. Furthermore, the accuracy of simulation models was validated through in silico site-directed mutagenesis based on the key residues. By identifying dynamic structural changes and energy signatures, this study provides valuable information for finding safer alternatives to OPs.

Assessing novel analogues of nilutamide as a human androgen receptor antagonist: A detailed investigation of drug design using a bioisosteric methodology including ADMET profiling, molecular docking studies and molecular dynamics simulation

Cancer is a significant health and economic concern worldwide. Prostate cancer (PC) ranks as the fourth leading cause of global death and is the second most prevalent malignancy in males. Androgens are essential for the progress and growth of the prostate gland. PC is caused by androgens binding to receptors, which activates genes that promotes the development of PC. Nilutamide (NLM) is an antiandrogen medicine used in the treatment of PC. However, throughout treatment, it induces various toxicities and leads to resistance in patients. The objective of the work was to designed and evaluated safer NLM analogues using computational approaches with optimized pharmacokinetic profiles and less toxicity. Newer bioisosteres of the designed NLM analogues and their ADMET scores were calculated using the MolOpt and ADMETlab 3.0 tools, respectively. We conducted docking investigations of the designed ligands using AutoDock Vina software. The MolOpt web server produces 1575 bioisosteres of NLM using the scaffold transformation method. The 47 bioisosteres were selected based on pharmacokinetic profiles, drug likeness (DL) and drug score (DS) prediction scores and were determined to be optimum to excellent in comparison to NLM. The analogues NLM28, NLM31, NLM34, NLM38, NLM40, NLM44, NLM45, and NLM47 exhibited favorable interactions and docking scores with the protein (PDB ID: 2AM9). The molecular dynamics (MD) simulation results revealed that the NLM34 and NLM40 complexes were found stable during the 100 ns run. The findings indicate that the NLM analogues, particularly NLM34 and NLM40 have the potential to be used as promising antiandrogen agents for PC therapy.

Exploiting the Achilles' heel of cancer through a structure-based drug-repurposing approach and experimental validation of top drugs using the TRAP assay

Telomerase, a reverse transcriptase implicated in replicative immortality of cancers, remains a challenging target for therapeutic intervention due to its structural complexity and the absence of clinically approved small-molecule inhibitors. In this study, we explored drug repurposing as a pragmatic approach to address this gap, leveraging FDA-approved drugs to accelerate the identification of potential telomerase inhibitors. Using a structure-based drug discovery framework, we screened the DrugBank database through a previously validated pharmacophore model for the FVYL pocket in the hTERT thumb domain, the established binding site of BIBR1532. This was followed by molecular docking, pharmacokinetic filtering, and molecular dynamics (MD) simulations to evaluate the stability of protein-ligand complexes. Binding free energy calculations (MM-PBSA and MM-GBSA) were employed for cross-validation, identifying five promising candidates. Experimental validation using the Telomerase Repeat Amplification Protocol (TRAP) assay confirmed the inhibitory potential of Raltitrexed, showing significant inhibition with IC50 8.899 µM in comparison to control. Decomposition analysis and Structure-Activity Relationship (SAR) studies further offered insights into the binding mechanism, reinforcing the utility of the FVYL pocket as a druggable site. Raltitrexed's dual mechanism of action, targeting both telomerase and thymidylate synthase, underscores its potential as a versatile anticancer agent, suitable for combination therapies or standalone treatment. As the top lead, Raltitrexed demonstrates the potential of repurposed drugs in telomerase-targeted therapies, offering a time and cost-effective strategy for advancing its clinical development. The study also provides a robust framework for future drug development, addressing challenges in targeting telomerase for anticancer therapy.

In Silico Evaluation of Potential Hit Molecules Against Multiple Serotypes of Dengue Virus Envelope Glycoprotein

Dengue Fever, a widespread mosquito-borne disease caused by the dengue virus (DENV), poses a major health threat in tropical and subtropical regions worldwide, resulting in millions of infections yearly. Severe cases of dengue fever have a mortality rate of around fifteen percent. Currently, there are no antiviral treatments for this disease and the only FDA-approved vaccine has been known to have adverse effects, especially in children. Thus, there is an urgent need for new therapeutics for Dengue fever. The largest issue with developing an antiviral treatment is that DENV has four serotypes that each differ slightly enough to pose problems with one compound inhibiting all four. This study addresses that challenge to some extent by focusing on in silico screening of potential hits targeting the envelope glycoprotein, which is relatively conserved across these four serotypes. Using pharmacophore screening and in silico evaluation of ligands, we identified compounds which could potentially have high affinity to the envelope glycoprotein for two of the four DENV serotypes. These in silico results were validated experimentally using bio-layer interferometry. These findings lay a foundation for in vitro analysis and hit-to-lead studies, advancing the development of antivirals that can inhibit multiple serotypes of the dengue virus.

Binding Free Energy Analysis of Colicin D, E3 and E8 to Their Respective Cognate Immunity Proteins Using Computational Simulations

Colicins are antimicrobial proteins produced by bacteria for the purpose of destroying neighboring bacteria. Colicin activity is neutralized by a specific cognate immunity protein in order to protect the host. This study investigates the structural and binding mechanisms underlying the interaction of colicin-D, -E3 and -E8 to their respective immunity proteins (ImD, Im3 and Im8) using structure prediction, molecular dynamics (MD) simulations and MM-PBSA approach of free energy calculations. High-confidence colicin-immunity (Col-Im) complex structures predicted using AlphaFold2 were subjected to MD simulations of 150 ns with GROMACS and were analyzed for the binding free energy calculation using gmx_MMPBSA. Results showed that the complex of Col_E3-Im3 exhibited the most favorable binding free energy, driven by strong van der Waals and electrostatic interactions. Col_D-ImD and Col_E8-Im8 also showed the favorable binding. Electrostatics and hydrogen bonding emerged as a key factor driving binding and stability, while polar solvation acted as a destabilizing factor across all systems. These outcomes provide an understanding of the molecular mechanisms of Col-Im systems, with potential applications for developing natural antimicrobials for food safety.

Leveraging AlphaFold models to predict androgenic effects of endocrine-disrupting chemicals through zebrafish androgen receptor analysis

The androgen receptor (AR) activation by androgens is vital for tissue development, sexual differentiation, and reproductive attributes in zebrafish (Danio rerio). However, our understanding of the molecular mechanisms behind their activation remains limited. In this study, we employed both ab initio (AlphaFold) and homology (SWISS-MODEL) structure models of zebrafish androgen receptor ligand-binding domain (zAR-LBD) to explore the binding specificity, binding affinity, and molecular interactions of endogenous hormones (testosterone (T), 11-ketotestosterone (11-KT), and dihydrotestosterone (DHT)) in a computational simulation. Molecular docking analysis showed that both structures formed the same interactions and similar patterns of binding energy with androgens. Molecular Dynamics (MD) simulation analysis revealed that hydrogen bond occupancy aligned with in vitro findings related to androgenic effect. When comparing complexes modeled by SWISS-MODEL and AlphaFold, significant differences were observed in root mean square deviation (RMSD) and root mean square fluctuations (RMSF). The AlphaFold structures also exhibited a clear separation between ligands in principal component analysis. Further correlation analysis between in silico features and in vitro EC50 values identified MMPBSA energies as the most significant contributors to ligand-specific variance in the in silico complexes (p < 0.05). Overall, this integrative approach offers significant insights into the molecular mechanisms underlying zebrafish AR activity.

Insight into the interaction of serum albumin with antihypertensive peptide Val-Ala-Pro from bovine casein hydrolysate based on the biolayer interferometry, multi-spectroscopic analysis and computational evaluation

Food-derived angiotensin-converting enzyme inhibitory peptide (ACEIP) has an effect in supportive therapeutic on hypertension. Bovine serum albumin (BSA) as a model transporter protein to explore the interaction mechanisms with casein-hydrolyzed ACEIP Val-Ala-Pro (VAP) by multi-spectroscopic, biolayer interferometry (BLI), isothermal titration calorimetry (ITC), molecular docking, and molecular dynamics simulations. Multi-spectroscopic analysis showed that the non-covalent complexes formed by VAP and BSA resulted in decreased hydrophobicity and α-helix contents on BSA, revealing the unfolding of the BSA structure. BLI revealed the reversible binding process of BSA to VAP. ITC confirmed that the combination of VAP to BSA was a spontaneous process mainly driven by entropy. Molecular docking and molecular dynamic simulations showed that VAP was primarily bound in site II of BSA by hydrogen bonding, hydrophobic interactions, van der Waals force, and electrostatic force. This study provides a systematic method to reveal the structure-activity relationship of ACEIPs.

Small-Molecule FICD Inhibitors Suppress Endogenous and Pathologic FICD-Mediated Protein AMPylation

The AMP transferase, FICD, is an emerging drug target fine-tuning stress signaling in the endoplasmic reticulum (ER). FICD is a bifunctional enzyme, catalyzing both AMP addition (AMPylation) and removal (deAMPylation) from the ER-resident chaperone BiP/GRP78. Despite increasing evidence linking excessive BiP/GRP78 AMPylation to human diseases, small molecules that inhibit pathogenic FICD variants are lacking. Using an in vitro high-throughput screen, we identify two small-molecule FICD inhibitors, C22 and C73. Both molecules significantly inhibit FICD-mediated BiP/GRP78 AMPylation in intact cells while only weakly inhibiting BiP/GRP78 deAMPylation. C22 and C73 also inhibit pathogenic FICD variants and improve proinsulin processing in β cells. Our study identifies and validates FICD inhibitors, highlighting a novel therapeutic avenue against pathologic protein AMPylation.

In vitro, in silico, and STD-NMR studies of flavonoids from Hypericum helianthemoides (Spach) Boiss. against Leishmania major pteridine reductase 1 (LmPTR1)

Apigenin (1) and 3I,8II-biapigenin (2), a dimer of apigenin, were isolated from the aerial parts of Hypericum helianthemoides (Spach) Boiss. (Hypericaceae family). This study aimed to evaluate the in vitro inhibitory effects of flavonoids 1 and 2 against Leishmania major pteridine reductase-1 (LmPTR1), an essential enzyme for the growth of Leishmania parasites and other trypanosomatid protozoa. The second objective was to understand the binding interactions and structural properties of LmPTR1 inhibition at the atomic level through extensive in silico analyses and Saturation-Transfer Difference (STD)-NMR studies. Anti-LmPTR1 results showed that the dimeric form (2) was active (IC50 of 34.65 μM), while the monomeric form (1) was inactive. Computational analyses yielded a grid score of -52.14 kcal/mol and a free energy binding score of -38.23 kcal/mol. A stable ligand-receptor complex at the LmPTR1 binding site was observed for 2. Moreover, several important binding residues in the catalytic triad (Y194 and K198) and the substrate loop (L226, S227, S229, V230, and M233) interacted with 2. The STD-NMR results corroborated the computational simulations, indicating that H-6I and H-6II of the conjugated ring system on the biapigenin structure showed the highest interaction with the LmPTR1 active site. MTT assay results for 2 against human normal fibroblast cells (BJ cells) exhibited no cytotoxicity at concentrations of 50 and 100 μM. Overall, 3I,8II-biapigenin (2) displayed promise as a candidate for in vivo studies and anti-leishmanial drug development. Further evaluation of the anti-leishmanial and anti-LmPTR1 activities of bioflavonoid 2, along with its analogues, is warranted.

Investigation of serotonin-receptor interactions, stability and signal transduction pathways via molecular dynamics simulations

Serotonin-receptor binding plays a key role in several neurological and biological processes, including mood, sleep, hunger, cognition, learning, and memory. In this article, we performed molecular dynamics simulation to examine the key residues that play an essential role in the binding of serotonin to the G-protein-coupled 5-HT1B receptor (5HT1BR) via electrostatic interactions. Key residues for electrostatic interactions were identified via bond distance analysis and frustration analysis methods. An end-point free energy calculation method determines the stability of the 5-HT1BR due to serotonin binding. The single-point mutation of the polar/charged amino acid residues (Asp129, Thr134) on the binding sites and the calculation of binding free energy validate the quantitative contribution of these residues to the stability of the serotonin-receptor complex. The principal component analysis reflects that the serotonin-bound 5-HT1BR is more stabilized than the apo-receptor regarding dynamical changes. The difference dynamic cross-correlations map shows the correlation between the transmembranes and mini-Go, which indicates that the signal transduction happens between mini-Go and the receptor. Allosteric pathway analysis reveals the key nodes and key pathways for signal transduction in 5-HT1BR. These results provide useful insights into the study of signal transduction pathways and mutagenesis to regulate the binding and functionality of the complex. The developed protocols can be applied to study local non-covalent interactions and long-range allosteric communications in any protein-ligand system for computer-aided drug design.

Nanohydrogel of Curcumin/Berberine Co-Crystals Induces Apoptosis via Dual Covalent/Noncovalent Inhibition of Caspases in Endometrial Cancer Cell Lines: The Synergy Between Pharmacokinetics and Pharmacodynamics

Endometrial cancer remains a significant therapeutic challenge due to drug resistance and heterogeneity. This study leverages the synergistic potential of curcumin (CUR) and berberine (BBR) co-crystals encapsulated in a nanohydrogel to address these challenges through a pharmacokinetically and pharmacodynamically targeted therapeutic strategy. The nanohydrogel formulation significantly improves the solubility, stability, and bioavailability of CUR/BBR co-crystals, optimizing their therapeutic delivery and sustained release under physiological and tumor microenvironment conditions. On the other hand, the dual inhibitory mechanism of CUR and BBR, with CUR covalently binding to the active site of caspase-3 and BBR non-covalently targeting the allosteric site, achieves enhanced apoptotic activity by disrupting both the catalytic and conformational functions of caspase-3. In vitro cytotoxicity assays demonstrate remarkable efficacy of the CUR/BBR nanohydrogel, achieving an IC50 of 12.36 μg/mL against HEC-59 endometrial cancer cells, significantly outperforming the individual components and the standard drug Camptothecin (IC50: 17.27 μg/mL). Caspase-3/7 assays confirm enhanced apoptosis induction for the nanohydrogel formulation compared to co-crystals alone and Camptothecin. Molecular dynamics simulations and binding free energy analyses further validate the synergistic interaction of CUR and BBR in their dual binding mode. This study introduces a novel therapeutic approach by enhancing drug delivery and dual targeting mechanisms, demonstrating the potential of CUR-BBR nanohydrogel as a robust therapy for EC. This strategy offers a promising platform for addressing drug resistance and improving outcomes in endometrial cancer therapy.

D-glucose-conjugated thioureas containing 2-aminopyrimidine as potential multitarget inhibitors for type 2 diabetes mellitus: Synthesis and biological activity study

α-d-Glucose-conjugated thioureas 8a-w of substituted 4,6-diaryl-2-aminopyrimindines were designed, synthesized, and screened for their antidiabetic inhibitory activity. The thioureas with the strongest potential inhibitory activity included 8f (IC50 = 11.32 ± 0.34 μM for α-amylase), 8g (IC50 = 10.35 ± 0.88 μM for α-glucosidase), 8e (IC50 = 2.53 ± 0.03 nM for DPP-4), and 8c (IC50 = 3.93 ± 0.03 nM for PTP1B). The inhibitors 8g, 8e, and 8c were competitive α-glucosidase, non-competitive DDP-4, and non-competitive PTP1B inhibitors, respectively. In addition, compounds 8a, 8c, 8e, 8f, 8g, 8h, and 8j were noncytotoxic for 3T3 cell line. Induced fit docking study showed the key active interactions of each ligand with residues in the active site of each of these enzymes. Molecular dynamics simulation study on the representative complexes 8f/4W93 and 8e/3W2T in enzymes 4W93 and 3W2T, respectively, displayed the bioactive interactions between the residues and the corresponding potent inhibitor in the active site. Some of the various effects of the electron-donating and electron-withdrawing substituents on benzene of pyrimidine ring to inhibitory activities against enzymes related to T2DM were discussed. The calculations based on MM-GBSA showed the effects of the solvation to the active binding of the specific ligand in the active pocket of an enzyme.

Based on Molecular Docking, Molecular Dynamics Simulation and MM/PB(GB)SA to Study Potential Inhibitors of PRRSV-Nsp4

Porcine reproductive and respiratory syndrome (PRRS) is one of the most serious infectious immunosuppressive diseases in the world. The nonstructural protein Nsp4 can be used as an ideal target for anti-PRRSV replication inhibitors. However, little is known about potential inhibitors that target Nsp4 to affect PRRSV replication. The purpose of this study was to screen potential natural inhibitors that affect PRRSV replication by inhibiting Nsp4. Five compounds with strong binding affinity to Nsp4 were selected by structure-based molecular docking method. The complexes of naringin dihydrochalcone (NDC), agathisflavone (AGT), and amentoflavone (AMF) with Nsp4 were stable throughout the molecular dynamics simulation. According to MM/PBSA analysis, the free energies of binding of NDC, AGT, and AMF to Nsp4 were less than-30 Kcal/mol. In conclusion, these three compounds are worthy of further investigation as novel inhibitors of PRRSV. This study provides a theoretical basis for the development of anti-PRRSV natural drugs.

Antioxidant effect, DNA-binding, and transport of the flavonoid acacetin influenced by the presence of redox-active Cu(II) ion: Spectroscopic and in silico study

Acacetin (AC) is a natural polyphenol from the group of flavonoids. It is well established that the behavior of flavonoids depends on the presence of redox-active substances; therefore, we aim to investigate their biological activity following the interaction with Cu(II) ion. Our study demonstrates that AC can effectively bind Cu(II) ions, as confirmed by UV-Vis and EPR spectroscopy as well as DFT calculations. AC appears as a potent scavenger against the model ABTS radical cation by itself, but this ability is significantly limited upon Cu(II) coordination. The possible mild synergistic effect of AC in the presence of vitamin C and glutathione was also shown by the ABTS•+ test. In contrast, an inhibitory effect was observed in the presence of Cu(II) ions. The equimolar addition of AC to the model Fenton-like system containing Cu(II) did not have a noticeable effect on the concentration of hydroxyl radicals produced, but in its excess the formation of •OH decreased, as proved by EPR spin trapping. Absorption titrations and gel electrophoresis revealed effective binding to calf thymus (CT)-DNA with a stronger interaction for the Cu(II)-AC complex. The detailed mode of binding to biomolecules was described using molecular docking and molecular dynamics. Obtained results indicate that the double helix of DNA unwinds after interaction with the Cu(II)-AC complex. Fluorescence spectroscopy, employing human serum albumin (HSA), suggested a potential transport capacity for both AC and its Cu(II) complex.

Molecular Dynamics Simulation Studies of Beta-Glucogallin and Dihydro Dehydro Coniferyl Alcohol from Syzygium cumini for its Antimicrobial Activity on Staphylococcus aureus

With the escalating threat of antimicrobial resistance (AMR), discovering novel therapeutic agents against resistant pathogens like Staphylococcus aureus is crucial. This study explores phytochemicals from Syzygium cumini for their potential efficacy against AMR S. aureus infections, elucidating their mechanisms through in silico methods. We investigated 83 compounds from S. cumini, sourced from PubMed, using rigorous docking analysis against the ATP binding domain AgrC of S. aureus with AMdock with Autodock Vina v1.5.2. Drug-likeness predictions were assessed using SwissADME v2023 and Pass online v2.0. Molecular dynamics (MD) simulations identified promising compounds, focusing on stability and interaction dynamics. Beta-Glucogallin (BEG) and Dihydro Dehydro Coniferyl alcohol (DIH) emerged as significant hits. MD simulations with GROMACS v2020.6 revealed stable BEG and DIH complexes with AgrC, forming six hydrogen bonds with six key amino acids (Arg-303, Asp-338, Glu-342, Glu-384, Lys-389, Gly-396), indicating strong and stable bonding. The binding affinities for DIH and BEG are -73.474 ± 11.104 kJ/mol and -6.319 ± 18.823 kJ/mol with 4BXI, respectively. Our findings highlight BEG and DIH as promising candidates against AMR S. aureus infections, showing favourable binding affinities and stable interactions with AgrC. This study underscores the importance of natural products in combating AMR and demonstrates the utility of computational methodologies in drug discovery. Further experimental validation is warranted to fully exploit these phytochemicals' therapeutic potential.

In silico identification of a phosphate marine steroid from Indonesian marine compounds as a potential inhibitor of phosphatidylinositol mannosyltransferase (PimA) in Mycobacterium tuberculosis

A higher death rate is associated with multiple factors, including medication resistance and co-infection with the human immunodeficiency virus (HIV). This shows the need to obtain new and effective drug candidates in improving tuberculosis (TB) treatment. In addition, the phosphatidylinositol mannosyltransferase (PimA) enzyme starts the production of phosphatidyl-myo-inositol. PimA has been identified as a key enzyme and an important area for further research in the development of anti-TB drugs. Previous research investigated various applications including marine resources driven by a deeper understanding of the distinctive features of the ecosystem and the diverse array of organisms. Therefore, this research aims to investigate the potential of Indonesian marine compounds as inhibitors of PimA, with a focus on binding energy, interaction modes, and stability using docking and molecular dynamics (MD) investigation methodologies. The results show that a total of 84 Indonesian marine compounds are effectively docked to the PimA to obtain compounds 21, 27, and 33 for further investigation. Based on the MD analysis, compound 27 (desulfohaplosamate) is the most promising candidate among the new MTB-PimA inhibitors. Compounds bind to PimA, as shown by a strong affinity of -30.09 kJ/mol, and form hydrogen bonds with the key amino acid residue Gly16. Furthermore, a stable complex is formed to easily analyze the antibacterial agents targeting MTB in the future.

A dual-drive strategy for enhanced protein crystallization with sodium alginate/hyaluronic acid film: Protein adsorption and supersaturation regulation

Protein crystallization is essential for determining the three-dimensional structures of biomacromolecules and advancing biopharmaceutical development, yet it remains a major challenge in structural biology due to common issues like slow nucleation rates and inconsistent crystal quality. Herein, a dual-drive crystallization (DDC) strategy, relying on a composite film of sodium alginate (SA) and hyaluronic acid (HA), is reported to synergistically regulate both protein adsorption and solution supersaturation. Driven by the electrostatic interactions of SA and the water absorption properties of HA, the SA/HA film achieves enhanced crystallization efficiency and controlled crystal quality mainly. It significantly reduces lysozyme nucleation time by over 66.0 % and better controls crystal size distribution. Molecular simulations further reveal a strong electrostatic interaction energy of -17.0 kcal·mol-1 between protein and SA, which enhances protein adsorption and then promotes cluster formation, nucleation, and crystal growth. Additionally, the DDC strategy efficiently promotes the crystallization of both thaumatin and proteinase K, enhancing the crystallization success rate for proteins with opposite charges. These results highlight the advantages and promising potential of SA/HA film-assisted protein crystallization for effectively producing protein crystals suitable for diverse applications.

Further exploration of the quantitative distance-energy and contact number-energy relationships for predicting the binding affinity of protein-ligand complexes

Accurate estimation of the strength of the protein-ligand interaction is important in the field of drug discovery. The binding strength can be determined by using experimental binding affinity assays which are both time and labor consuming and costly. Predicting the binding affinity/energy in silico is an alternative approach, particularly for virtual screening of large data sets. In general, the distance-based terms such as electrostatic and van der Waals interactions are among the key determinants of binding energy. In this work, the distance-binding energy relationships, i.e., E ∝ -d-k, are further explored, extended, and developed for protein-ligand binding affinity prediction. The contributions of different atom-type pairs were considered synthetically and jointly. Additionally, the contact number-energy relationships (E ∝ -nk) were also explored for protein-ligand binding affinity prediction. Significantly, the power exponents of the distances or contact numbers in the energy functions are not restricted by the existing theories concerning van der Waals and electrostatic energies (expressed as ar6-br12 and cr). The performances of the new distance-based or contact number-based models are better than the performances of those sophisticated non-machine-learning-based scoring functions developed before. The exploration and extension of the distance-energy and contact number-energy relationships may offer insights into the development of more effective methods for predicting the protein-ligand binding affinity accurately and analyzing the protein-ligand interactions rationally.

Designing novel cabozantinib analogues as p-glycoprotein inhibitors to target cancer cell resistance using molecular docking study, ADMET screening, bioisosteric approach, and molecular dynamics simulations

Introduction

One of the foremost contributors to mortality worldwide is cancer. Chemotherapy remains the principal strategy for cancer treatment. A significant factor leading to the failure of cancer chemotherapy is the phenomenon of multidrug resistance (MDR) in cancer cells. The primary instigator of MDR is the over expression of P-glycoprotein (P-gp), a protein that imparts resistance and facilitates the ATP-dependent efflux of various anticancer agents. Numerous efforts have been made to inhibit P-gp function with the aim of restoring the effectiveness of chemotherapy due to its broad specificity. The main objective has been to create compounds that either serve as direct P-gp inhibitors or interact with cancer therapies to modulate transport. Despite substantial in vitro achievements, there are currently no approved drugs available that can effectively "block" P-gp mediated resistance. Cabozantinib (CBZ), a multi-kinase inhibitor, is utilized in the treatment of various carcinomas. CBZ has been shown to inhibit P-gp efflux activity, thereby reversing P-gp mediated MDR. Consequently, P-gp has emerged as a critical target for research in anti-cancer therapies.

Methods

The purpose of this study was to computationally identify new andsafer analogues of CBZ using bioisosteric approach, focusing on improved pharmacokinetic properties andreduced toxicity. The physicochemical, medicinal, and ADMET profiles of generated analogues were computed using the ADMETLab 3.0 server. We also predicted the drug likeness (DL) and drug score (DS) of analogues. The molecular docking studies of screened analogues against the protein (PDB ID: 3G5U) were conducted using AutoDock Vina flowing by BIOVIA Discovery Studio for visualizing interactions.Molecular dynamics (MD) simulation of docked ligands was done using Schrödinger suite.

Results and Discussion

The docking scores for the ligands CBZ01, CBZ06, CBZ11, CBZ13, CBZ25, CBZ34, and CBZ38 ranged from -8.0 to -6.4 kcal/mol against the protein (PDB ID: 3G5U). A molecular dynamics (MD) simulation of CBZ01, CBZ13, and CBZ38 was conducted using the Schrödinger suite, revealing that these complexesmaintained stability throughout the 100 ns simulation.

Conclusion

An integrated computational approach combining bioisosteric approach, molecular docking, drug likeness calculations, and MD simulations highlights the promise of ligands CBZ01 and CBZ13 as candidates for the development of potential anticancer agents for the treatment of various cancers.

Structural insights into SOD1: from in silico and molecular dynamics to experimental analyses of ALS-associated E49K and R115G mutants

Protein stability is a crucial characteristic that influences both protein activity and structure and plays a significant role in several diseases. Cu/Zn superoxide dismutase 1 (SOD1) mutations serve as a model for elucidating the destabilizing effects on protein folding and misfolding linked to the lethal neurological disease, amyotrophic lateral sclerosis (ALS). In the present study, we have examined the structure and dynamics of the SOD1 protein upon two ALS-associated point mutations at the surface (namely, E49K and R115G), which are located in metal-binding loop IV and Greek key loop VI, respectively. Our analysis was performed through multiple algorithms on the structural characterization of the hSOD1 protein using computational predictions, molecular dynamics (MD) simulations, and experimental studies to understand the effects of amino acid substitutions. Predictive results of computational analysis predicted the deleterious and destabilizing effect of mutants on hSOD1 function and stability. MD outcomes also indicate that the mutations result in structural destabilization by affecting the increased content of β-sheet structures and loss of hydrogen bonds. Moreover, comparative intrinsic and extrinsic fluorescence results of WT-hSOD1 and mutants indicated structural alterations and increased hydrophobic surface pockets, respectively. As well, the existence of β-sheet-dominated structures was observed under amyloidogenic conditions using FTIR spectroscopy. Overall, our findings suggest that mutations in the metal-binding loop IV and Greek key loop VI lead to significant structural and conformational changes that could affect the structure and stability of the hSOD1 molecule, resulting in the formation of toxic intermediate species that cause ALS.

Methods for Theoretical Treatment of Local Fields in Proteins and Enzymes

Electric fields generated by protein scaffolds are crucial in enzymatic catalysis. This review surveys theoretical approaches for detecting, analyzing, and comparing electric fields, electrostatic potentials, and their effects on the charge density within enzyme active sites. Pioneering methods like the empirical valence bond approach rely on evaluating ionic and covalent resonance forms influenced by the field. Strategies employing polarizable force fields also facilitate field detection. The vibrational Stark effect connects computational simulations to experimental Stark spectroscopy, enabling direct comparisons. We highlight how protein dynamics induce fluctuations in local fields, influencing enzyme activity. Recent techniques assess electric fields throughout the active site volume rather than only at specific bonds, and machine learning helps relate these global fields to reactivity. Quantum theory of atoms in molecules captures the entire electron density landscape, providing a chemically intuitive perspective on field-driven catalysis. Overall, these methodologies show protein-generated fields are highly dynamic and heterogeneous, and understanding both aspects is critical for elucidating enzyme mechanisms. This holistic view empowers rational enzyme engineering by tuning electric fields, promising new avenues in drug design, biocatalysis, and industrial applications. Future directions include incorporating electric fields as explicit design targets to enhance catalytic performance and biochemical functionalities.

Studying the Signaling Mechanism of Neuropilin-1's Intracellular Disorder Region via Conformational Mining and Dynamic Interaction Characterization

Many single-pass membrane proteins contain an intrinsically disordered region (IDR) within their intracellular domain, playing a key role in regulating cellular signaling. However, understanding the functional mechanisms of these disordered regions has remained a challenge. In this study, we focus on the cytoplasmic IDR of neuropilin-1 (NRP-1 IDR) and employ a combination of experimental and computational methods to investigate its dynamics and function. We compare several enhanced sampling molecular simulations, structural statistics-based methods, and AI-driven conformation mining techniques, emphasizing the strengths and limitations of each with respect to sampling diversity and energy landscape exploration. Subsequently, we investigate the broad array of potential binding partners for the NRP-1 IDR and employ AlphaFold3 for complex structure prediction, highlighting the promiscuous binding behavior of the NRP-1 IDR. Finally, we focus on high-confidence binding partners, GIPC-1 and SNX-5, validating the interaction of the NRP-1 IDR with these proteins and investigating the effects of membrane context and phosphorylation on these interactions. Our findings provide critical insights into how a flexible cytoplasmic region in signal-transmembrane proteins can modulate transmembrane signaling.

Molecular dynamics simulation-driven focused virtual screening and experimental validation of Fisetin as an inhibitor of Helicobacter pylori HtrA protease

Helicobacter pylori (H. pylori, Hp) is a primary contributor to various stomach diseases, including gastritis and gastric cancer. This bacterium can colonize gastric epithelial cells, compromising their integrity and leading to the development of these conditions. While antibiotics are the mainstay of treatment for H. pylori infections, their widespread use has led to serious issues with drug resistance. High-temperature requirement A (HtrA) protein is an active serine protease secreted by H. pylori, which can destroy gastric epithelium, thus helping H. pylori to colonize gastric mucosa efficiently. In this study, we identified three compounds-Quercetin, Fisetin, and Geniposide-as potential natural compounds that might specifically interact with the HtrA protein, based on molecular docking and molecular dynamics simulations (MDs). The casein hydrolysis experiment indicated that Fisetin could inhibit the activity of HtrA in hydrolyzing casein at the concentration of 50 μM m. Additionally, our in vitro antibacterial experiments further showed that Fisetin could effectively inhibit the growth of H. pylori in a concentration-dependent manner, with an inhibition rate of 80% achieved at a concentration of 10 μM. In summary, these results suggest that Fisetin has an inhibitory effect on the growth of H. pylori, and this study may be the first to reveal its obviously inhibitory effect on HtrA protein. Our findings imply that Fisetin could be a potential candidate for further research as a therapeutic agent targeting protein HtrA, providing a new direction for the exploration of lead compounds and potential drugs against H. pylori infections.

Molecular simulations reveal intricate coupling between agonist-bound β-adrenergic receptors and G protein

G protein-coupled receptors (GPCRs) and G proteins transmit signals from hormones and neurotransmitters across cell membranes, initiating downstream signaling and modulating cellular behavior. Using advanced computer modeling and simulation, we identified atomistic-level structural, dynamic, and energetic mechanisms of norepinephrine (NE) and stimulatory G protein (Gs) interactions with β-adrenergic receptors (βARs), crucial GPCRs for heart function regulation and major drug targets. Our analysis revealed distinct binding behaviors of NE within β1AR and β2AR despite identical orthosteric binding pockets. β2AR had an additional binding site, explaining variations in NE binding affinities. Simulations showed significant differences in NE dissociation pathways and receptor interactions with the Gs. β1AR binds Gs more strongly, while β2AR induces greater conformational changes in the α subunit of Gs. Furthermore, GTP and GDP binding to Gs may disrupt coupling between NE and βAR, as well as between βAR and Gs. These findings may aid in designing precise βAR-targeted drugs.