Discovery of phyto-compounds as novel inhibitors against NDM-1 and VIM-1 protein through virtual screening and molecular modelling

Marine natural compounds as potential CBP bromodomain inhibitors for treating cancer: an in-silico approach using molecular docking, ADMET, molecular dynamics simulations and MM-PBSA binding free energy calculations

The cAMP-responsive element binding protein (CREB) binding protein (CBP), a bromodomain-containing protein, engages with multiple transcription factors and enhances the activation of many genes. CBP bromodomain acts as an epigenetic reader and plays an important role in the CBP-chromatin interaction which makes it an important drug target for treating many diseases. Though inhibiting CBP bromodomain was reported to have great potential in cancer therapeutics, approved CBP bromodomain inhibitor is yet to come. We utilized various in silico approaches like molecular docking, ADMET, molecular dynamics (MD) simulations, MM-PBSA calculations, and in silico PASS predictions to identify potential CBP bromodomain inhibitors from marine natural compounds as they have been identified as having distinctive chemical structures and greater anticancer activities. To develop a marine natural compound library for this investigation, Lipinski's rule of five was used. Sequential investigations utilizing molecular docking, ADMET studies, 100 ns MD simulations, and MM-PBSA calculations revealed that three marine compounds-ascididemin, neoamphimedine, and stelletin A-demonstrated superior binding affinity compared to the standard inhibitor, 69 A. These compounds also exhibited suitable drug-like properties, a favorable safety profile, and formed stable protein-ligand complexes. The in-silico PASS tool predicted that these compounds have significant potential for anticancer activity. Among them, ascididemin demonstrated the highest binding affinity in both molecular docking and MM-PBSA calculations, as well as a better stability profile in MD simulations. Hence, ascididemin can be a potential inhibitor of CBP bromodomain. However, in vitro and in vivo validation is required for further confirmation of these findings.

Graphical abstract

Supplementary Information

The online version contains supplementary material available at 10.1007/s40203-024-00258-5.

A computational odyssey: uncovering classical β-lactamase inhibitors in dry fruits

In the antibacterial arsenal, β-lactams have held a prominent position, but increasing resistance due to unauthorized use and genetic factors requires new strategies. Combining β-lactamase inhibitors with broad-spectrum β-lactams proves effective in combating this resistance. ESBL producers demand new inhibitors, leading to the exploration of plant-derived secondary metabolites for potent β-lactam antibiotics or alternative inhibitors. Using virtual screening, molecular docking, ADMET analysis, and molecular dynamic simulation, this study actively analyzed the inhibitory activity of figs, cashews, walnuts, and peanuts against SHV-1, NDM-1, KPC-2, and OXA-48 β-lactamases. Using AutoDock Vina, the docking affinities of various compounds for target enzymes were initially screened, revealing 12 bioactive compounds with higher affinities for the target enzymes compared to Avibactam and Tazobactam. Top-scoring metabolites, including Oleanolic acid, Protocatechuic acid, and Tannin, were subjected to MD simulation studies to further analyze the stability of the docked complexes using WebGro. The simulation coordinates, in terms of RMSD, RMSF, SASA, Rg, and hydrogen bonds formed, showed that these phytocompounds are stable enough to retain in the active sites at various orientations. The PCA and FEL analysis also showed the stability of the dynamic motion of Cα residues of phytochemical-bound enzymes. The pharmacokinetic analysis of the top phytochemicals was performed to analyze their bioavailability and toxicity. This study provides new insights into the therapeutic potential of phytochemicals of selected dry fruits and contributes to future experimental studies to identify βL inhibitors from plants.Communicated by Ramaswamy H. Sarma.

Identification of potent inhibitors targeting Tribolium castaneum GSTe2 via structure-based screening and molecular dynamics simulation

Red flour beetle, Tribolium castaneum, has a major negative impact during storage of agricultural products and reveals the negative impacts on human health. Insect-specific epsilon glutathione S-transferase (GSTs) which requires reduced glutathione (GSH) as an essential substrate not only develop insecticide resistance but also play important role in insect metamorphosis. Inhibition of the insect metamorphosis and the development of insecticide resistance could play an important role in pest control, so T. castaneum GSTe2 (TcGSTe2) in our previous study could be an important target protein for this purpose. This study aimed to find a potential TcGSTe2 inhibitors through in silico mothods, including molecular modeling, molecular docking, ADMET assay, followed by molecular dynamics (MD) simulation, principal component analysis and MM/PBSA analysis. The results showed that ZINC000169293362 and ZINC000095566957 were selected as potential TcGSTe2 inhibitors with high-binding affinity and without any toxicity from 3618 of GSH-like compounds obtained from ZINC database. MD simulation results revealed that TcGSTe2-ZINC000169293362 had more stability than that of reference GSH. Moreover, TcGSTe2-ZINC000169293362 and TcGSTe2-ZINC000095566957 showed lower binding free energy (-27.53 ± 0.16 kcal/mol and -18.83 ± 0.15 kcal/mol, respectively) compared with TcGSTe2-GSH (-8.90 ± 0.30 kcal/mol). This study could provide new insight into reduction of insecticide resistance and be used to design new inhibitors of insect GSTs.Communicated by Ramaswamy H. Sarma.

Computational modelling of potential Zn-sensitive non-β-lactam inhibitors of imipenemase-1 (IMP-1)

Antibiotic resistance (AR) remains one of the leading global health challenges, mostly implicated in disease-related deaths. The Enterobacteriaceae-producing metallo-β-lactamases (MBLs) are critically involved in AR pathogenesis through Zn-dependent catalytic destruction of β-lactam antibiotics, yet with limited successful clinical inhibitors. The efficacy of relevant broad-spectrum β-lactams including imipenem and meropenem are seriously challenged by their susceptibility to the Zn-dependent carbapenemase hydrolysis, as such, searching for alternatives remains imperative. In this study, computational molecular modelling and virtual screening methods were extensively applied to identify new putative Zn-sensitive broad-spectrum inhibitors of MBLs, specifically imipenemase-1 (IMP-1) from the IBScreen database. Three ligands, STOCK3S-30154, STOCK3S-30418 and STOCK3S-30514 selectively displayed stronger binding interactions with the enzymes compared to reference inhibitors, imipenem and meropenem. For instance, the ligands showed molecular docking scores of -9.450, -8.005 and -10.159 kcal/mol, and MM-GBSA values of -40.404, -31.902 and -33.680 kcal/mol respectively against the IMP-1. Whereas, imipenem and meropenem showed docking scores of -9.038 and -10.875 kcal/mol, and MM-GBSA of -31.184 and -32.330 kcal/mol respectively against the enzyme. The ligands demonstrated good thermodynamic stability and compactness in complexes with IMP-1 throughout the 100 ns molecular dynamics (MD) trajectories. Interestingly, their binding affinities and stabilities were significantly affected in contacts with the remodelled Zn-deficient IMP-1, indicating sensitivity to the carbapenemase active Zn site, however, with non-β-lactam scaffolds, tenable to resist catalytic hydrolysis. They displayed ideal drug-like ADMET properties, thus, representing putative Zn-sensitive non-β-lactam inhibitors of IMP-1 amenable for further experimental studies.

Prediction of Phytochemicals for Their Potential to Inhibit New Delhi Metallo β-Lactamase (NDM-1)

The effectiveness of all antibiotics in the β-lactam group to cure bacterial infections has been impaired by the introduction of the New Delhi Metallo-β-lactamase (NDM-1) enzyme. Attempts have been made to discover a potent chemical as an inhibitor to this enzyme in order to restore the efficacy of antibiotics. However, it has been a challenging task to develop broad-spectrum inhibitors of metallo-β-lactamases. Lack of sequence homology across metallo-β-lactamases (MBLs), the rapidly evolving active site of the enzyme, and structural similarities between human enzymes and metallo-β-lactamases, are the primary causes for the difficulty in the development of these inhibitors. Therefore, it is imperative to concentrate on the discovery of an effective NDM-1 inhibitor. This study used various in silico approaches, including molecular docking and molecular dynamics simulations, to investigate the potential of phytochemicals to inhibit the NDM-1 enzyme. For this purpose, a library of about 59,000 phytochemicals was created from the literature and other databases, including FoodB, IMPPAT, and Phenol-Explorer. A physiochemical and pharmacokinetics analysis was performed to determine possible toxicity and mutagenicity of the ligands. Following the virtual screening, phytochemicals were assessed for their binding with NDM-1using docking scores, RMSD values, and other critical parameters. The docking score was determined by selecting the best conformation of the protein-ligand complex. Three phytochemicals, i.e., butein (polyphenol), monodemethylcurcumin (polyphenol), and rosmarinic acid (polyphenol) were identified as result of pharmacokinetics and molecular docking studies. Furthermore, molecular dynamics simulations were performed to determine structural stabilities of the protein-ligand complexes. Monodemethylcurcumin, butein, and rosmarinic acid were identified as potential inhibitors of NDM-1 based on their low RMSD, RMSF, hydrogen bond count, average Coulomb-Schrödinger interaction energy, and Lennard-Jones-Schrödinger interaction energy. The present investigation suggested that these phytochemicals might be promising candidates for future NDM-1 medication development to respond to antibiotic resistance.

Betaxolol as a Potent Inhibitor of NDM-1-Positive E. coli That Synergistically Enhances the Anti-Inflammatory Effect in Combination with Meropenem

With significant human and economic losses, increasing bacterial resistance is a serious global threat to human life. Due to their high efficacy, broad spectrum, and cost-effectiveness, beta-lactams are widely used in the clinical management of bacterial infection. The emergence and wide spread of New Delhi metallo-β-lactamase (NDM-1), which can effectively inactivate β-lactams, has posed a challenge in the design of effective new antimicrobial treatments. Medicine repurposing is now an important tool in the development of new alternative medicines. We present a known glaucoma therapeutic, betaxolol (BET), which with a 50% inhibitory concentration (IC50) of 19.3 ± 0.9 μM significantly inhibits the hydrolytic activity of the NDM-1 enzyme and may represent a potential NDM-1 enzyme inhibitor. BET combined with meropenem (MEM) showed bactericidal synergism in vitro. The efficacy of BET was further evaluated against systemic bacterial infections in BALB/c mice. The results showed that BET+MEM decreased the numbers of leukocytes and inflammatory factors in peripheral blood, as well as the organ bacterial load and pathological damage. Molecular docking and kinetic simulations showed that BET can form hydrogen bonds and hydrophobic interactions directly with key amino acid residues in the NDM-1 active site. Thus, we demonstrated that BET inhibited NDM-1 by competitively binding to it and that it can be developed in combination with MEM as a new therapy for the management of infections caused by medicine-resistant bacteria.