High-Throughput Virtual Screening, Molecular Dynamics Simulation, and Enzyme Kinetics Identified ZINC84525623 as a Potential Inhibitor of NDM-1

2-[(E)-(2-carboxybenzylidene) amino] ethan ammonium-like amino acid zwitterions: crystal structure, functional studies and its molecular dynamic simulation study with drug target receptors

The novel synthetic amino acid-like zwitterion containing imine bond ionic compound 2-[(E)-(2-carboxy benzylidene) amino] ethan ammonium salt, C10H12N2O2, was synthesized. Computational functional characterization is now being used to predict novel compounds. Here, we report on a titled combination that has been crystallizing in orthorhombic space group Pcc2 with Z = 4. The zwitterions form centrosymmetric dimers to polymeric supramolecular network via intermolecular N-H… O hydrogen bonds between the carboxylate groups and ammonium ion. The components are linked by ionic (N+-H-O-) and hydrogen bonds (N+-H-O), forming a complex three-dimensional supramolecular network. Further, molecular computational docking characterization study was performed with compound against multi-disease drug target biomolecule of anticancer target molecule of HDAC8 (PDB ID 1T69) receptor and antiviral molecular target protease (PDB ID 6LU7) to evaluate the interaction stability, conformational changes and to get insights into the natural dynamics on different timescales in solution. HighlightsThe novel zwitter ionic amino acid compound 2-[(E)-(2-carboxybenzylidene) amino] ethan ammonium salt, C10H12N2O2.The crystal structure determined for this compound illustrates the presence of intermolecular ionic N+-H-O- and N+-H-O hydrogen bonds between the carboxylate groups and ammonium ion, which influence the formation of a complex three-dimensional supramolecular polymeric network.Molecular docking studies helps to understand the conformational stability and interaction stabilityThe novel molecule can be considered for anticancer treatment.

Worldwide trend discovery of structural and functional relationship of metallo-β-lactamase for structure-based drug design: A bibliometric evaluation and patent analysis

Metallo-β-lactamase (MBL) is an enzyme produced by clinically important bacteria that can inactivate many commonly used antibiotics, making them a significant concern in treating bacterial infections and the risk of having high antibiotic resistance issues among the community. This review presents a bibliometric and patent analysis of MBL worldwide research trend based on the Scopus and World Intellectual Property Organization databases in 2013-2022. Based on the keywords related to MBL in the article title, abstract, and keywords, 592 research articles were retrieved for further analysis using various tools such as Microsoft Excel to determine the frequency analysis, VOSviewer for bibliometric networks visualization, and Harzing's Publish or Perish for citation metrics analysis. Standard bibliometric parameters were analysed to evaluate the field's research trend, such as the growth of publications, topographical distribution, top subject area, most relevant journal, top cited documents, most relevant authors, and keyword trend analysis. Within 10 years, MBL discovery has shown a steady and continuous growth of interest among the community of researchers. United States of America, China, and the United Kingdom are the top 3 countries contribute high productivity to the field. The patent analysis also shows several impactful filed patents, indicating the significance of development research on the structural and functional relationship of MBL for an effective structure-based drug design (SBDD). Developing new MBL inhibitors using SBDD could help address the research gap and provide new successful therapeutic options for treating MBL-producing bacterial infections.

The Power of Molecular Dynamics Simulations and Their Applications to Discover Cysteine Protease Inhibitors

A large family of enzymes with the function of hydrolyzing peptide bonds, called peptidases or cysteine proteases (CPs), are divided into three categories according to the peptide chain involved. CPs catalyze the hydrolysis of amide, ester, thiol ester, and thioester peptide bonds. They can be divided into several groups, such as papain-like (CA), viral chymotrypsin-like CPs (CB), papainlike endopeptidases of RNA viruses (CC), legumain-type caspases (CD), and showing active residues of His, Glu/Asp, Gln, Cys (CE). The catalytic mechanism of CPs is the essential cysteine residue present in the active site. These mechanisms are often studied through computational methods that provide new information about the catalytic mechanism and identify inhibitors. The role of computational methods during drug design and development stages is increasing. Methods in Computer-Aided Drug Design (CADD) accelerate the discovery process, increase the chances of selecting more promising molecules for experimental studies, and can identify critical mechanisms involved in the pathophysiology and molecular pathways of action. Molecular dynamics (MD) simulations are essential in any drug discovery program due to their high capacity for simulating a physiological environment capable of unveiling significant inhibition mechanisms of new compounds against target proteins, especially CPs. Here, a brief approach will be shown on MD simulations and how the studies were applied to identify inhibitors or critical information against cysteine protease from several microorganisms, such as Trypanosoma cruzi (cruzain), Trypanosoma brucei (rhodesain), Plasmodium spp. (falcipain), and SARS-CoV-2 (Mpro). We hope the readers will gain new insights and use our study as a guide for potential compound identifications using MD simulations.

Aggregation and cytotoxicity of food additive dye (Azorubine)-albumin adducts: a multi-spectroscopic, microscopic and computational analysis

Protein and peptide misfolding is a central factor in the formation of pathological aggregates and fibrils linked to disorders like Alzheimer's and Parkinson's diseases. Therefore, it's essential to understand how food additives, particularly Azorubine, affect protein structures and their ability to induce aggregation. In this study, human serum albumin (HSA) was used as a model protein to investigate the binding and conformational changes caused by azorubine, a common food and drink colorant. The research revealed that azorubine destabilized the conformation of HSA at both physiological (pH 7.4) and acidic (pH 3.5) conditions. The loss of tryptophan fluorescence in HSA suggested significant structural alterations, particularly around aromatic residues. Far UV-CD analysis demonstrated disruptions in HSA's secondary structure, with a notable reduction in α-helical structures at pH 7.4. At pH 3.5, Azorubine induced even more extensive perturbations, resulting in a random coil conformation at higher azorubine concentrations. The study also investigated aggregation phenomena through turbidity measurements, RLS analysis, and TEM imaging. At pH 3.5, larger insoluble aggregates formed, while at pH 7.4, only conformational changes occurred without aggregate formation. Cytotoxicity assessments on neuroblastoma (SH-SY5Y) cells highlighted the concentration-dependent toxicity of albumin aggregates. Molecular dynamics simulations reaffirmed the stable interaction between azorubine and HSA. This research provides valuable insights into the mechanisms by which azorubine influences protein conformations. To further advance our understanding and contribute to the broader knowledge in this area, several future directions can be considered such as exploring other proteins, studying dose-response relationship, gaining mechanistic insights, biological relevance, toxicity assessment, identifying alternative food colorants, and mitigation strategies to prevent adverse effects of azorubine on serum proteins.Communicated by Ramaswamy H. Sarma.

Screening of Multitarget-Directed Natural Compounds as Drug Candidates for Alzheimer's Disease Using In Silico Techniques: Their Extraction and In Vitro Validation

Alzheimer's disease (AD) is a neurodegenerative disorder that impairs neurocognitive function. Acetylcholinesterase (AChE) and β-site APP cleaving enzyme 1 (BACE1) are the two main proteins implicated in AD. Indeed, the major available commercial drugs (donepezil, rivastigmine, and galantamine) against Alzheimer's are AChE inhibitors. However, none of these drugs are known to reverse or reduce the pathophysiological condition of the disease since there are multiple contributing factors to AD. Therefore, there is a need to develop a multitarget-directed ligand approach for its treatment. In the present study, plant bioactive compounds were screened for their AChE and BACE1 inhibition potential by conducting molecular docking studies. Considering their docking score and pharmacokinetic properties, limonin, peimisine, serratanine B, and withanolide A were selected as the lead compounds. Molecular dynamics simulations of these protein-ligand complexes confirmed the conformational and energetically stabilized enzyme-inhibitor complexes. The inhibition potential of the lead compounds was validated by in vitro enzyme assay. Withanolide A inhibited AChE (IC50 value of 107 μM) and showed mixed-type inhibition. At this concentration, it inhibited BACE1 activity by 57.10% and was stated as most effective. Both the compounds, as well as their crude extracts, were found to have no cytotoxic effect on the SH-SY5Y cell line.

Antioxidant, LC-MS Analysis, and Cholinesterase Inhibitory Potentials of Phoenix dactylifera Cultivar Khudari: An In Vitro Enzyme Kinetics and In Silico Study

We evaluated the therapeutic potentials of Khudari fruit pulp, a functional food and cultivar of Phoenix dactylifera, against neurological disorders. Our results demonstrate a good amount of phytochemicals (total phenolic content: 17.77 ± 8.21 µg GA/mg extract) with a high antioxidant potential of aqueous extract (DPPH assay IC50 = 235.84 ± 11.65 µg/mL) and FRAP value: 331.81 ± 4.56 µmol. Furthermore, the aqueous extract showed the marked inhibition of cell-free acetylcholinesterase (electric eel) with an IC50 value of 48.25 ± 2.04 µg/mL, and an enzyme inhibition kinetics study revealed that it exhibits mixed inhibition. Thereafter, we listed the 18 best-matched phytochemical compounds present in aqueous extract through LC/MS analysis. The computational study revealed that five out of eighteen predicted compounds can cross the BBB and exert considerable aqueous solubility. where 2-{5-[(1E)-3-methylbuta-1,3-dien-1-yl]-1H-indol-3-yl}ethanol (MDIE) indicates an acceptable LD50. value. A molecular docking study exhibited that the compounds occupied the key residues of acetylcholinesterase with ΔG range between -6.91 and -9.49 kcal/mol, where MDIE has ∆G: -8.67 kcal/mol, which was better than that of tacrine, ∆G: -8.25 kcal/mol. Molecular dynamics analyses of 100 ns supported the stability of the protein-ligand complexes analyzed through RMSD, RMSF, Rg, and SASA parameters. TRP_84 and GLY_442 are the most critical hydrophobic contacts for the complex, although GLU_199 is important for H-bonds. Prime/MM-GBSA showed that the protein-ligand complex formed a stable confirmation. These findings suggest that the aqueous extract of Khudari fruit pulp has significant antioxidant and acetylcholinesterase inhibition potentials, and its compound, MDIE, forms stably with confirmation with the target protein, though this fruit of Khudari dates can be a better functional food for the treatment of Alzheimer's disease. Further investigations are needed to fully understand the therapeutic role of this plant-based compound via in vivo study.

Identification of a potential inhibitor for New Delhi metallo-β-lactamase 1 (NDM-1) from FDA approved chemical library- a drug repurposing approach to combat carbapenem resistance

Superbugs producing New Delhi metallo-β-lactamase 1 (NDM-1) enzyme is a growing crisis, that is adversely affecting the global health care system. NDM-1 empowers the bacteria to inactivate entire arsenal of β-lactam antibiotics including carbapenem (the last resort antibiotic) and remains ineffective to all the available β lactamase inhibitors used in the clinics. Limited therapeutic option available for rapidly disseminating NDM-1 producing bacteria makes it imperative to identify a potential inhibitor for NDM-1 enzyme. With drug repurposing approach, in this study, we used virtual screening of available Food and Drug Administration (FDA) approved chemical library (ZINC12 database) and captured 'adapalene' (FDA drug) as a potent inhibitor candidate for NDM-1 enzyme. Active site docking with NDM-1, showed adapalene with binding energy -9.21 kcal/mol and interacting with key amino acid residues (Asp124, His122, His189, His250, Cys208) in the active site of NDM-1. Further, molecular dynamic simulation of NDM-1 docked with the adapalene at 100 ns displayed a stable conformation dynamic, with relative RMSD and RMSF in the acceptable range. Subsequently, in vitro enzyme assays using recombinant NDM-1 protein demonstrated inhibition of NDM-1 by adapalene. Further, the combination of adapalene plus meropenem (carbapenem antibiotic) showed synergistic effect against the NDM-1 producing carbapenem (meropenem) resistant clinical isolates (Escherichia coli and Klebsiella pneumoniae). Overall, our data indicated that adapalene can be a potential inhibitor candidate for NDM-1 enzyme that can contribute to the development of a suitable adjuvant to save the activity of carbapenem antibiotic against infections caused by NDM-1 positive gram-negative bacteria. Communicated by Ramaswamy H. Sarma.

Identification of a Putative SARS-CoV-2 Main Protease Inhibitor through In Silico Screening of Self-Designed Molecular Library

There have been outbreaks of SARS-CoV-2 around the world for over three years, and its variants continue to evolve. This has become a major global health threat. The main protease (M^pro, also called 3CL^pro) plays a key role in viral replication and proliferation, making it an attractive drug target. Here, we have identified a novel potential inhibitor of M^pro, by applying the virtual screening of hundreds of nilotinib-structure-like compounds that we designed and synthesized. The screened compounds were assessed using SP docking, XP docking, MM-GBSA analysis, IFD docking, MD simulation, ADME/T prediction, and then an enzymatic assay in vitro. We finally identified the compound V291 as a potential SARS-CoV-2 M^pro inhibitor, with a high docking affinity and enzyme inhibitory activity. Moreover, the docking results indicate that His41 is a favorable amino acid for pi-pi interactions, while Glu166 can participate in salt-bridge formation with the protonated primary or secondary amines in the screened molecules. Thus, the compounds reported here are capable of engaging the key amino acids His41 and Glu166 in ligand-receptor interactions. A pharmacophore analysis further validates this assertion.

Genetic and enzymatic characterization of two novel blaNDM-36, -37 variants in Escherichia coli strains

The widespread of different NDM variants in clinical Enterobacterales isolates poses a serious public health concern, which requires continuous monitoring. In this study, three E. coli strains carrying two novel blaNDM variants of blaNDM-36, -37 were identified from a patient with refractory urinary tract infection (UTI) in China. We conducted antimicrobial susceptibility testing (AST), enzyme kinetics analysis, conjugation experiment, whole-genome sequencing (WGS), and bioinformatics analysis to characterize the blaNDM-36, -37 enzymes and their carrying strains. The blaNDM-36, -37 harboring E. coli isolates belonged to ST227, O9:H10 serotype and exhibited intermediate or resistance to all β-lactams tested except aztreonam and aztreonam/avibactam. The genes of blaNDM-36, -37 were located on a conjugative IncHI2-type plasmid. NDM-37 differed from NDM-5 by a single amino acid substitution (His261Tyr). NDM-36 differed from NDM-37 by an additional missense mutation (Ala233Val). NDM-36 had increased hydrolytic activity toward ampicillin and cefotaxime relative to NDM-37 and NDM-5, while NDM-37 and NDM-36 had lower catalytic activity toward imipenem but higher activity against meropenem in comparison to NDM-5. This is the first report of co-occurrence of two novel blaNDM variants in E. coli isolated from the same patient. The work provides insights into the enzymatic function and demonstrates the ongoing evolution of NDM enzymes.

The activity and mechanism of vidofludimus as a potent enzyme inhibitor against NDM-1-positive E. coli

New Delhi metallo-β-lactamase-1 (NDM-1) is the most important and prevalent enzyme among all metallo-β-lactamases. NDM-1 can hydrolyze almost all-available β-lactam antibiotics including carbapenems, resulting in multidrug resistance, which poses an increasing clinical threat. However, there is no NDM-1 inhibitor approved for clinical treatment. Therefore, identifying a novel and potential enzyme inhibitor against NDM-1-mediated infections is an urgent need. In this study, vidofludimus was identified as a potential NDM-1 inhibitor by structure-based virtual screening and an enzyme activity inhibition assay. Vidofludimus significantly inhibited NDM-1 hydrolysis activity with a significant dose-dependent effect. When the vidofludimus concentration was 10 μg/ml, the inhibition rate and 50% inhibitory concentration were 93.3% and 13.8 ± 0.5 μM, respectively. In vitro, vidofludimus effectively restored the antibacterial activity of meropenem against NDM-1-positive Escherichia coli (E. coli), and the minimum inhibitory concentration of meropenem was decreased from 64 μg/ml to 4 μg/ml, a 16-fold reduction. The combination of vidofludimus and meropenem showed a significant synergistic effect with a fractional inhibitory concentration index of 0.125 and almost all the NDM-1-positive E. coli were killed within 12 h. Furthermore, the synergistic therapeutic effect of vidofludimus and meropenem in vivo was evaluated in mice infected with NDM-1 positive E. coli. Compared with the control treatment, vidofludimus combined with meropenem significantly improved the survival rate of mice infected with NDM-1-positive E. coli (P < 0.05), decreased the white blood cell count, the bacterial burden and inflammatory response induced by NDM-1-positive E. coli (P < 0.05), and alleviated histopathological damage in infected mice. It was demonstrated by molecular dynamic simulation, site-directed mutagenesis and biomolecular interaction that vidofludimus could interact directly with the key amino acids (Met67, His120, His122 and His250) and Zn²⁺ in the active site of NDM-1, thereby competitively inhibiting the hydrolysis activity of NDM-1 on meropenem. In summary, vidofludimus holds promise as anNDM-1 inhibitor, and the combination of vidofludimus and meropenem has potential as a therapeutic strategy for NDM-1-mediated infections.

Virtual Screening of Novel 24-Dehydroxysterol Reductase (DHCR24) Inhibitors and the Biological Evaluation of Irbesartan in Cholesterol-Lowering Effect

Hyperlipidemia is a risk factor for the development of fatty liver and cardiovascular diseases such as atherosclerosis and coronary heart disease, and hence, cholesterol-lowering drugs are considered important and effective in preventing cardiovascular diseases. Thus, researchers in the field of new drug development are endeavoring to identify new types of cholesterol-lowering drugs. 3β-hydroxysterol-Δ(24)-reductase (DHCR24) catalyzes the conversion of desmosterol to cholesterol, which is the last step in the cholesterol biosynthesis pathway. We speculated that blocking the catalytic activity of DHCR24 could be a novel therapeutic strategy for treating hyperlipidemia. In the present study, by virtually screening the DrugBank database and performing molecular dynamics simulation analysis, we selected four potential DHCR24 inhibitor candidates: irbesartan, risperidone, tolvaptan, and conivaptan. All four candidates showed significant cholesterol-lowering activity in HepG2 cells. The experimental mouse model of hyperlipidemia demonstrated that all four candidates improved high blood lipid levels and fat vacuolation in the livers of mice fed with a high-fat diet. In addition, Western blot analysis results suggested that irbesartan reduced cholesterol levels by downregulating the expression of the low-density lipoprotein receptor. Finally, the immune complex activity assay confirmed the inhibitory effect of irbesartan on the enzymatic activity of DHCR24 with its half-maximal inhibitory concentration (IC50) value of 602 nM. Thus, to the best of our knowledge, this is the first study to report that blocking the enzymatic activity of DHCR24 via competitive inhibition is a potential strategy for developing new cholesterol-lowering drugs against hyperlipidemia or multiple cancers. Furthermore, considering that irbesartan is currently used to treat hypertension combined with type 2 diabetes, we believe that irbesartan should be a suitable choice for patients with both hypertension and hyperlipidemia.

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

Amid the rise of multi-drug resistance among bacterial pathogens, the drying of the development pipeline of new antibiotics is worrisome. In search of new effective alternatives, phytocompounds can be considered a good one because of their immense antimicrobial property, low toxicity and huge structural diversity. In the present study, 200 phytocompounds were targeted against two Metallo β-lactamase (MBL) enzymes (NDM-1 and VIM-1) through molecular docking and meropenem was used as a reference drug. The phytocompounds with docking score ≤-8.0 kcal/mol were screened for their pharmacokinetic properties. The three best selected phytocompounds are Coriandrinonediol, Oleanderolide and Uzarigenin. Molecular docking helps to understand binding affinity. The selected phytocompounds showed better result than meropenem. Molecular interaction study reveals their competitive mechanism of inhibition against the target proteins. Coriandrinonediol has docking score -8.3 kcal/mol (NDM-1) and -8.9 kcal/mol (VIM-1), and oleanderolide has docking score -8.2 kcal/mol (NDM-1) and -9.3 kcal/mol (VIM-1). Uzarigenin has the highest binding affinity (-10.4 kcal/mol) among the three against VIM-1 and the lowest binding affinity (-8.1 kcal/mol) against NDM-1. Molecular dynamic (MD) simulation study also supports the stability and flexibility of the above phytocompounds during the MD run. Among the abovementioned three phytocompounds, oleanderolide has given the best result against both target proteins. These phytocompounds are first time reported as MBL inhibitors and their promising in silico results encourage to promote them for further investigation for in vitro and in vivo clinical trials.Communicated by Ramaswamy H. Sarma.

Phytochemical rich Himalayan Rhododendron arboreum petals inhibit SARS-CoV-2 infection in vitro

Phytochemicals with potential to competitively bind to the host receptors or inhibit SARS-CoV-2 replication, may prove to be useful as adjunct therapeutics for COVID-19. We profiled and investigated the phytochemicals of Rhododendron arboreum petals sourced from Himalayan flora, undertook in vitro studies and found it as a promising candidate against SARS-CoV-2. The phytochemicals were reported in various scientific investigations to act against a range of virus in vitro and in vivo, which prompted us to test against SARS-CoV-2. In vitro assays of R. arboreum petals hot aqueous extract confirmed dose dependent reduction in SARS-CoV-2 viral load in infected Vero E6 cells (80% inhibition at 1 mg/ml; IC50 = 173 µg/ml) and phytochemicals profiled were subjected to molecular docking studies against SARS CoV-2 target proteins. The molecules 5-O-Feruloyl-quinic acid, 3-Caffeoyl-quinic acid, 5-O-Coumaroyl-D-quinic acid, Epicatechin and Catechin showed promising binding affinity with SARS-CoV-2 Main protease (M^Pro; PDB ID: 6LU7; responsible for viral replication) and Human Angiotensin Converting Enzyme-2 (ACE2; PDB ID: 1R4L; mediate viral entry in the host). Molecular dynamics (MD) simulation of 5-O-Feruloyl-quinic acid, an abundant molecule in the extract complexed with the target proteins showed stable interactions. Taken together, the phytochemical profiling, in silico analysis and in vitro anti-viral assay revealed that the petals extract act upon M^Pro and may be inhibiting SARS-CoV-2 replication. This is the first report highlighting R. arboreum petals as a reservoir of antiviral phytochemicals with potential anti-SARS-CoV-2 activity using an in vitro system.

Celecoxib, Glipizide, Lapatinib, and Sitagliptin as potential suspects of aggravating SARS-CoV-2 (COVID-19) infection: a computational approach

COVID-19 caused by SARS-CoV-2 has emerged as a potential threat to human life, especially to people suffering from chronic diseases. In this study, we investigated the ability of selected FDA-approved drugs to inhibit TACE (tumor necrosis factor α converting enzyme), which is responsible for the shedding of membrane-bound ACE2 (angiotensin-converting enzyme2) receptors into soluble ACE2. The inhibition of TACE would lead to an increased population of membrane-bound ACE2, which would facilitate ACE2-Spike protein interaction and viral entry. A total of 50 drugs prescribed in treating various chronic diseases in Saudi Arabia were screened by performing molecular docking using AutoDock4.2. Based on docking energy (≤ -9.00 kcal mol^-1), four drugs (Celecoxib, Glipizide, Lapatinib, and Sitagliptin) were identified as potential inhibitors of TACE, with binding affinities up to 10⁶-10⁷ M^-1. Analysis of the molecular docking suggests that these drugs were bound to TACE's catalytic domain and interact with the key residues such as His405, Glu406, and His415, which are involved in active site Zn²⁺ ion chelation. Molecular dynamics simulation was performed to confirm the stability of TACE-drugs complexes. RMSD (root mean square deviation), RMSF (root mean square fluctuation), Rg (radius of gyration), and SASA (solvent accessible surface area) were within the acceptable limits. Free energy calculations using Prime-MM/GBSA suggest that Celecoxib formed the most stable complex with TACE, followed by Glipizide, Sitagliptin, and Lapatinib. The finding of this study suggests a mechanism for drugs to aggravate SARS-CoV-2 infection and hence high mortality in patients suffering from chronic diseases.Communicated by Ramaswamy H. Sarma.

Towards combating antibiotic resistance by exploring the quantitative structure-activity relationship of NDM-1 inhibitors

The emergence of New Delhi metallo-beta-lactamase-1 (NDM-1) has conferred enteric bacteria resistance to almost all beta-lactam antibiotics. Its capability of horizontal transfer through plasmids, amongst humans, animal reservoirs and the environment, has added up to the totality of antimicrobial resistance control, animal husbandry and food safety. Thus far, there have been no effective drugs for neutralizing NDM-1. This study explores the structure-activity relationship of NDM-1 inhibitors. IC₅₀ values of NDM-1 inhibitors were compiled from both the ChEMBL database and literature. After curation, a final set of 686 inhibitors were used for machine learning model building using the random forest algorithm against 12 sets of molecular fingerprints. Benchmark results indicated that the KlekotaRothCount fingerprint provided the best overall performance with an accuracy of 0.978 and 0.778 for the training and testing set, respectively. Model interpretation revealed that nitrogen-containing features (KRFPC 4080, KRFPC 3882, KRFPC 677, KRFPC 3608, KRFPC 3750, KRFPC 4287 and KRFPC 3943), sulfur-containing substructures (KRFPC 2855 and KRFPC 4843), aromatic features (KRFPC 1566, KRFPC 1564, KRFPC 1642, KRFPC 3608, KRFPC 4287 and KRFPC 3943), carbonyl features (KRFPC 1193 and KRFPC 3025), aliphatic features (KRFPC 2975, KRFPC 297, KRFPC 3224 and KRFPC 669) are features contributing to NDM-1 inhibitory activity. It is anticipated that findings from this study would help facilitate the drug discovery of NDM-1 inhibitors by providing guidelines for further lead optimization.

Targeting and ultrabroad insight into molecular basis of Resistance-nodulation-cell division efflux pumps

Resistance-nodulation-cell devision (RND) efflux pump variants have attracted a great deal of attention for efflux of many antibiotic classes, which leads to multidrug-resistant bacteria. The present study aimed to discover the interaction between the RND efflux pumps and antibiotics, find the conserved and hot spot residues, and use this information to target the most frequent RND efflux pumps. Protein sequence and 3D conformational alignments, pharmacophore modeling, molecular docking, and molecular dynamics simulation were used in the first level for discovering the function of the residues in interaction with antibiotics. In the second level, pharmacophore-based screening, structural-based screening, multistep docking, GRID MIF, pharmacokinetic modeling, fragment molecular orbital, and MD simulation were utilized alongside the former level information to find the most proper inhibitors. Five conserved residues, containing Ala209, Tyr404, Leu415, Asp416, and Ala417, as well as their counterparts in other OMPs were evaluated as the crucial conserved residues. MD simulation confirmed that a number of these residues had a key role in the performance of the efflux antibiotics; therefore, some of them were hot spot residues. Fourteen ligands were selected, four of which interacted with all the crucial conserved residues. NPC100251 was the fittest OMP inhibitor after pharmacokinetic computations. The second-level MD simulation and FMO supported the efficacy of the NPC100251. It was exhibited that perhaps OMPs worked as the intelligent and programable protein. NPC100251 was the strongest OMPs inhibitor, and may be a potential therapeutic candidate for MDR infections.

Identification of a Potential Inhibitor (MCULE-8777613195-0-12) of New Delhi Metallo-β-Lactamase-1 (NDM-1) Using In Silico and In Vitro Approaches

New Delhi metallo-β-lactamase-1 (NDM-1), expressed in different Gram-negative bacteria, is a versatile enzyme capable of hydrolyzing β-lactam rings containing antibiotics such as penicillins, cephalosporins, and even carbapenems. Multidrug resistance in bacteria mediated by NDM-1 is an emerging threat to the public health, with an enormous economic burden. There is a scarcity in the availability of specific NDM-1 inhibitors, and also a lag in the development of new inhibitors in pharmaceutical industries. In order to identify novel inhibitors of NDM-1, we screened a library of more than 20 million compounds, available at the MCULE purchasable database. Virtual screening led to the identification of six potential inhibitors, namely, MCULE-1996250788-0-2, MCULE-8777613195-0-12, MCULE-2896881895-0-14, MCULE-5843881524-0-3, MCULE-4937132985-0-1, and MCULE-7157846117-0-1. Furthermore, analyses by molecular docking and ADME properties showed that MCULE-8777613195-0-12 was the most suitable inhibitor against NDM-1. An analysis of the binding pose revealed that MCULE-8777613195-0-12 formed four hydrogen bonds with the catalytic residues of NDM-1 (His120, His122, His189, and Cys208) and interacted with other key residues. Molecular dynamics simulation and principal component analysis confirmed the stability of the NDM-1 and MCULE-8777613195-0-12 complex. The in vitro enzyme kinetics showed that the catalytic efficiency (i.e., k_cat/K_m) of NDM-1 on various antibiotics decreased significantly in the presence of MCULE-8777613195-0-12, due to poor catalytic proficiency (k_cat) and affinity (K_m). The IC₅₀ value of MCULE-8777613195-0-12 (54.2 µM) was comparable to that of a known inhibitor, i.e., D-captopril (10.3 µM). In sum, MCULE-8777613195-0-12 may serve as a scaffold to further design/develop more potent inhibitors of NDM-1 and other β-lactamases.

A computational evaluation of FDA medicines’ ability to inhibit hypoxia-inducible factor prolyl hydroxylase-2 (PHD-2) for acute respiratory distress syndrome

COVID-19 infection is associated with a significant fatality rate in individuals suffering from severe acute respiratory distress syndrome (ARDS). Among the several possibilities, inhibition of hypoxia-inducible factor prolyl hydroxylase-2 or prolyl hydroxylase domain-containing protein 2 (PHD2) in a hypoxia-independent way is a prospective therapeutic target for the treatment of ARDS. Vadadustat, Roxadustat, Daprodustat, Desidustat, and Enarudustat are the available clinical trial inhibitors. This study is proposed to focus on the repurposing of FDA-approved drugs as effective PHD2 inhibitors. This computational study utilises e-pharmacophore hypothesis generation from the native ligand–protein complex (PDB ID: 5OX6) based on XP visualiser information. The hypothesis containing five essential features (AAANR) was incorporated for FDA database screening, followed by Glide XP molecular docking and Prime MM-GBSA binding free energy calculations. Top scored ligands were investigated and Fenbufen was identified as an effective PHD-2 inhibitor by comparing with the native co-crystal ligand (Vadadustat). The manual lead optimisation of the Fenbufen structure was adopted to improve inhibitory potency, by increasing the binding affinity and protein–ligand stability. The newly designed compounds B and C showed additional binding interactions, excellent docking scores, binding free energy, and an acceptable range of ADME properties. Also, Fenbufen and compound C owned preferable protein–ligand stability during MD simulation when compared with the co-crystallised clinical trial ligand. Based on our findings, we deduce that Fenbufen can be proposed as an effective repurposable candidate as its structural modification showed a remarkable improvement in PHD2 inhibition.

Design, synthesis, and biological evaluation of trizole-based heteroaromatic derivatives as Bcr-Abl kinase inhibitors

Bcr-Abl is a key driver in the pathophysiology of CML. Broadening the chemical diversity of Bcr-Abl kinase inhibitors to overcome drug resistance is a current medical demand for CML treatment. As a continuation to our research, a series of compounds with heteroaromatics-trizole scaffold as hinge binding moiety (HBM) were developed as Bcr-Abl inhibitors based on in silico modeling analysis. Biological results indicated that these compounds exhibited a significantly enhanced inhibition against Bcr-Abl^WT and Bcr-Abl^T315I in kinases assays, along with improved anti-proliferative activities in leukemia cell assays, compared with previous disclosed compounds. In particular, compounds 9f, 28c, 31, and 44c displayed comparable even better potency with that of Imatinib in enzymatic assay and cell assays including K562 cells and adriamycin-resistant K562/A cells. Moreover, compounds 9f, 28c, and 44c exhibited potent inhibition activities against K562R cells bearing T315I mutant with IC₅₀ of 13.35 μM, 40.14 μM, and 1.91 μM, respectively, outperforming that of Imatinib. Meanwhile, the inhibition of Bcr-Abl activity in Ba/F3 cells demonstrated that these compounds exerted effects mainly by acting on Bcr-Abl. Additionally, compounds 9f, 28c, and 44c effectively induced apoptosis, arrest the cell cycle at S or G₂/M phase, and inhibited phosphorylation of Bcr-Abl and STAT5 in a dose-dependent manner. Docking studies indicated that trizole indeed retained the hydrophobic interaction of aromatic heterocycles with hinge region, and ADME prediction suggested that tested compounds had a favorable safety profile. Therefore, aromatic heterocycles incorporated with trizole could serve as a promising HBM for Bcr-Abl inhibitors with proline as fexibile linker, and compounds 9f, 28c, especially 44c could be served as a starting point for further optimization.

Risedronate and Methotrexate Are High-Affinity Inhibitors of New Delhi Metallo-β-Lactamase-1 (NDM-1): A Drug Repurposing Approach

Bacteria expressing New Delhi metallo-β-lactamase-1 (NDM-1) can hydrolyze β-lactam antibiotics (penicillins, cephalosporins, and carbapenems) and, thus, mediate multidrug resistance. The worldwide dissemination of NDM-1 poses a serious threat to public health, imposing a huge economic burden in the development of new antibiotics. Thus, there is an urgent need for the identification of novel NDM-1 inhibitors from a pool of already-known drug molecules. Here, we screened a library of FDA-approved drugs to identify novel non-β-lactam ring-containing inhibitors of NDM-1 by applying computational as well as in vitro experimental approaches. Different steps of high-throughput virtual screening, molecular docking, molecular dynamics simulation, and enzyme kinetics were performed to identify risedronate and methotrexate as the inhibitors with the most potential. The molecular mechanics/generalized Born surface area (MM/GBSA) and molecular dynamics (MD) simulations showed that both of the compounds (risedronate and methotrexate) formed a stable complex with NDM-1. Furthermore, analyses of the binding pose revealed that risedronate formed two hydrogen bonds and three electrostatic interactions with the catalytic residues of NDM-1. Similarly, methotrexate formed four hydrogen bonds and one electrostatic interaction with NDM-1’s active site residues. The docking scores of risedronate and methotrexate for NDM-1 were –10.543 kcal mol⁻¹ and −10.189 kcal mol⁻¹, respectively. Steady-state enzyme kinetics in the presence of risedronate and methotrexate showed a decreased catalytic efficiency (i.e., kcat/Km) of NDM-1 on various antibiotics, owing to poor catalytic proficiency and affinity. The results were further validated by determining the MICs of imipenem and meropenem in the presence of risedronate and methotrexate. The IC₅₀ values of the identified inhibitors were in the micromolar range. The findings of this study should be helpful in further characterizing the potential of risedronate and methotrexate to treat bacterial infections.

Insights from the molecular docking analysis of colistin with the PmrA protein model from Acinetobacter baumannii

Acinetobacter baumannii (AB) is one of the most common causes of nosocomial infections. Therefore, it is of interest to design and develop drugs against Acinetobacter baumannii. A strain of AB showing MIC 32 µg/ml against colistin was isolated from a hospital environment in Iran. Hence, we document data to glean insights from the molecular docking analysis of colistin with the PmrA protein from this bacterium.

Exploring the Binding Pattern of Geraniol with Acetylcholinesterase through In Silico Docking, Molecular Dynamics Simulation, and In Vitro Enzyme Inhibition Kinetics Studies

Acetylcholinesterase (AChE) inhibition is a key element in enhancing cholinergic transmission and subsequently relieving major symptoms of several neurological and neuromuscular disorders. Here, the inhibitory potential of geraniol and its mechanism of inhibition against AChE were elucidated in vitro and validated via an in silico study. Our in vitro enzyme inhibition kinetics results show that at increasing concentrations of geraniol and substrate, Vmax did not change significantly, but Km increased, which indicates that geraniol is a competitive inhibitor against AChE with an IC₅₀ value 98.06 ± 3.92 µM. All the parameters of the ADME study revealed that geraniol is an acceptable drug candidate. A docking study showed that the binding energy of geraniol (−5.6 kcal mol⁻¹) was lower than that of acetylcholine (−4.1 kcal mol⁻¹) with AChE, which exhibited around a 12.58-fold higher binding affinity of geraniol. Furthermore, molecular dynamics simulation revealed that the RMSD of AChE alone or in complex with geraniol fluctuated within acceptable limits throughout the simulation. The mean RMSF value of the complex ensures that the overall conformation of the protein remains conserved. The average values of Rg, MolSA, SASA, and PSA of the complex were 3.16 Å, 204.78, 9.13, and 51.58 Ų, respectively. We found that the total SSE of AChE in the complex was 38.84% (α-helix: 26.57% and β-sheets: 12.27%) and remained consistent throughout the simulation. These findings suggest that geraniol remained inside the binding cavity of AChE in a stable conformation. Further in vivo investigation is required to fully characterize the pharmacokinetic properties, optimization of dose administration, and efficacy of this plant-based natural compound.

Concatenation of molecular docking and molecular simulation of BACE-1, γ-secretase targeted ligands: in pursuit of Alzheimer's treatment

INTRODUCTION

Alzheimer's disease (AD), the most predominant cause of dementia, has evolved tremendously with an escalating frequency, mainly affecting the elderly population. An effective means of delaying, preventing, or treating AD is yet to be achieved. The failure rate of dementia drug trials has been relatively higher than in other disease-related clinical trials. Hence, multi-targeted therapeutic approaches are gaining attention in pharmacological developments.

AIMS

As an extension of our earlier reports, we have performed docking and molecular dynamic (MD) simulation studies for the same 13 potential ligands against beta-site APP cleaving enzyme 1 (BACE-1) and γ-secretase as a therapeutic target for AD. The In-silico screening of these ligands as potential inhibitors of BACE-1 and γ-secretase was performed using AutoDock enabled PyRx v-0.8. The protein-ligand interactions were analyzed in Discovery Studio 2020 (BIOVIA). The stability of the most promising ligand against BACE-1 and γ-secretase was evaluated by MD simulation using Desmond-2018 (Schrodinger, LLC, NY, USA).

RESULTS

The computational screening revealed that the docking energy values for each of the ligands against both the target enzymes were in the range of -7.0 to -10.1 kcal/mol. Among the 13 ligands, 8 (55E, 6Z2, 6Z5, BRW, F1B, GVP, IQ6, and X37) showed binding energies of ≤-8 kcal/mol against BACE-1 and γ-secretase. For the selected enzyme targets, BACE-1 and γ-secretase, 6Z5 displayed the lowest binding energy of -10.1 and -9.8 kcal/mol, respectively. The MD simulation study confirmed the stability of BACE-6Z5 and γ-secretase-6Z5 complexes and highlighted the formation of a stable complex between 6Z5 and target enzymes.

CONCLUSION

The virtual screening, molecular docking, and molecular dynamics simulation studies revealed the potential of these multi-enzyme targeted ligands. Among the studied ligands, 6Z5 seems to have the best binding potential and forms a stable complex with BACE-1 and γ-secretase. We recommend the synthesis of 6Z5 for future in-vitro and in-vivo studies.

High-throughput screening to identify potential inhibitors of the Zα domain of the adenosine deaminase 1 (ADAR1)

Adenosine deaminases acting on RNA 1 (ADAR1) are enzymes involved in editing adenosine to inosine in the dsRNAs of cells associated with cancer development. The p150 isoform of ADAR1 is the only isoform containing the Zα domain that binds to both Z-DNA and Z-RNA. The Zα domain is suggested to modulate the immune response and could be a suitable target for antiviral treatment and cancer immunotherapy. In this study, we aimed to identify potential inhibitors for ADAR1 protein that bind the Zα domain using molecular docking and simulation tools. Virtual docking and molecular dynamics simulation approaches were used to screen the potential activity of 2115 FDA-approved compounds on the Zα domain of ADAR1 and filtered for to obtain the top-scoring hits. The top three compounds with the best XP Gscore—namely alendronate (−7.045), etidronate (−6.923), and zoledronate (−6.77)—were subjected to 50 ns simulations to characterize complex stability and identify the fundamental interactions that contribute to inhibition of the ADAR1 Zα domain. The three compounds were shown to interact with Lys169, Lys170, Asn173, and Tyr177 of the Zα domain-like helical backbone of Z-RNA. The study provides a comprehensive and novel insights of repurposes drugs for the inhibition of ADAR1 function.

Design, synthesis, and biological evaluation of novel Bcr-AblT315I inhibitors incorporating amino acids as flexible linker

Despite the success of imatinib in CML therapy through Bcr-Abl inhibition, acquired drug resistance occurs over time in patients. In particular, the resistance caused by T315I mutation remains a challenge in clinic. Herein, we embarked on a structural optimization campaign aiming at discovery of novel Bcr-Abl inhibitors toward T315I mutant based on previously reported dibenzoylpiperazin derivatives. We proposed that incorporation of flexible linker could achieve potent inhibition of Bcr-Abl^T315I by avoiding steric clash with bulky sidechain of Ile315. A library of 28 compounds with amino acids as linker has been developed and evaluated. Among them, compound AA2 displayed the most potent activity against Bcr-Abl^WT and Bcr-Abl^T315I, as well as toward Bcr-Abl driven K562 and K562R cells. Further investigations indicated that AA2 could induce apoptosis of K562 cells and down regulate phosphorylation of Bcr-Abl. In summary, the compounds with amino acid as novel flexible linker exhibited certain antitumor activities, providing valuable hints for the discovery of novel Bcr-Abl inhibitors to overcome T315I mutant resistance, and AA2 could be considered as a candidate for further optimization.

High-Throughput Screening and Molecular Dynamics Simulation of Natural Product-like Compounds against Alzheimer's Disease through Multitarget Approach

Alzheimer’s disease (AD) is a progressive neurological disorder that affects 50 million people. Despite this, only two classes of medication have been approved by the FDA. Therefore, we have planned to develop therapeutics by multitarget approach. We have explored the library of 2029 natural product-like compounds for their multi-targeting potential against AD by inhibiting AChE, BChE (cholinergic pathway) MAO-A, and MOA-B (oxidative stress pathway) through in silico high-throughput screening and molecular dynamics simulation. Based on the binding energy of these target enzymes, approximately 189 compounds exhibited a score of less than −10 kcal/mol against all targets. However, none of the control inhibitors exhibited a binding affinity of less than −10 kcal/mol. Among these, the top 10 hits of compounds against all four targets were selected for ADME-T analysis. As a result, only F0850-4777 exhibited an acceptable range of physicochemical properties, drug-likeness, pharmacokinetics, and suitability for BBB permeation with high GI-A and non-toxic effects. The molecular dynamics study confirmed that F0850-4777 remained inside the binding cavity of targets in a stable conformation throughout the simulation and Prime-MM/GBSA study revealed that van der Waals’ energy (ΔG_vdW) and non-polar solvation or lipophilic energy (ΔG_{Sol_Lipo}) contribute favorably towards the formation of a stable protein–ligand complex. Thus, F0850-4777 could be a potential candidate against multiple targets of two pathophysiological pathways of AD and opens the doors for further confirmation through in vitro and in vivo systems.

Identification of Butyrylcholinesterase and Monoamine Oxidase B Targeted Ligands and their Putative Application in Alzheimer's Treatment: A Computational Strategy

BACKGROUND

With the burgeoning worldwide aging population, the incidence of Alzheimer's disease (AD) and its associated disorders is continuously rising. To appraise other relevant drug targets that could lead to potent enzyme targeting, 13 previously predicted ligands (shown favorable binding with AChE (acetylcholinesterase) and GSK-3 (glycogen synthase kinase) were screened for targeting 3 different enzymes, namely butyrylcholinesterase (BChE), monoamine oxidase A (MAO-A), and monoamine oxidase B (MAO-B) to possibly meet the unmet medical need of better AD treatment.

MATERIALS AND METHODS

The study utilized in silico screening of 13 ligands against BChE, MAO-A and MAOB using PyRx-Python prescription 0.8. The visualization of the active interaction of studied compounds with targeted proteins was performed by Discovery Studio 2020 (BIOVIA).

RESULTS

The computational screening of studied ligands revealed the docking energies in the range of -2.4 to -11.3 kcal/mol for all the studied enzymes. Among the 13 ligands, 8 ligands (55E, 6Z2, 6Z5, BRW, F1B, GVP, IQ6, and X37) showed the binding energies of ≤ -8.0 kcal/mol towards BChE, MAO-A and MAO-B. The ligand 6Z5 was found to be the most potent inhibitor of BChE and MAO-B, with a binding energy of -9.7 and -10.4 kcal mol, respectively. Molecular dynamics simulation of BChE-6Z5 and MAO-B-6Z5 complex confirmed the formation of a stable complex.

CONCLUSION

Our computational screening, molecular docking, and molecular dynamics simulation studies revealed that the above-mentioned enzymes targeted ligands might expedite the future design of potent anti-AD drugs generated on this chemical scaffold.

Recent research and development of NDM-1 inhibitors

Bacteria carrying New Delhi metallo-β-lactamase-1 (New Delhi metallo-β-lactamase, NDM-1) resistance gene is a new type of "superbug", which can hydrolyze almost all β-lactam antibiotics, rapidly spread among the same species and even spread among different species. NDM-1 belongs to the class B1 broad-spectrum enzyme of β-lactamase. The two positively charged zinc ions in the active center have electrostatic interaction with the hydroxyl ions in them to seize the hydrogen atom near the water molecule to form a bridging ring water molecule, which strengthens its nucleophilicity and attacks the carbonyl group on the lactam ring; thus, catalyzing the hydrolysis of β-lactam antibiotics. Since NDM-1 has an open active site and unique electrostatic structure, it essentially provides a wider range of substrate specificity. Due to its flexible hydrolysis mechanism and more and more variants also aggravate the threat of drug-resistant bacteria infection, there is still no effective inhibitor in clinic, which is a serious threat to human health and public health safety. The electron-rich substituents of NDM-1 inhibitors coordinate with two positively charged zinc ions in the active center of the enzyme through ion-dipole interaction to produce NDM-1 inhibitory activity. In this review, the research progress of NDM-1 enzyme and its inhibitors in the past 5 years was reviewed. The crystal structure, active center structure, surrounding important amino acid residues, newly discovered inhibitors and their action mechanism are classified and summarized in detail, which can be used as a reference for the development of effective drugs against drug-resistant bacteria targeting NDM-1.

Mutations in passive residues modulate 3D-structure of NDM (New Delhi metallo-β-lactamase) protein that endue in drug resistance: a MD simulation approach

The ability of antimicrobial resistance developed by bacteria enhanced the complexity of bacterial treatment leading a serious threat to human health. Production of β-lactamase by bacteria that inactivates β-lactam is a generic cause of resistance. One such β-lactamase enzyme is New Delhi Metallo-β-lactamase (NDM) which is recently reported to have clinically more importance and recognized as an antibiotic resistance marker. Mutations in active and passive residues of NDM protein play a fateful role in the substrate and inhibitor specificity. In this study, in silico point mutations of residues near the active site and flexible regions of protein were investigated. Hybrid modelling and molecular dynamics (MD) simulations were carried to build up the mutant models and monitored structural stability. Molecular docking results articulated that mutant proteins had lesser binding affinities with methicillin, oxacillin and doripenem drugs. Further, to scrutinize the structural alterations and rescore the binding energies per-residue basis, MD simulations of wildtype (WT) and mutant (MT) NDM proteins with methicillin, oxacillin and doripenem were performed. Our results demonstrated that mutations in N193A, S217A, G219A and T262A residues led to protein destabilization and amend their binding affinities with methicillin, oxacillin and doripenem. The present study exploited computational approaches which displayed differential binding of drugs with WT and MT NDM proteins that confer resistance to oxacillin and doripenem. The study features the significance of passive residues, thus provides a clue to accelerate the process of designing an ergastic antibiotic against NDM protein. Communicated by Ramaswamy H. Sarma.

Dieckol and Its Derivatives as Potential Inhibitors of SARS-CoV-2 Spike Protein (UK Strain: VUI 202012/01): A Computational Study

The high risk of morbidity and mortality associated with SARS-CoV-2 has accelerated the development of many potential vaccines. However, these vaccines are designed against SARS-CoV-2 isolated in Wuhan, China, and thereby may not be effective against other SARS-CoV-2 variants such as the United Kingdom variant (VUI-202012/01). The UK SARS-CoV-2 variant possesses D614G mutation in the Spike protein, which impart it a high rate of infection. Therefore, newer strategies are warranted to design novel vaccines and drug candidates specifically designed against the mutated forms of SARS-CoV-2. One such strategy is to target ACE2 (angiotensin-converting enzyme2)-Spike protein RBD (receptor binding domain) interaction. Here, we generated a homology model of Spike protein RBD of SARS-CoV-2 UK strain and screened a marine seaweed database employing different computational approaches. On the basis of high-throughput virtual screening, standard precision, and extra precision molecular docking, we identified BE011 (Dieckol) as the most potent compounds against RBD. However, Dieckol did not display drug-like properties, and thus different derivatives of it were generated in silico and evaluated for binding potential and drug-like properties. One Dieckol derivative (DK07) displayed good binding affinity for RBD along with acceptable physicochemical, pharmacokinetic, drug-likeness, and ADMET properties. Analysis of the RBD-DK07 interaction suggested the formation of hydrogen bonds, electrostatic interactions, and hydrophobic interactions with key residues mediating the ACE2-RBD interaction. Molecular dynamics simulation confirmed the stability of the RBD-DK07 complex. Free energy calculations suggested the primary role of electrostatic and Van der Waals' interaction in stabilizing the RBD-DK07 complex. Thus, DK07 may be developed as a potential inhibitor of the RBD-ACE2 interaction. However, these results warrant further validation by in vitro and in vivo studies.

Identification of natural compounds (proanthocyanidin and rhapontin) as high-affinity inhibitors of SARS-CoV-2 Mpro and PLpro using computational strategies

Introduction

The emergence of a new and highly pathogenic coronavirus (SARS-CoV-2) in Wuhan (China) and its spread worldwide has resulted in enormous social and economic losses. Amongst many proteins encoded by the SARS-CoV-2 genome, the main protease (Mpro) or chymotrypsin-like cysteine protease (3CLpro) and papain-like protease (PLpro) serve as attractive drug targets.

Material and methods

We screened a library of 2267 natural compounds against Mpro and PLpro using high throughput virtual screening (HTVS). Fifty top-scoring compounds against each protein in HTVS were further evaluated by standard-precision (SP) docking. Compounds with SP docking energy of ≤ -8.0 kcal/mol against Mpro and ≤ -5.0 kcal/mol against PLpro were subjected to extra-precision (XP) docking. Finally, six compounds against each target proteins were identified and subjected to Prime/MM-GBSA free energy calculations. Compounds with the lowest Prime/MM-GBSA energy were subjected to molecular dynamics simulation to evaluate the stability of protein-ligand complexes.

Results

Proanthocyanidin and rhapontin were identified as the most potent inhibitors of Mpro and PLpro, respectively. Analysis of protein-inhibitor interaction revealed that both protein-inhibitor complexes were stabilized by hydrogen bonding and hydrophobic interactions. Proanthocyanidin interacted with the catalytic residues (His41 and Cys145) of Mpro, while rhapontin contacted the active site residues (Trp106, His272, Asp286) of PLpro. The docking energies of proanthocyanidin and rhapontin towards their respective targets were -10.566 and -10.022 kcal/mol.

Conclusions

This study's outcome may support application of proanthocyanidin and rhapontin as a scaffold to build more potent inhibitors with desirable drug-like properties. However, it requires further validation by in vitro and in vivo studies.

Quinoline yellow dye stimulates whey protein fibrillation via electrostatic and hydrophobic interaction: A biophysical study

Amyloid fibril formation of proteins is associated with a number of neurodegenerative diseases. Several small molecules can accelerate the amyloid fibril formation in vitro and in vivo. However, the molecular mechanism of amyloid fibrillation is still unclear. In this study, we investigated how the food dye quinoline yellow (QY) induces amyloid fibrillation in α-lactalbumin (α-LA), a major whey protein, at pH 2.0. We used several spectroscopy techniques and a microscopy technique to explore how QY provokes amyloid fibrillation in α-LA. From turbidity and Rayleigh light scattering experiments, we found that QY promotes α-LA aggregation in a concentration-dependent manner; the optimal concentration for α-LA aggregation was 0.15 to 10.00 mM. Below 0.1 mM, no aggregation occurred. Quinoline yellow-induced aggregation was a rapid process that escaped the lag phase, but it depended on the concentrations of both α-LA and QY. We also demonstrated that aggregation switched the secondary structure of α-LA from α-helices to cross-β-sheets. We then confirmed the amyloid-like structure of aggregated α-LA by transmission electron microscopy measurements. Molecular docking and simulation confirmed the stability of the α-LA-QY complex due to the formation of 1 hydrogen bond with Lys99 and 2 electrostatic interactions with Arg70 and Lys99, along with hydrophobic interactions with Leu59 and Tyr103. This study will aid in our understanding of how small molecules induce aggregation of proteins inside the stomach (low pH) and affect the digestive process.

Critical Review on the Chemical Aspects of Cannabidiol (CBD) and Harmonization of Computational Bioactivity Data

Cannabidiol (CBD) is a non-psychotropic phytocannabinoid which represents one of the constituents of the "phytocomplex" of Cannabis sativa. This natural compound is attracting growing interest since when CBD-based remedies and commercial products were marketed. This review aims to exhaustively address the extractive and analytical approaches that have been developed for the isolation and quantification of CBD. Recent updates on cutting-edge technologies were critically examined in terms of yield, sensitivity, flexibility and performances in general, and are reviewed alongside original representative results. As an add-on to currently available contributions in the literature, the evolution of the novel, efficient synthetic approaches for the preparation of CBD, a procedure which is appealing for the pharmaceutical industry, is also discussed. Moreover, with the increasing interest on the therapeutic potential of CBD and the limited understanding of the undergoing biochemical pathways, the reader will be updated about recent in silico studies on the molecular interactions of CBD towards several different targets attempting to fill this gap. Computational data retrieved from the literature have been integrated with novel in silico experiments, critically discussed to provide a comprehensive and updated overview on the undebatable potential of CBD and its therapeutic profile.

Stabilization of a potential anticancer thiosemicarbazone derivative in Sudlow site I of human serum albumin: In vitro spectroscopy coupled with molecular dynamics simulation

Human Serum Albumin (HSA) is the most important protein in human blood plasma and can acts as a major transporting agent for various drug molecules with flexible binding interaction. To elucidate the interaction of a newly designed potential anticancer thiosemicarbazone based luminophore (E)-1-(4-(diethylamino)-2-hydroxybenzylidene)-4,4-dimethyl-thiosemicarbazide (DAHTS) with HSA under physiological condition, in vitro optical spectroscopic experiments viz UV-Vis absorption, steady state fluorescence, fluroscence anisotropy, time resolved fluorscence (TRF) and cicular dichroism (CD) spectroscopy have been scrutinised. The experimental findings have been corroborated with in silico molecular docking analysis and Molecular Dynamics (MD) simulation. The spectroscopic results demonstrated that the conventionally anion-favouring Sudlow site I of HSA copiously adapt neutral DAHTS molecule with moderate binding affinity. The mean fluorescence lifetime of the sole tryptophan (Trp-214) present in the macromolecule experiences an appreciable diminution with an increase in concentration of the synthesized molecule. DAHTS localize itself close to Trp-214 within subdomain IIA (Sudlow site I) and surrounded by multiple hydrophobic amino acid residues (Val-235, Val-231, Ala-229, Phe-228, Val-325, Phe-326, Leu-327, Met-329, Phe-330, Leu-331, Tyr-332, Leu-346, Leu-347, Val-482, Leu-349, Ala-350, Ala-210, Trp-214, Ala- 213 and Val-216) in HSA. The distinct fluorescence lifetime, diverse pathways and changing rate of population indicates that the rotamerisation of Trp-214 residue is controlled by the guest molecule. Sudlow site I of HSA behaves flexibly and induces an allosteric modulation in the macromolecule resulting a minor deformation in the protein secondary structure as observed in CD (observed 11% change of α-helix content) as well as in MD simulation. The integrated multi-spectroscopic research described herein provides several important information about the binding interaction of a thiosemicarbazone Schiff base with HSA, which can be very significant for thiosemicarbazone based drug designing for academia as well as industry.

ACSS3 represses prostate cancer progression through downregulating lipid droplet-associated protein PLIN3

Current endocrine therapy for prostate cancer (PCa) mainly inhibits androgen/androgen receptor (AR) signaling. However, due to increased intratumoural androgen synthesis and AR variation, PCa progresses to castration-resistant prostate cancer (CRPC), which ultimately becomes resistant to endocrine therapy. A search for new therapeutic perspectives is urgently needed. Methods: By screening lipid metabolism-related gene sets and bioinformatics analysis in prostate cancer database, we identified the key lipid metabolism-related genes in PCa. Bisulfite genomic Sequence Polymerase Chain Reaction (PCR) (BSP) and Methylation-Specific Polymerase Chain Reaction (PCR) (MSP) were preformed to detect the promoter methylation of ACSS3. Gene expression was analyzed by qRT-PCR, Western blotting, IHC and co-IP. The function of ACSS3 in PCa was measured by CCK-8, Transwell assays. LC/MS, Oil Red O assays and TG and cholesterol measurement assays were to detect the levels of TG and cholesterol in cells. Resistance to Enzalutamide in C4-2 ENZR cells was examined in a xenograft tumorigenesis model in vivo. Results: We found that acyl-CoA synthetase short chain family member 3 (ACSS3) was downregulated and predicted a poor prognosis in PCa. Loss of ACSS3 expression was due to gene promoter methylation. Restoration of ACSS3 expression in PCa cells significantly reduced LD deposits, thus promoting apoptosis by increasing endoplasmic reticulum (ER) stress, and decreasing de novo intratumoral androgen synthesis, inhibiting CRPC progression and reversing Enzalutamide resistance. Mechanistic investigations demonstrated that ACSS3 reduced LD deposits by regulating the stability of the LD coat protein perilipin 3 (PLIN3). Conclusions: Our study demonstrated that ACSS3 represses prostate cancer progression through downregulating lipid droplet-associated protein PLIN3.

Siphonocholin isolated from red sea sponge Siphonochalina siphonella attenuates quorum sensing controlled virulence and biofilm formation

Increasing incidence of multi-drug resistant bacterial pathogens, especially in clinical settings, has been developed into a grave health situation. The drug resistance problem demands the necessity for alternative unique therapeutic policies. One such tactic is targeting the quorum sensing (QS) controlled virulence and biofilm production. In this study, we evaluated a marine steroid Siphonocholin (Syph-1) isolated from Siphonochalina siphonella against Chromobacterium violaceum (CV) 12472, Pseudomonas aeruginosa (PAO1), Methicillin-resistant Staphylococcus aureus (MRSA) and Acinetobacter baumannii (BAA) for biofilm and pellicle formation inhibition, and anti-QS property. MIC of Syph-1 against MRSA, CV, PAO1 was found as 64 µg/mL and 256 µg/mL against BAA. At selected sub-MICs, Syph-1 significantly (P ≤ 0.05) decreased the production of QS regulated virulence functions of CV12472 (violacein) and PAO1 [elastase, total protease, pyocyanin, chitinase, exopolysaccharides, and swarming motility]. The Syph-1 significantly decreased (p = 0.005) biofilm formation ability of tested bacterial pathogens, at sub-MIC level (PAO1 > MRSA > CV > BAA) and pellicle formation in A. baumannii (at 128 µg/mL). Molecular docking and simulation results indicated that Siph-1 was bound at the active site of BfmR N-terminal domain with high affinity. This study highlights the anti-QS and anti-biofilm activity of Syph-1 against bacterial pathogens reflecting its broad spectrum anti-infective potential.

Identifying novel inhibitor of quorum sensing transcriptional regulator (SdiA) of Klebsiella pneumoniae through modelling, docking and molecular dynamics simulation

In this study, attempts have been made to identify novel inhibitor(s) of SdiA (a homolog of LuxR transcription regulator) of Klebseilla pneumoniae using various computational techniques. 4LFU was used as a template to model the structure of SdiA. ProCheck, Verify3D, Ramachandran plot scores and ProSA-Web confirmed the good quality of the model as the root mean square deviation (RMSD) between SdiA model, and 4LFU template was estimated to be 0.21 Å. The secondary structural contents of SdiA model were predicted using PDBsum. The only binding site of SdiA was identified (area = 523.083 Ų and volume = 351.044 ų) using CASTp. Molecular docking at three different levels [high throughput virtual screening, standard-precision (SP) and extra-precision (XP) dockings] with increasingly stringent conditions was performed using Glide on Selleck's express pick library (L3600). A total of 61 ligands were found to bind with high affinities to the active site of SdiA. Further, the effect of solvent on protein-ligand interaction was evaluated by performing molecular mechanics-general born surface area (Prime/MM-GBSA). On the basis of Prime/MM-GBSA score, molecular dynamics simulation (50 ns) was performed on the ligand (WAY-390139-A) showing lowest binding energy to confirm the stability of protein-ligand complex. Docking energy and the corresponding binding affinity of WAY-390139-A towards SdiA were estimated to be -13.005 kcal mol^-1 and 3.46 × 10⁹ M^-1, respectively. Our results confirm that WAY-390139-A binds at the autoinducer binding site of SdiA with high affinity and stability and can be further exploited as potential drug against K. pneumoniae after experimental validation.Communicated by Ramaswamy H. Sarma.

Oncoglabrinol C, a new flavan from Oncocalyx glabratus protects endothelial cells against oxidative stress and apoptosis, and modulates hepatic CYP3A4 activity

Active herbal or natural compounds have high chemical diversity and specificity than synthetic drugs. Recently, we have validated the hypoglycemic salutation of Oncocalyx glabratus in rodent model, and demonstrated the activation of PPARα/γ by its newly ioslated flavan derivative Oncoglabrinol C (5,3′-Dihydroxyflavan 7-4′-O-digallate) in liver cells (HepG2). Here we evaluated the potential of Oncoglabrinol C against Dichlorofluorescin (DCFH) and Methylglyoxal (MGO) induced endothelial cells (HUVEC) oxidative and apoptotic damage, including activation of PXR-mediated hepatic CYP3A4. Our MTT assay showed protection of ~57% and ~63.5% HUVEC cells by 10 and 20 μg/ml doses of Oncoglabrinol C, respectively through attenuating DCFH triggered free-radicals. Also, the two doses effectively protected ~53% and ~65.5% cells, respectively by reversing MGO toxicity. In DCFH and MGO treated cells, Oncoglabrinol C (20 μg/ml) effectively downregulated caspase 3/7 activity by ~33% and ~43.5%, respectively. Moreover, in reporter gene (dual-luciferase) assay, Oncoglabrinol C (20 μg/ml) moderately activated hepatic CYP3A4. Molecular docking of Oncoglabrinol C indicated its strong interactions with cellular caspase 3/7, PPARα/γ and PXR proteins, which supported its anti-apoptotic (antagonistic) as well as pro-hypoglycemic and PXR/CYP activating (agonistic) activities. Taken together, our findings demonstrated the potential of Oncoglabrinol C in reversing the endothelial oxidative and apoptotic damage as well as in the activation of hepatic CYP3A4. This warrants further evaluations of Oncoglabrinol C and related compounds towards developing effective and safe drugs against diabetes associated cardiovascular disorders.

Food color 'Azorubine' interferes with quorum sensing regulated functions and obliterates biofilm formed by food associated bacteria: An in vitro and in silico approach

Quorum sensing (QS) plays a crucial role in different stages of biofilm development, virulence production, and subsequently to the growth of bacteria in food environments. Biofilm mediated spoilage of food is one of the ongoing challenge faced by the food industry worldwide as it incurs substantial economic losses and leads to various health issues. In the present investigation, we studied the interference of quorum sensing, its regulated virulence functions, and biofilm in food-associated bacteria by colorant azorubine. In vitro bioassays demonstrated significant inhibition of QS and its coordinated virulence functions in Chromobacterium violaceum 12472 (violacein) and Pseudomonas aeruginosa PAO1 (elastase, protease, pyocyanin, and alginate). Further, the decrease in the production EPS (49–63%) and swarming motility (61–83%) of the pathogens was also recorded at sub-MICs. Azorubine demonstrated broad-spectrum biofilm inhibitory potency (50–65%) against Chromobacterium violaceum, Pseudomonas aeruginosa, E. coli O157:H7, Serratia marcescens, and Listeria monocytogenes. ROS generation due to the interaction between bacteria and azorubine could be responsible for the biofilm inhibitory action of the food colorant. Findings of the in vitro studies were well supported by molecular docking and simulation analysis of azorubine and QS virulence proteins. Azorubine showed strong binding to PqsA as compared to other virulent proteins (LasR, Vfr, and QscR). Thus, it is concluded that azorubine is a promising candidate to ensure food safety by curbing the menace of bacterial QS and biofilm-based spoilage of food and reduce economic losses.

Specific NDM-1 Inhibitor of Isoliquiritin Enhances the Activity of Meropenem against NDM-1-positive Enterobacteriaceae in vitro

NDM-1-positive Enterobacteriaceae have caused serious clinical infections, with high mortality rates. Carbapenem was the ultimate expectation for the treatment of such infections in clinical practice. However, since the discovery of plasmid-mediated New Delhi metallo-β-lactamase-1 (NDM-1), the efficient therapeutic effects of carbapenems have been increasingly restricted. Here, we identified isoliquiritin, a novel specific inhibitor of the NDM-1 enzyme that restored the activity of carbapenem against NDM-1-producing E. coli isolates and K. pneumoniae isolates without affecting the growth of bacteria. A checkerboard test, growth curve assays and time-kill assays confirmed the significant synergistic effect of isoliquiritin combined with meropenem in vitro. It is worth noting that isoliquiritin only inhibited the activity of NDM-1 and had no obvious inhibitory effect on other class B metallo-β-lactamases (VIM-1) or NDM-1 mutants (NDM-5). The FIC indices of meropenem with isoliquiritin on NDM-1-positive E. coli and K. pneumoniae were all less than 0.5. Isoliquiritin had no influences on the expression of NDM-1-positive strains at concentrations below 64 µg/mL. Collectively, our results show that isoliquiritin is a potential adjuvant therapy drug that could enhance the antibacterial effect of carbapenems, such as meropenem, on NDM-1-positive Enterobacteria and lay the foundation for subsequent clinical trials.

Quinoline yellow (food additive) induced conformational changes in lysozyme: a spectroscopic, docking and simulation studies of dye-protein interactions

Quinoline yellow (QY) is a synthetic yellow dye widely used as a coloring agent for various foodstuffs. In the current study, we have examined the role of QY on the aggregation propensity of hen egg-white lysozyme (HEWL) under physiological conditions. The dye induced conformational changes in HEWL leading to aggregate formation were identified by circular dichroism (CD), turbidity analysis, fluorescence measurement and microscopic (TEM) imaging. Molecular docking and molecular dynamics simulation studies were also employed to strengthen binding and aggregation results. Our results indicate that 25-100 µM of QY induces aggregation in HEWL, while lower QY concentrations (5 and 10 µM) does not have any effect on the aggregation propensity of HEWL. The kinetics of HEWL aggregation demonstrate nucleation independent aggregation of HEWL without lag phase. On the other hand, far UV-CD analysis illustrated the loss of α-helical structure with the increasing concentration of QY. TEM results also support the formation of aggregate structures in HEWL when exposed to QY. Molecular docking and simulation studies revealed that the HEWL-QY complex is stable as compared to individual entities. In silico analysis also illustrated that QY-induced aggregation of HEWL proceeds through the formation of hydrogen bonds, electrostatic (Pi-Anion) and Pi-Sulfur interactions. The above-mentioned results highlight the possible detrimental effect by food additive dyes, particularly in protein misfolding.

Computer-aided screening for suppressor of variegation 4-20 homolog 1 inhibitors and their preliminary activity validation in human osteosarcoma

Histone methylation/demethylation facilitate to maintain balanced histone methylation levels and underpin gene regulation, playing the key roles in epigenetic regulation. Suppressor of variegation 4-20 homolog 1 (SUV420H1), a member of class Histone Lysine Methyltransferase and a key enzyme in the epigenetic regulation of the pathways controlling metabolism and tumorigenesis, is crucial to maintain cell homeostasis. The inhibition of SUV420H1 has emerged as a promising candidate for drug development and cancer therapy. Herein, two potential and potent SUV420H1 inhibitors (ZINC08398384, ZINC08439608) were identified through in silico approach and in vitro biological experiments. In vitro biological tests demonstrated that these compounds can inhibit the proliferation of U2OS cells and restrict its migration ability. And the level of dimethylation of lysine 20 on histone H4 (H4K20me2) was markedly decreased by these compounds-treatment in a dose-dependent manner. These results indicated that ZINC08398384 and ZINC08439608 are potential SUV420H1 inhibitors and could be developed as promising drug candidates applied to cancer epigenetic therapy.Communicated by Ramaswamy H. Sarma.