Search

Abstract Several computational methods have been developed to identify neutralizing antibodies (NAbs) covering four dengue virus serotypes (DENV-1 to DENV-4); however, limitations of the dataset and the resulting performance remain. Here, we developed a new computational framework to predict potent and stable NAbs against DENV-1 to DENV-4 using only antibody (CDR-H3) and epitope sequences as input. Specifically, our proposed computational framework employed sequence-based ML and molecular dynamic simulation (MD) methods to achieve more accurate identification. First, we built a novel dataset (n = 1108) by compiling the interactions of CDR-H3 and epitope sequences with the half maximum inhibitory concentration (IC50) values, which represent neutralizing activities. Second, we achieved an accurately predictive ML model that showed high AUC values of 0.879 and 0.885 by tenfold cross-validation and independent tests, respectively. Finally, our computational framework could be applied to filter approximately 2.5 million unseen antibodies into two final candidates that showed strong and stable binding to all four serotypes. In addition, the most potent and stable candidate (1B3B9_V21) was evaluated for its development potential as a therapeutic agent by molecular docking and MD simulations. This study provides an antibody computational approach to facilitate the high-throughput identification of NAbs and accelerate the development of therapeutic antibodies.

Abstract Background The high virulence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), responsible for coronavirus disease 2019 (COVID-19), has triggered global health and economic concerns. The absence of specific antiviral treatments and the side effects of repurposed drugs present persistent challenges. This study explored a promising antiviral herbal extract against SARS-CoV-2 from selected Thai medicinal plants based on in vitro efficacy and evaluated its antiviral lead compounds by molecular docking. Methods Twenty-two different ethanolic-aqueous crude extracts (CEs) were rapidly screened for their potential activity against porcine epidemic diarrhea virus (PEDV) as a surrogate using a plaque reduction assay. Extracts achieving ≥ 70% anti-PEDV efficacy proceeded to the anti-SARS-CoV-2 activity test using a 50% tissue culture infectious dose method in Vero E6 cells. Molnupiravir and extract-free media served as positive and negative controls, respectively. Potent CEs underwent water/ethyl acetate fractionation to enhance antiviral efficacy, and the fractions were tested for anti-SARS-CoV-2 performance. The fraction with the highest antiviral potency was identified using liquid chromatography–high-resolution mass spectrometry (LC–HRMS). Molecular docking analyses of these compounds against the main protease (Mpro) of SARS-CoV-2 (6LU7) were performed to identify antiviral lead molecules. The top three hits were further evaluated for their conformational stability in the docked complex using molecular dynamics (MD) simulation. Results The water fraction of mulberry (Morus alba Linn.) leaf CE (WF-MLCE) exhibited the most potent anti-SARS-CoV-2 efficacy with low cytotoxicity profile (CC50 of ~ 0.7 mg/mL), achieving 99.92% in pre-entry mode and 99.88% in postinfection treatment mode at 0.25 mg/mL. Flavonoids and conjugates were the predominant compounds identified in WF-MLCE. Molecular docking scores of several flavonoids against SARS-CoV-2 Mpro demonstrated their superior antiviral potency compared to molnupiravir. Remarkably, myricetin-3-O-β-D-galactopyranoside, maragrol B, and quercetin 3-O-robinobioside exhibited binding energies of ~ − 9 kcal/mol. The stability of each ligand–protein complex of these compounds with the Mpro system showed stability during MD simulation. These three molecules were pronounced as antiviral leads of WF-MLCE. Given the low cytotoxicity and high antiviral potency of WF-MLCE, it holds promise as a candidate for future therapeutic development for COVID-19 treatment, especially considering its economic and pharmacological advantages.

Tyrosinase, a pivotal enzyme in melanin synthesis, is a primary target for the development of depigmenting agents. In this work, in vitro and in silico techniques were employed to identify novel tyrosinase inhibitors from a set of 12 anilino-1,4-naphthoquinone derivatives. Results from the mushroom tyrosinase activity assay indicated that, among the 12 derivatives, three compounds (1, 5, and 10) demonstrated the most significant inhibitory activity against mushroom tyrosinase, surpassing the effectiveness of the kojic acid. Molecular docking revealed that all studied derivatives interacted with copper ions and amino acid residues at the enzyme active site. Molecular dynamics simulations provided insights into the stability of enzyme–inhibitor complexes, in which compounds 1, 5, and particularly 10 displayed greater stability, atomic contacts, and structural compactness than kojic acid. Drug likeness prediction further strengthens the potential of anilino-1,4-naphthoquinones as promising candidates for the development of novel tyrosinase inhibitors for the treatment of hyperpigmentation disorders.

This research aimed to explore binding interactions between pea protein isolate (PPI) and selected strawberry flavorings including vanillin, γ-decalactone, furaneol, and (Z)-3-hexen-1-ol within an aqueous system. The results showed that binding affinities of PPI with all various functional group of flavor compounds decreased as temperature increased from 5 °C to 25 °C. Notably, at 25 °C, γ-decalactone displayed the highest binding affinity, followed by vanillin, (Z)-3-hexen-1-ol, and furaneol. Lowest binding was observed for furaneol, explained by its greater lipophilicity (lower partition coefficient values or LogP value) and molecular structure in each functional group in the flavor compounds. Thermodynamically, the interaction between PPI and each selected flavor compound was spontaneous, with evidence suggesting primary forces being hydrophobic interactions or hydrogen bonding/van der Waals forces. Computational molecular docking further confirmed these interaction types. This research provides insights into the interactions between PPI and strawberry flavorings, aiding in the selection of optimal flavor compound proportion for protein-rich products.

Our study employed molecular dynamics (MD) simulations to assess the binding affinity between short peptides derived from the tumor-associated antigen glypican 3 (GPC3) and the major histocompatibility complex (MHC) molecule HLA-A*11:01 in hepatocellular carcinoma. We aimed to improve the reliability of in silico predictions of peptide-MHC interactions, which are crucial for developing targeted cancer therapies. We used five algorithms to discover four peptides (TTDHLKFSK, VINTTDHLK, KLIMTQVSK, and STIHDSIQY), demonstrating the substantial potential for HLA-A11:01 presentation. The Anchored Peptide-MHC Ensemble Generator (APE-Gen) was used to create the initial structure of the peptide-MHC complex. This was followed by a 200 ns molecular dynamics (MD) simulation using AMBER22, which verified the precise positioning of the peptides in the binding groove of HLA-A*11:01, specifically at the A and F pockets. Notably, the 2nd residue, which serves as a critical anchor within the 2nd pocket, played a pivotal role in stabilising the binding interactions.VINTTDHLK (ΔGSIE = −14.46 ± 0.53 kcal/mol and ΔGMM/GBSA = −30.79 ± 0.49 kcal/mol) and STIHDSIQY (ΔGSIE and ΔGMM/GBSA = −14.55 ± 0.16 and −23.21 ± 2.23 kcal/mol) exhibited the most effective binding potential among the examined peptides, as indicated by both their binding free energies and its binding affinity on the T2 cell line (VINTTDHLK: IC50 = 0.45 nM; STIHDSIQY: IC50 = 0.35 nM). The remarkable concordance between in silico and in vitro binding affinity results was of particular significance, indicating that MD simulation is a potent instrument capable of bolstering confidence in in silico peptide predictions. By employing MD simulation as a method, our study provides a promising avenue for improving the prediction of potential peptide-MHC interactions, thereby facilitating the development of more effective and targeted cancer therapies.

Abstract The prevalence of HIV-1 infection continues to pose a significant global public health issue, highlighting the need for antiretroviral drugs that target viral proteins to reduce viral replication. One such target is HIV-1 protease (PR), responsible for cleaving viral polyproteins, leading to the maturation of viral proteins. While darunavir (DRV) is a potent HIV-1 PR inhibitor, drug resistance can arise due to mutations in HIV-1 PR. To address this issue, we developed a novel approach using the fragment molecular orbital (FMO) method and structure-based drug design to create DRV analogs. Using combinatorial programming, we generated novel analogs freely accessible via an on-the-cloud mode implemented in Google Colab, Combined Analog generator Tool (CAT). The designed analogs underwent cascade screening through molecular docking with HIV-1 PR wild-type and major mutations at the active site. Molecular dynamics (MD) simulations confirmed the assess ligand binding and susceptibility of screened designed analogs. Our findings indicate that the three designed analogs guided by FMO, 19–0–14–3, 19–8–10–0, and 19–8–14–3, are superior to DRV and have the potential to serve as efficient PR inhibitors. These findings demonstrate the effectiveness of our approach and its potential to be used in further studies for developing new antiretroviral drugs.

Background: Anti-SARS-CoV-2 and immunomodulatory drugs are important for treating clinically severe patients with respiratory distress symptoms. Alpha- and gamma-mangostins (AM and GM) were previously reported as potential 3C-like protease (3CLpro) and Angiotensin-converting enzyme receptor 2 (ACE2)-binding inhibitors in silico. Objective: We aimed to evaluate two active compounds, AM and GM, from Garcinia mangostana for their antivirals against SARS-CoV-2 in live virus culture systems and their cytotoxicities using standard methods. Also, we aimed to prove whether 3CLpro and ACE2 neutralization were major targets and explored whether any additional targets existed. Methods: We tested the translation and replication efficiencies of SARS-CoV-2 in the presence of AM and GM. Initial and subgenomic translations were evaluated by immunofluorescence of SARS-CoV-2 3CLpro and N expressions at 16 h after infection. The viral genome was quantified and compared with the untreated group. We also evaluated the efficacies and cytotoxicities of AM and GM against four strains of SARS-CoV-2 (wild-type B, B.1.167.2, B.1.36.16, and B.1.1.529) in Vero E6 cells. The potential targets were evaluated using cell-based anti-attachment, time-of-drug addition, in vitro 3CLpro activities, and ACE2-binding using a surrogated viral neutralization test (sVNT). Moreover, additional targets were explored using combinatorial network-based interactions and Chemical Similarity Ensemble Approach (SEA). Results: AM and GM reduced SARS-CoV-2 3CLpro and N expressions, suggesting that initial and subgenomic translations were globally inhibited. AM and GM inhibited all strains of SARS-CoV-2 at EC50 of 0.70–3.05 μM, in which wild-type B was the most susceptible strain (EC50 0.70–0.79 μM). AM was slightly more efficient in the variants (EC50 0.88–2.41 μM), resulting in higher selectivity indices (SI 3.65–10.05), compared to the GM (EC50 0.94–3.05 μM, SI 1.66–5.40). GM appeared to be more toxic than AM in both Vero E6 and Calu-3 cells. Cell-based anti-attachment and time-of-addition suggested that the potential molecular target could be at the post-infection. 3CLpro activity and ACE2 binding were interfered with in a dose-dependent manner but were insufficient to be a major target. Combinatorial network-based interaction and chemical similarity ensemble approach (SEA) suggested that fatty acid synthase (FASN), which was critical for SARS-CoV-2 replication, could be a target of AM and GM. Conclusion: AM and GM inhibited SARS-CoV-2 with the highest potency at the wild-type B and the lowest at the B.1.1.529. Multiple targets were expected to integratively inhibit viral replication in cell-based system.

Background: Hepatocellular carcinoma (HCC) is the most prevalent primary liver cancer. Anomianthus dulcis (Dunal) J.Sinclair (syn. Uvaria dulcis ) has been used in Thai traditional medicine in various therapeutic indications. Phytochemical constituents of A. dulcis have been isolated and identified. However, their effects on liver cancer and the associated mechanisms have not been elucidated. Methods: Dry flowers of A. dulcis were extracted using organic solvents, and chromatographic methods were used to purify the secondary metabolites. The chemical structures of the pure compounds were elucidated by analysis of spectroscopic data. Cytotoxicity against HCC cells was examined using SRB assay, and the effects on cell proliferation were determined using flow cytometry. The mechanisms underlying HCC inhibition were examined by molecular docking and verified by Western blot analysis. Results: Among 3 purified flavonoids, pinocembrin, pinostrobin, and chrysin, and 1 indole alkaloid (3-farnesylindole), only pinocembrin showed inhibitory effects on the proliferation of 2 HCC cell lines, HepG2 and Li-7, whereas chrysin showed specific toxicity to HepG2. Pinocembrin was then selected for further study. Flow cytometric analyses revealed that pinocembrin arrested the HCC cell cycle at the G1 phase with a minimal effect on cell death induction. Pinocembrin exerted the suppression of STAT3, as shown by the molecular docking on STAT3 with a better binding affinity than stattic, a known STAT3 inhibitor. Pinocembrin also suppressed STAT3 phosphorylation at both Tyr705 and Ser727. Cell cycle regulatory proteins under the modulation of STAT3, namely cyclin D1, cyclin E, CDK4, and CDK6, are substantially suppressed in their expression levels. Conclusion: Pinocembrin extracted from A. dulcis exerted a significant growth inhibition on HCC cells via suppressing STAT3 signaling pathways and its downstream-regulated genes.

Neurodegenerative diseases (NDDs) are marked by progressive degeneration of neurons within the central nervous system. A notable rise in the prevalence of NDDs has been noticed in the recent past. There is an undeniable requirement for the discovery of innovative therapies aimed at treating NDDs, as current medications predominantly address symptoms rather than provide cures. Approved therapies often experience a decline in therapeutic efficacy over time and are associated with significant side effects. The current investigation explores the potential of spilanthol, the major bioactive compound isolated from Acmella paniculata, in attenuating NDDs through a multi-faceted approach combining in silico, and in vitro methodologies. In silico pharmacokinetic and toxicity screening of spilanthol indicated favorable characteristics for oral delivery, blood–brain barrier permeability, and minimal toxicity. Network pharmacology predicts that spilanthol attenuates neuroinflammation in NDDs by suppressing the toll-like receptor signaling pathway. Molecular docking and dynamics simulations demonstrate robust binding affinities between spilanthol and key proteins in the TLR4 pathway. In vitro experiments conducted using BV-2 microglial cells demonstrate the potential of spilanthol to reduce the production of proinflammatory cytokines and mediators such as NO, TNF-α, and IL-6 induced by lipopolysaccharide. The cumulative findings of the present study indicate that spilanthol mitigates neurodegeneration by alleviating neuroinflammation.

After a proofreading check, some experimental data were inconsistent with the supplementary information in the original publication [...]