Investigating the anti-cancer compounds from Calliandra harrisii for precision medicine in pancreatic cancer via in-silico drug design and GC-MS analysis

Pancreatic cancer is a fatal illness caused by mutations in multiple genes. Pancreatic cancer damages the organ that helps in digestion, resulting in symptoms including fatigue, bloating, and nausea. The use of medicinal plants has been crucial in the treatment of numerous disorders. The medicinal plant Calliandra Harrisi has been widely exploited for its possibilities in biology and medicine. The current study aimed to assess the biopotential of biologically active substances against pancreatic cancer. The GC-MS data of these phytochemicals from Calliandra Harrisi were further subjected to computational approaches with pancreatic cancer genes to evaluate their potential as therapeutic candidates. Molecular docking analysis revealed that N-[Carboxymethyl] maleamic acid is the leading molecule responsible for protein denaturation inhibition, having the highest binding affinity of 6.8 kJ/mol among all other compounds with KRAS inflammatory proteins. Furthermore, ADMET analysis and Lipinski's rule validation were also performed revealing its higher absorption in the gastrointestinal tract. The results of the hepatotoxicity test demonstrated that phytochemicals are non-toxic, safe to use, and do not cause necrosis, fibrosis, or vacuolar degeneration even at excessive levels. Calliandra Harrisi has phytoconstituents that have a variety of pharmacological uses in consideration.

Imaging metabolic mechanisms and the binding behavior of nutrients/transporters of edible Matricaria flowers VOCs

To promote the consumption of flowers and to utilize the nutritional value of proteins, the efficacy of the beneficial components of flowers has been intensively studied. Anthemis nobilis was used as the study object, and all its volatile components (VOCs) were fingerprinted using headspace solid-phase micro-extraction gas-mass spectrometry (HS-SPME/GC-MS). GC-MS fingerprints of five parts of Anthemis nobilis were established using three proteins, bovine lactoferrin (BLF), bovine lactoglobulin (β-Lg), and human serum albumin (HSA), as nutrient transporters. The interactions between the volatile components from different parts of the mother chrysanthemum plant and the nutrient/transport proteins were investigated. The results of fingerprinting showed that the flavor components were dominated by alkenes. In addition, this study revealed that among the three nutrient transporters, the strongest binding to the adsorbed volatile components was HSA, followed by BLF, and β-Lg was second. In addition, a characteristic molecule, camphene, was screened. Integrated molecular simulation using fluorescence spectroscopy was used to validate the results of the interaction of the nutrient/transport proteins systems with characteristic molecule. The properties of the characteristic molecules such as absorption, distribution, metabolism, excretion and toxicity in vivo were analyzed using ADMET to provide a theoretical basis for the preparation of flower-flavored dairy products.

Exploration of comprehensive marine natural products database against dengue viral non-structural protein 1 using high-throughput computational studies

Dengue virus (DENV) non-structural protein 1 (NS1) is a versatile quasi-protein essential for the multiplication of the virus. This study applied high-throughput virtual screening (HTVS) and molecular dynamics (MD) simulation to detect the potential marine natural compounds against the NS1 of DENV. The structure of the NS1 protein was retrieved from Protein Data Bank with (PDB ID: 4O6B). Missing residues were added using modeler software. Molecular operating environment (MOE) programme was used to prepare the protein before docking. Virtual screening was performed on PyRx software to identify natural compounds retrieved from Comprehensive Marine Natural Products Database (CMNPD) against the NS1 protein, and best-docked compounds were examined by molecular docking and molecular dynamic (MD) simulation. Out of 31,561 marine compounds, the top 10 compounds showed docking scores lesser than -8.0 kcal/mol. One of the best hit compounds, CMNPD6802, was further analyzed using MD simulation study at 100 nanoseconds and Molecular Mechanics with Generalized Born and Surface Area Solvation (MM/GBSA). Based on its total binding energy, determined using the MM/GBSA approach, CMNPD6802 was ranked first. Its pharmacokinetic properties concerning the target protein NS1 were also evaluated. The results of the MD simulation showed that CMNPD6802 remained in close contact with the protein throughout the activation period, mapped using principal component analysis. These findings suggest that CMNPD6802 could serve as an NS1 inhibitor and may be a potential candidate for treating DENV infections.Communicated by Ramaswamy H. Sarma.

Chemical profile of phenolic extracts from rapeseed meal and inhibitory effects on α-glucosidase: UPLC-MS/MS analysis, multispectral approaches, molecular simulation and ADMET analysis

Rapeseed meal (RSM) is the by-product of rapeseed processing that enriches phenolic compounds. However, the comprehensive characterization of its phenolic substances in terms of composition and potential activities remains incomplete, leading to limited utilization in the food industry. In this study, the phenolic profile from RSM (referred to as RMP) was identified, and their inhibitory effects on α-glucosidase were investigated. UPLC-MS/MS analysis showed that a total of 466 phenolic compounds were detected in RMP. The primary components were sinapic acid (SA), caffeic acid (CA), salicylic acid (SAA), and astragalin (AS). Multispectral approaches demonstrated significant inhibitory capacity of RMP against α-glucosidase with a half inhibition value (IC50) of 0.32 mg/mL, with a stronger inhibition compared to CA/SAA/AS (IC50: 4.0, 5.9, and 0.9 mg/mL) in addition to the previously reported SA, suggesting a synergistic effect. Both RMP and CA/SAA/AS altered the secondary structure of α-glucosidase to quench its intrinsic fluorescence. Molecular simulation results revealed that hydrogen bonds and van der Waals forces primarily contributed to the interaction between CA/SAA/AS and α-glucosidase, as well as verified the stability of the binding process over the entire simulation duration. The ADMET analysis showed that CYP2D6 was not inhibited by CA/SAA/AS, which had no AMES toxicity, hepatotoxicity, and skin sensitization. This finding suggests the potential of RMP against α-glucosidase for the treatment of diabetes.

Exploring Medicinal Herbs' Therapeutic Potential and Molecular Docking Analysis for Compounds as Potential Inhibitors of Human Acetylcholinesterase in Alzheimer's Disease Treatment

Background and Objectives: Alzheimer's disease (AD) stands as a pervasive neurodegenerative ailment of global concern, necessitating a relentless pursuit of remedies. This study aims to furnish a comprehensive exposition, delving into the intricate mechanistic actions of medicinal herbs and phytochemicals. Furthermore, we assess the potential of these compounds in inhibiting human acetylcholinesterase through molecular docking, presenting encouraging avenues for AD therapeutics. Materials and Methods: Our approach entailed a systematic exploration of phytochemicals like curcumin, gedunin, quercetin, resveratrol, nobiletin, fisetin, and berberine, targeting their capability as human acetylcholinesterase (AChE) inhibitors, leveraging the PubChem database. Diverse bioinformatics techniques were harnessed to scrutinize molecular docking, ADMET (absorption, distribution, metabolism, excretion, and toxicity), and adherence to Lipinski's rule of five. Results: Results notably underscored the substantial binding affinities of all ligands with specific amino acid residues within AChE. Remarkably, gedunin exhibited a superior binding affinity (-8.7 kcal/mol) compared to the reference standard. Conclusions: These outcomes accentuate the potential of these seven compounds as viable candidates for oral medication in AD treatment. Notably, both resveratrol and berberine demonstrated the capacity to traverse the blood-brain barrier (BBB), signaling their aptitude for central nervous system targeting. Consequently, these seven molecules are considered orally druggable, potentially surpassing the efficacy of the conventional drug, donepezil, in managing neurodegenerative disorders.

In-silico investigation of 4-nitro-N-1H-pyrazol-3-ylbenzamide towards its potential use against SARS-CoV-2: a DFT, molecular docking and molecular dynamics study

In the present research work, we report the synthesis and characterization of novel pyrazole derivative obtained by the condensation reaction of 4-nitro benzaldehyde group with one equivalent of the 2-amino pyrazole yielding 4-nitro-N-1H-pyrazol-3-ylbenzamide with high yield. The two symmetry-independent molecules (molecule A and molecule B) differ about the central C-N bond, with the dihedral angles between the pyrazole ring system and the nitrobenzene ring being 13.90° and 18.64°, respectively. By optimizing the symmetry-independent dimer molecules, the rotational barrier between the conformers is found to be within the 2.5-5.5 kcal/mol range. QTAIM and RDG based NCI isosurface revealed the presence of strong N-H…N and C-H…O hydrogen bonds which stabilize the two independent centrosymmetric inversion-related dimers. Further, weak and short directional interactions such as C-H…N, H…H and C-H…π were also analyzed systematically using various topological parameters. The compound is found to adhere to the Lipinski's rule of five and exhibit good pharmacokinetic properties. The results of molecular docking studies performed against SARS-CoV-2 virus main protease (PDB IDs: 6LU7, 6W9C and 6WQF) revealed that the compound showed better docking scores. Molecular docking studies verified the inhibition activity of the synthesized novel compound. Finally, the binding free energy and contributed energies were calculated using MM-GBSA method. The 6LU7-ligand complex showed highest binding free energy and among all other interactions, the contributions of the covalent binding and van der Waals energy are found to be significant.Communicated by Ramaswamy H. Sarma.

Computer-aided identification of dengue virus NS2B/NS3 protease inhibitors: an integrated molecular modelling approach for screening of phytochemicals

Globally, dengue (DENV) fever has appeared as the most widespread vector-borne disease, affecting more than 100 million individuals annually. No approved anti-DENV therapy or preventive vaccine is available yet. DENV NS3 protein is associated with protease activity and is essential for viral replication process within the host cell. NS2B is linked with NS3 protein as a cofactor. Hence, NS3/NS2B is a potential druggable target for developing inhibitors against dengue virus. In the present study, a dataset of Beta vulgaris L.-based natural compounds was developed. Virtual ligand screening of 30 phytochemicals was carried out to find novel inhibitors against the NS2B/NS3 protein. Spatial affinity, drug-likeness, and binding behaviors of selected phytochemicals were analyzed. Post-simulation analysis, including Principal Component Analysis (PCA), MMGBSA, and Co-relation analysis, was also performed to provide deep insight for elucidating protein-ligand complexes. This computer-aided screening scrutinized four potent phytochemicals, including betavulgaroside II, vitexin xyloside, epicatechin, and isovitexin2-O-xyloside inhibitors exhibiting optimal binding with viral NS3/NS2B protein. Our study brings novel scaffolds against DENV NS2B/NS3 of serotype-2 to act as lead molecules for further biological optimization. In future, this study will prompt the exploration and development of adjuvant anti-DENV therapy based on natural compounds.Communicated by Ramaswamy H. Sarma.

Unleashing Nature's potential: a computational approach to discovering novel VEGFR-2 inhibitors from African natural compound using virtual screening, ADMET analysis, molecular dynamics, and MMPBSA calculations

One of the characteristic features of cancer is angiogenesis, the process by which new, aberrant blood vessels are formed from pre-existing blood vessels. The process of angiogenesis begins when VEGF binds to its receptor, the VEGF receptor (VEGFR). The formation of new blood vessels provides nutrients that can promote the growth of cancer cells. When it comes to new blood vessel formation, VEGFR2 is a critical player. Therefore, inhibiting VEGFR2 is an effective way to target angiogenesis in cancer treatment. The aim of our research was to find new VEGFR-2 inhibitors by performing a virtual screening of 13313 from African natural compounds using different in silico techniques. Using molecular docking calculations and ADMET properties, we identified four compounds that exhibited a binding affinity ranging from -11.0 kcal/mol to -11.5 Kcal/mol when bound to VEGFR-2. These four compounds were further analyzed with 100 ns simulations to determine their stability and binding energy using the MM-PBSA method. After comparing the compounds with Regorafenib, a drug approved for anti-angiogenesis treatment, it was found that all the candidates (EANPDB 252, NANPDB 4577, and NANPDB 4580), with the exception of EANPDB 76, could target VEGFR-2 similarly effectively to Regorafenib. Therefore, we recommend three of these agents for anti-angiogenesis treatment because they are likely to deactivate VEGFR-2 and thus inhibit angiogenesis. However, it should be noted that the safety and suitability of these agents for clinical use needs further investigation, as the computer-assisted study did not include in vitro or in vivo experiments.

Identification of phytoconstituents from Albizia lebbeck as potential therapeutics against HIV-1 reverse transcriptase associated with infective endocarditis: In silico and in vitro approaches

Acquired immune deficiency syndrome (AIDS) is an unadorned disease affected via the human immunodeficiency virus (HIV), which has become the most infectious diseases worldwide. HIV-1 RT has been shown to be present in the cardiac tissue of patients with HIV-associated infective endocarditis, and to be associated with the development of valvular lesions and other cardiac abnormalities. The use of anti-retroviral therapies has helped to control the virus and reduce the incidence of HIV-1 associated infective endocarditis. Though, these treatments have several adjacent effects, and the improvement of drug-resistant stresses of the virus has become a significant challenge in HIV treatment. This study is to identify A. lebbeck phytoconstituents with HIV-1 RT inhibitory activity for potential therapeutic use against HIV-1 RT associated with infective endocarditis. We performed in silico and in vitro screening of natural cardiovascular phytoconstituents from Albizia lebbeck, a medicinal plant that has been traditionally used for the management of numerous diseases. The in silico results showed that all three compounds (geraldone, luteolin, and isookanin) exhibited affinities of solid binidng to the active amino acids of HIV-1 RT's DNA-polymerase (DNA-p) and Ribonuclease-H (RNA-H) active positions, suggesting their potential as HIV-1 RT inhibitors. In vitro assessment of the three compounds at a concentration of 1 mg/mL revealed that Geraldone exhibited the most effective inhibitory consequence on HIV-1 RT activity (83.45%), followed by Isookanin (75.88%) and Luteolin (66.36%). These findings suggest that these compounds have the potential to inhibit HIV-1 RT associated with infective endocarditis and could assist as main compounds for emerging unique anti-HIV-1 agents. Further studies are needed to confirm the in vitro and in vivo efficacy of these molecules and assess their safety and efficiency as anti-HIV-1 drugs.

Identification of anti-cyanobacterial leads targeting carbonic anhydrase from phytochemical database using in silico approach

In cyanobacteria, carbonic anhydrase (zinc metalloenzyme) is a major enzyme that converts CO₂ to HCO₃- maintaining the carbon concentration around the vicinity of RuBisCo, leading to cyanobacterial biomass generation. Anthropogenic activities, disposal of leached micro nutrients effluents from industries into the aquatic environment results in cyanobacterial blooms. The harmful cyanobacteria release cyanotoxins in open-water system which on ingression through oral route causes major health issues like hepatotoxicity and immunotoxicity. A database was prepared consisting of approximately 3k phytochemicals curated from previous literatures, earlier identified by GC-MS analysis. The phytochemicals were subjected to online servers to identify the novel lead molecules which followed ADMET and drug-like candidates. The identified leads were optimized by density functional theory method using B3YLP/G* level of theory. Carbonic anhydrase chosen as target to observe the binding interaction through molecular docking simulations. From the molecules included in the database the highest binding energy exhibited by alpha-tocopherol succinate and mycophenolic acid were found to be -9.23 kcal/mol and -14.41 kcal/mol and displayed interactions with GLY A102, GLN B30, ASP A41, LYS A105 including Zn²⁺ and their adjacent amino acids CYS 101, HIS 98, CYS 39 in both chain A and chain A-B of carbonic anhydrase. The Identified molecular orbitals decipher computed global electrophilicity values (Energy gap, electrophilicity and Softness) of alpha-tocopherol succinate and mycophenolic acid were found to be (5.262, 1.948, 0.380) eV and (4.710, 2.805, 0.424) eV demonstrates both molecules are effective and stable. The identified leads may serve as a better anti-carbonic anhydrase agent because they accommodate in the binding site and hampers the catalytic activity of Carbonic anhydrase thus inhibiting the generation of cyanobacterial biomass. This identified lead molecules may serve as a substructure to design novel phytochemicals against carbonic anhydrase present in cyanobacteria. Further in vitro study is necessary to evaluate the efficacy of these molecules.

In Silico Subtractive Proteomics and Molecular Docking Approaches for the Identification of Novel Inhibitors against Streptococcus pneumoniae Strain D39

Streptococcus pneumoniae is a notorious Gram-positive pathogen present asymptomatically in the nasophayrnx of humans. According to the World Health Organization (W.H.O), pneumococcus causes approximately one million deaths yearly. Antibiotic resistance in S. pneumoniae is raising considerable concern around the world. There is an immediate need to address the major issues that have arisen as a result of persistent infections caused by S. pneumoniae. In the present study, subtractive proteomics was used in which the entire proteome of the pathogen consisting of 1947 proteins is effectively decreased to a finite number of possible targets. Various kinds of bioinformatics tools and software were applied for the discovery of novel inhibitors. The CD-HIT analysis revealed 1887 non-redundant sequences from the entire proteome. These non-redundant proteins were submitted to the BLASTp against the human proteome and 1423 proteins were screened as non-homologous. Further, databases of essential genes (DEGG) and J browser identified almost 171 essential proteins. Moreover, non-homologous, essential proteins were subjected in KEGG Pathway Database which shortlisted six unique proteins. In addition, the subcellular localization of these unique proteins was checked and cytoplasmic proteins were chosen for the druggability analysis, which resulted in three proteins, namely DNA binding response regulator (SPD_1085), UDP-N-acetylmuramate-L-alanine Ligase (SPD_1349) and RNA polymerase sigma factor (SPD_0958), which can act as a promising potent drug candidate to limit the toxicity caused by S. pneumoniae. The 3D structures of these proteins were predicted by Swiss Model, utilizing the homology modeling approach. Later, molecular docking by PyRx software 0.8 version was used to screen a library of phytochemicals retrieved from PubChem and ZINC databases and already approved drugs from DrugBank database against novel druggable targets to check their binding affinity with receptor proteins. The top two molecules from each receptor protein were selected based on the binding affinity, RMSD value, and the highest conformation. Finally, the absorption, distribution, metabolism, excretion, and toxicity (ADMET) analyses were carried out by utilizing the SWISS ADME and Protox tools. This research supported the discovery of cost-effective drugs against S. pneumoniae. However, more in vivo/in vitro research should be conducted on these targets to investigate their pharmacological efficacy and their function as efficient inhibitors.

Virtual screening, molecular docking, molecular dynamics and quantum chemical studies on (2-methoxy-4-prop-2-enylphenyl) N-(2-methoxy-4-nitrophenyl) carbamate: a novel inhibitor of hepatocellular carcinoma

HDAC protein is associated with hepatocellular carcinoma. Different medicinal plants were selected for this study to analyze the inhibitory efficacy against the target protein, HDAC. Using virtual screening, we filtered out the best compounds, and molecular docking (XP) was carried out for the top compounds which filtered out. The molecular docking results showed that the title compound (2-methoxy-4-prop-2-enylphenyl) N-(2-methoxy-4-nitrophenyl) carbamate (MEMNC) has the highest docking score of about -7.7 kcal/mol against the targeted protein histone deacetylase (HDAC) compared with the other selected phytocompounds. From the molecular dynamics analysis, the RMSD and RMSF plots depicted the overall stability of the protein-ligand complex. Toxicity properties show the acceptable range of various kinds of toxicity that were predicted using the ProTox-II server. In addition, DFT quantum chemical and physicochemical properties of the MEMNC molecule were reported. Initially, the molecular structure of the MEMNC molecule was optimized and harmonic vibrational frequencies were calculated using DFT/B3LYP method with a cc-pVTZ basis set using Gaussian 09 program. The calculated vibrational wavenumber values were assigned based on Potential Energy Distribution calculations using the VEDA 4.0 program and correlated well with the previous literature values. The molecule has bioactivity as a result of intramolecular charge transfer interactions, as demonstrated by frontier molecular orbital analysis. Molecular electrostatic potential surface and Mulliken atomic charge distribution analyses validate the reactive sites of the molecule. Thus, the title compound can be used as a potential inhibitor of HDAC protein, which paves the way for designing novel drugs to treat Hepatocellular carcinoma.Communicated by Ramaswamy H. Sarma.

Discovery of VEGFR inhibitors through virtual screening and energy assessment

Vascular endothelial growth factor receptor-2 (VEGFR-2) is crucial in promoting tumor angiogenesis and cancer metastasis. Thus, inhibition of VEGFR-2 has appeared as a good tactic for cancer treatment. To find out novel VEGFR-2 inhibitors, first, the PDB structure of VEGFR-2, 6GQO, was selected based on atomic nonlocal environment assessment (ANOLEA) and PROCHECK assessment. 6GQO was then further used for structure-based virtual screening (SBVS) of different molecular databases, including US-FDA approved drugs, US-FDA withdrawn drugs, may bridge, MDPI, and Specs databases using Glide. Based on SBVS, receptor fit, drug-like filters, and absorption, distribution, metabolism, excretion, and toxicity (ADMET) analysis of 427877 compounds, the best 22 hits were selected. From the 22 hits, hit 5 complex with 6GQO was put through molecular mechanics/generalized born surface area (MM/GBSA) study and hERG binding. The MM/GBSA study revealed that hit 5 possesses lesser binding free energy with more inferior stability in the receptor pocket than the reference compound. The VEGFR-2 inhibition assay of hit 5 disclosed an IC₅₀ of 165.23 nM against VEGFR-2, which can be possibly enhanced through structural modifications.

Discovering potential stabilizers for KRAS22RT G-quadruplex DNA: an alternative next generation approach to treat pancreatic cancer

KRAS is the signature gene responsible for the occurrence of pancreatic cancer, which is a complex, multifactorial and intractable lethal malignancy. Prevention and treatment of the ailment have always been a key motivation behind the search for new therapeutic drug molecules. G-quadruplexes are non-canonical guanine-rich secondary structures, commonly formed at eukaryotic telomeric ends, oncogenic promotors and G-rich regions of the DNA. These G-quadruplexes play a crucial role in the regulation of gene expression and maintenance of genome integrity, therefore, they are considered as emerging potential therapeutic drug targets. The present study is concerned with the discovery of a potential stabilizer for KRAS22RT G-quadruplex DNA, located in the NHE region of the promotor, while inhibiting the upregulation of KRAS proto-oncogene, as an alternative approach for the treatment of pancreatic cancer. Various chemical libraries have been virtually screened against the targeted G4 structure and 143 compounds showed promising results. However, molecular dynamic studies, ADME and toxicity analyses predicted that three compounds belonging to the class of tetra-substituted phenanthrolines (i.e., 7i, 7j and 7k) can not only effectively stabilize KRAS22RT G4 structure but also have least toxic effects in the in vivo system. Therefore, it is highly recommended to further investigate their effectiveness and efficacy through experimental analysis in laboratory.Communicated by Ramaswamy H. Sarma.

Drug and Anti-Viral Peptide Design to Inhibit the Monkeypox Virus by Restricting A36R Protein

Most recently, monkeypox virus (MPXV) has emanated as a global public health threat. Unavailability of effective medicament against MPXV escalates demand for new therapeutic agent. In this study, in silico strategies were conducted to identify novel drug against the A36R protein of MPXV. The A36R protein of MPXV is responsible for the viral migration, adhesion, and vesicle trafficking to the host cell. To block the A36R protein, 4893 potential antiviral peptides (AVPs) were retrieved from DRAMP and SATPdb databases. Finally, 57 sequences were screened based on peptide filtering criteria, which were then modeled. Likewise, 31 monkeypox virus A36R protein sequences were collected from NCBI protein database to find consensus sequence and to predict 3D protein model. The refined and validated models of the A36R protein and AVP peptides were used to predict receptor-ligand interactions using DINC 2 server. Three peptides that showed best interactions were SATPdb10193, SATPdb21850, and SATPdb26811 with binding energies -6.10, -6.10, and -6.30 kcal/mol, respectively. Small molecules from drug databases were also used to perform virtual screening against the A36R protein. Among databases, Enamine-HTSC showed strong affinity with docking scores ranging from -8.8 to 9.8 kcal/mol. Interaction of target protein A36R with the top 3 peptides and the most probable drug (Z55287118) examined by molecular dynamic (MD) simulation. Trajectory analyses (RMSD, RMSF, SASA, and Rg) confirmed the stable nature of protein-ligand and protein-peptide complexes. This work suggests that identified top AVPs and small molecules might interfere with the function of the A36R protein of MPXV.

LC-MS/MS Phytochemical Profiling, Antioxidant Activity, and Cytotoxicity of the Ethanolic Extract of Atriplex halimus L. against Breast Cancer Cell Lines: Computational Studies and Experimental Validation

Atriplex halimus L., also known as Mediterranean saltbush, and locally as "Lgtef", an halophytic shrub, is used extensively to treat a wide variety of ailments in Morocco. The present study was undertaken to determine the antioxidant activity and cytotoxicity of the ethanolic extract of A. halimus leaves (AHEE). We first determined the phytochemical composition of AHEE using a liquid chromatography (LC)-tandem mass spectrometry (MS/MS) technique. The antioxidant activity was evaluated using different methods including DPPH scavenging capacity, β-carotene bleaching assay, ABTS scavenging, iron chelation, and the total antioxidant capacity assays. Cytotoxicity was investigated against human cancer breast cells lines MCF-7 and MDA-MB-231. The results showed that the components of the extract are composed of phenolic acids and flavonoids. The DPPH test showed strong scavenging capacity for the leaf extract (IC₅₀ of 0.36 ± 0.05 mg/mL) in comparison to ascorbic acid (IC₅₀ of 0.19 ± 0.02 mg/mL). The β-carotene test determined an IC₅₀ of 2.91 ± 0.14 mg/mL. The IC₅₀ values of ABTS, iron chelation, and TAC tests were 44.10 ± 2.92 TE µmol/mL, 27.40 ± 1.46 mg/mL, and 124 ± 1.27 µg AAE/mg, respectively. In vitro, the AHE extract showed significant inhibitory activity in all tested tumor cell lines, and the inhibition activity was found in a dose-dependent manner. Furthermore, computational techniques such as molecular docking and ADMET analysis were used in this work. Moreover, the physicochemical parameters related to the compounds' pharmacokinetic indicators were evaluated, including absorption, distribution, metabolism, excretion, and toxicity prediction (Pro-Tox II).

Homology modeling, virtual screening, molecular docking, molecular dynamic (MD) simulation, and ADMET approaches for identification of natural anti-Parkinson agents targeting MAO-B protein

Monoamine oxidase-B (MAO-B) is a flavin-dependent enzyme involved in various neurodegenerative disorders. Here, a dataset of 142 chalcone derivatives, collected from various natural plants, was screened by combining structure-based virtual screening and ADMET approaches. The goal is to discover novel natural chalcones as potential MAO-B inhibitors. With the help of the Gaussian 09.5 software, the 3D chemical structures of compounds were optimized using the DFT method. The 3D structure of the hMAO-B enzyme was built using the Modeller software. The optimized structures were subjected to virtual screening by Autodock Vina, implicated in PyRx software. Among the 142 natural substances, 43 were selected based on their binding affinity. Then, the pharmacokinetic proprieties and toxicity of these compounds were evaluated using ADMET analysis. Ten compounds were predicted to have ADMET characteristics with no side effects. The binding modes and interactions of the top selected compounds were then evaluated using AutoDock 4.2. Compounds P60 and P81 were found to be potential inhibitors of MAO-B compared to rasagiline, safinamid, and selegiline, the reference drugs. The stability of the selected compounds was confirmed by MD simulation. Based on this finding, compounds P60 and P81 could be considered potential hMAO-B inhibitors.

SARS-CoV-2 Inhibitors from Nigella Sativa

The recently encountered severe acute respiratory syndrome coronavirus 2 creates huge predicaments among various countries. Lack of specific treatment of COVID-19 disease demands urgency in drug design against SARS-CoV-2 targets. Nigella sativa the miraculous herb native to South and Southwest Asia and belonging to the family Ranunculaceae, due to its beneficial bioactive properties, was used by us for performing in silico study to analyze the potential of its compounds so that they can target and inhibit SARS-COV-2 proteins including its main protease, the papain-like protease, its helicase, and also the RNA-dependent RNApolymerase, RNA-binding protein, Endoribonuclease, receptor-binding domain, and the RNA-binding domain of nucleocapsid phosphoprotein. The procedure of molecular docking was done with the help of AutoDock–Vina 1.1.2. and along with it the ADMET properties of the best suited ligands were found and Lipinski screening was performed. Among 58 ligands screened, various compounds showed binding energy less than the standard drug chloroquine. Three compounds alpha-hederin, rutin, and nigellamine A2 had the least binding energy with the specific SARS-Cov-2 proteins suggesting their best potential as SARS-CoV-2 inhibitor. Hence, in the future, studies including the in vitro and also the in vivo studies can be carried out for analyzing their true potential and encourage use of nutraceuticals like Nigella sativa to inhibit this virus.

HIV-1 Protease and Reverse Transcriptase Inhibitory Activities of Curcuma aeruginosa Roxb. Rhizome Extracts and the Phytochemical Profile Analysis: In Vitro and In Silico Screening

Human immunodeficiency virus type-1 (HIV-1) infection causes acquired immunodeficiency syndrome (AIDS). Currently, several anti-retroviral drugs are available, but adverse effects of these drugs have been reported. Herein, we focused on the anti-HIV-1 activity of Curcuma aeruginosa Roxb. (CA) extracted by hexane (CA-H), ethyl acetate (CA-EA), and methanol (CA-M). The in vitro HIV-1 protease (PR) and HIV-1 reverse transcriptase (RT) inhibitory activities of CA extracts were screened. CA-M potentially inhibited HIV-1 PR (82.44%) comparable to Pepstatin A (81.48%), followed by CA-EA (67.05%) and CA-H (47.6%), respectively. All extracts exhibited moderate inhibition of HIV-1 RT (64.97 to 76.93%). Besides, phytochemical constituents of CA extracts were identified by GC-MS and UPLC-HRMS. Fatty acids, amino acids, and terpenoids were the major compounds found in the extracts. Furthermore, drug-likeness parameters and the ability of CA-identified compounds on blocking of the HIV-1 PR and RT active sites were in silico investigated. Dihydroergocornine, 3β,6α,7α-trihydroxy-5β-cholan-24-oic acid, and 6β,11β,16α,17α,21-Pentahydroxypregna-1,4-diene-3,20-dione-16,17-acetonide showed strong binding affinities at the active residues of both HIV-1 PR and RT. Moreover, antioxidant activity of CA extracts was determined. CA-EA exhibited the highest antioxidant activity, which positively related to the amount of total phenolic content. This study provided beneficial data for anti-HIV-1 drug discovery from CA extracts.

Caesalpinia mimosoides Leaf Extract Promotes Neurite Outgrowth and Inhibits BACE1 Activity in Mutant APP-Overexpressing Neuronal Neuro2a Cells

Alzheimer’s disease (AD) is implicated in the imbalance of several proteins, including Amyloid-β (Aβ), amyloid precursor protein (APP), and BACE1. APP overexpression interferes with neurite outgrowth, while BACE1 plays a role in Aβ generation. Medicinal herbs with effects on neurite outgrowth stimulation and BACE1 inhibition may benefit AD. This study aimed to investigate the neurite outgrowth stimulatory effect, along with BACE1 inhibition of Caesalpinia mimosoides (CM), using wild-type (Neuro2a) and APP (Swedish mutant)-overexpressing (Neuro2a/APPSwe) neurons. The methanol extract of CM leaves stimulated neurite outgrowth in wild-type and APP-overexpressing cells. After exposure to the extract, the mRNA expression of the neurite outgrowth activation genes growth-associated protein-43 (GAP-43) and teneurin-4 (Ten-4) was increased in both Neuro2a and Neuro2a/APPSwe cells, while the mRNA expression of neurite outgrowth negative regulators Nogo receptor (NgR) and Lingo-1 was reduced. Additionally, the extract suppressed BACE1 activity in the APP-overexpressing neurons. Virtual screening demonstrated that quercetin-3′-glucuronide, quercetin-3-O-glucoside, clausarinol, and theogallin were possible inhibitors of BACE1. ADMET was analyzed to predict drug-likeness properties of CM-constituents. These results suggest that CM extract promotes neurite outgrowth and inhibits BACE1 activity in APP-overexpressing neurons. Thus, CM may serve as a source of drugs for AD treatment. Additional studies for full identification of bioactive constituents and to confirm the neuritogenesis in vivo are needed for translation into clinic of the present findings.

In silico identification of novel chemical compounds with antituberculosis activity for the inhibition of InhA and EthR proteins from Mycobacterium tuberculosis

Tuberculosis (TB) continuously poses a major public health concern around the globe, with a mounting death toll of approximately 1.4 million in 2019. Reduced bioavailability, elevated toxicity, increased side effects, and resistance of multiple first-line and second-line TB medications, including isoniazid, ethionamide necessitate studies of new drugs. The method of computational biology and bioinformatics approach allows virtual screening of a large number of drugs, reduces growing side effects of medications, and predicts potential drug resistance over time. In this study, we have analyzed fifty small molecules with antituberculosis properties using in silico approach including molecular docking, drug-likeness assessment, ADMET (absorption, distribution, metabolism, excretion, toxicity) profile evaluation, P450 site of metabolism prediction, and molecular dynamics simulation. Among those fifty compounds, 3-[3-(4-Fluorophenyl)-1,2,4-oxadiazol-5-yl]-N-(2-methylphenyl) piperidine-1-carboxamide (C22) and 5-(4-Ethyl-phenyl)-2-(1H-tetrazol-5-ylmethyl)-2H-tetrazole (C29) were found to pass the two-step molecular docking, P450 site of metabolism prediction and pharmacokinetics analysis successfully. Their binding stability for target proteins has been evaluated through root mean square deviation and root mean square fluctuation, Radius of gyration analysis from 10 ns Molecular Dynamics Simulation (MDS). Our identified drugs (C22 and C29) performed better than the control drugs (Isoniazid, Ethionamide) regarding binding affinity and molecular stability with the regulatory proteins (InhA, EthR) of Mycobacterium tuberculosis. The study proposed these compounds as effective therapeutic agents for Tuberculosis drug discovery, but further in vitro and in vivo testing are needed to substantiate their potential as novel drugs and modes of action.

Identification of Spiro-Fused [3-azabicyclo[3.1.0]hexane]oxindoles as Potential Antitumor Agents: Initial In Vitro Evaluation of Anti-Proliferative Effect and Actin Cytoskeleton Transformation in 3T3 and 3T3-SV40 Fibroblast

Novel heterocyclic compounds containing 3-spiro[3-azabicyclo[3.1.0]hexane]oxindole framework (4a, 4b and 4c) have been studied as potential antitumor agents. The in silico ADMET (adsorption, distribution, metabolism, excretion and toxicity) analysis was performed on 4a-c compounds with promising antiproliferative activity, previously synthetized and screened against human erythroleukemic cell line K562 tumor cell line. Cytotoxicity of 4a-c against murine fibroblast 3T3 and SV-40 transformed murine fibroblast 3T3-SV40 cell lines were evaluated. The 4a and 4c compounds were cytotoxic against 3T3-SV40 cells in comparison with those of 3T3. In agreement with the DNA cytometry studies, the tested compounds have achieved significant cell-cycle perturbation with higher accumulation of cells in G0/G1 phase. Using confocal microscopy, we found that with 4a and 4c treatment of 3T3 cells, actin filaments disappeared, and granular actin was distributed diffusely in the cytoplasm in 82-97% of cells. The number of 3T3-SV40 cells with stress fibers increased to 7-30% against 2% in control. We discovered that transformed 3T3-SV40 cells after treatment with compounds 4a and 4c significantly reduced the number of cells with filopodium-like membrane protrusions (from 86 % in control cells to 6-18% after treatment), which indirectly suggests a decrease in cell motility. We can conclude that the studied compounds 4a and 4c have a cytostatic effect, which can lead to a decrease in the number of filopodium-like membrane protrusions.

Cholinesterase inhibitory activity of tinosporide and 8-hydroxytinosporide isolated from Tinospora cordifolia: In vitro and in silico studies targeting management of Alzheimer's disease

Tinosporide and 8-hydroxytinosporide isolated from Tinospora cordifolia were evaluated for acetylcholinesterase (AChE) and butylcholinesterase (BuChE) inhibitory activities. The structure of the compound was confirmed by spectroscopic analysis, whereas cholinesterase inhibition was investigated by Ellman method using donepezil as standard drug and the data were presented as IC₅₀ (μg/ml ± SEM). Furthermore, donepezil, tinosporide and 8-hydroxytinosporide were executed for docking analysis. The results from the isolated compounds TC-16R confirmed as tinosporide promisingly inhibited AChE with IC₅₀ value of 13.45 ± 0.144, whereas TC-19R confirmed as 8-hydroxytinosporide moderately inhibited AChE with IC₅₀ value of 46.71 ± 0.511. In case of BuChE inhibition, the IC₅₀ values were found to be 408.50 ± 17.197 and 317.26 ± 6.918 for tinosporide and 8-hydroxytinosporide, respectively. The in silico studies revealed that the ligand tinosporide fit with the binding sites and inhibited AChE. Overall, the study findings suggested that tinosporide would be a complementary noble molecule of donepezil which is correlated with its pharmacological activity through in vitro studies, while 8-hydroxytinosporide modestly inhibited BuChE and the results are very close to the standard donepezil.

Cytotoxic Activity against A549 Human Lung Cancer Cells and ADMET Analysis of New Pyrazole Derivatives

Two new pyrazole derivatives, namely compound 1 and compound 2, have been synthesized, and their biological activity has been evaluated. Monocrystals of the obtained compounds were thoroughly investigated using single-crystal X-ray diffraction analysis, FTIR spectroscopy, and NMR spectroscopy. The results gathered from all three techniques are in good agreement, provide complete information about the structures of 1 and 2, and confirm their high purity. Thermal properties were studied using thermogravimetric analysis; both 1 and 2 are stable at room temperature. In order to better characterize 1 and 2, some physicochemical and biological properties have been evaluated using ADMET analysis. The cytotoxic activity of both compounds was determined using the MTT assay on the A549 cell line in comparison with etoposide. It was determined that compound 2 was effective in the inhibition of human lung adenocarcinoma cell growth and may be a promising compound for the treatment of lung cancer.

Exploring TEAD2 as a drug target for therapeutic intervention of cancer: A multi-computational case study

Transcriptional enhanced associate domain (TEAD) is a family of transcription factors that plays a significant role during embryonic developmental processes, and its dysregulation is responsible for tumour progression. TEAD is considered as druggable targets in various diseases, namely cancer, cardiovascular diseases and neurodegenerative disorders. Previous structural studies revealed the importance of the central hydrophobic pocket of TEAD as a potential target for small-molecule inhibitors and demonstrated flufenamic acid (FLU) (a COX-2 enzyme inhibitor) to bind and inhibit TEAD2 functions. However, to date, no drug candidates that bind specifically to TEAD2 with high selectivity and efficacy have been developed or proposed. Within this framework, we present here a case study where we have identified potential TEAD2 inhibitor candidates by integrating multiple computational approaches. Among the candidates, the top two ranked compounds ZINC95969481 (LG1) which is a fused pyrazole derivative and ZINC05203789 (LG2), a fluorene derivative resulted in much favourable binding energy scores than the reference ligand, FLU. The drug likeliness of the best compounds was also evaluated in silico to ensure the bioavailability of these compounds particularly LG1 as compared to FLU thus providing a strong rationale for their development as leads against TEAD. Molecular dynamics simulations results highlighted the role of key residues contributing to favourable interactions in TEAD2-LG1 complex with much favourable interaction and binding free energy values with respect to the reference compound. Altogether, this study provides a starting platform to be more exploited by future experimental research towards the development of inhibitors against TEAD, a persuasive strategy for therapeutic intervention in cancer treatment.

Virtual Screening of Natural Compounds as Potential PI3K-AKT1 Signaling Pathway Inhibitors and Experimental Validation

A computational screening for natural compounds suitable to bind the AKT protein has been performed after the generation of a pharmacophore model based on the experimental structure of AKT1 complexed with IQO, a well-known inhibitor. The compounds resulted as being most suitable from the screening have been further investigated by molecular docking, ADMET (Absorption, Distribution, Metabolism, Excretion, and Toxicity) analysis and toxicity profiles. Two compounds selected at the end of the computational analysis, i.e., ZINC2429155 (also named STL1) and ZINC1447881 (also named AC1), have been tested in an experimental assay, together with IQO as a positive control and quercetin as a negative control. Only STL1 clearly inhibited AKT activation negatively modulating the PI₃K/AKT pathway.

Mushroom-derived bioactive compounds potentially serve as the inhibitors of SARS-CoV-2 main protease: An in silico approach

Background and aim

Coronavirus Disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has now become the world pandemic. There is a race to develop suitable drugs and vaccines for the disease. The anti-HIV protease drugs are currently repurposed for the potential treatment of COVID-19. The drugs were primarily screened against the SARS-CoV-2 main protease. With an urgent need for safe and effective drugs to treat the virus, we have explored natural products isolated from edible and medicinal mushrooms that have been reported to possess anti-HIV protease.

Experimental procedures

We have examined 36 compounds for their potential to be SARS-CoV-2 main protease inhibitors using molecular docking study. Moreover, drug-likeness properties including absorption, distribution, metabolism, excretion and toxicity were evaluated by in silico ADMET analysis.

Results

Our AutoDock study showed that 25 of 36 candidate compounds have the potential to inhibit the main viral protease based on their binding affinity against the enzyme's active site when compared to the standard drugs. Interestingly, ADMET analysis and toxicity prediction revealed that 6 out of 25 compounds are the best drug-like property candidates, including colossolactone VIII, colossolactone E, colossolactone G, ergosterol, heliantriol F and velutin.

Conclusion

Our study highlights the potential of existing mushroom-derived natural compounds for further investigation and possibly can be used to fight against SARS-CoV-2 infection.

Taxonomy classification by evise

Disease, Infectious Disease, Respiratory System Disease, Covid-19, Traditional Medicine, Traditional Herbal Medicine, Phamaceutical Analysis.

Computational selection of flavonoid compounds as inhibitors against SARS-CoV-2 main protease, RNA-dependent RNA polymerase and spike proteins: A molecular docking study

An outbreak of Coronavirus disease 2019 (COVID-19) caused by SARS-CoV-2 has been recognized as a global health concern. Since, no specific antiviral drug is proven effective for treatment against COVID-19, identification of new therapeutics is an urgent need. In this study, flavonoid compounds were analyzed for its inhibitory potential against important protein targets of SARS-CoV-2 using computational approaches. Virtual docking was performed for screening of flavonoid compounds retrieved from PubChem against the main protease of SARS-CoV-2 using COVID-19 docking server. The cut off of dock score was set to >-9 kcal/mol and screened compounds were individually docked against main protease, RNA-dependent RNA polymerase, and spike proteins using AutoDock 4.1 software. Finally, lead flavonoid compounds were subjected to ADMET analysis. A total of 458 flavonoid compounds were virtually screened against main protease target and 36 compounds were selected based on the interaction energy value >-9 kcal/mol. Furthermore, these compounds were individually docked against protein targets and top 10 lead compounds were identified. Among the lead compounds, agathisflavone showed highest binding energy value of -8.4 kcal/mol against main protease, Albireodelphin showed highest dock score of -9.8 kcal/mol and -11.2 kcal/mol against RdRp, and spike proteins, respectively. Based on the high dock score and ADMET properties, top 5 lead molecules such as Albireodelphin, Apigenin 7-(6″-malonylglucoside), Cyanidin-3-(p-coumaroyl)-rutinoside-5-glucoside, Delphinidin 3-O-beta-D-glucoside 5-O-(6-coumaroyl-beta-D-glucoside) and (-)-Maackiain-3-O-glucosyl-6″-O-malonate were identified as potent inhibitors against main protease, RdRp, and spike protein targets of SARS-CoV-2. These all compounds are having non-carcinogenic and non-mutagenic properties. This study finding suggests that the screened compounds include Albireodelphin, Apigenin 7-(6″-malonylglucoside), Cyanidin-3-(p-coumaroyl)-rutinoside-5-glucoside, Delphinidin 3-O-beta-D-glucoside 5-O-(6-coumaroyl-beta-D-glucoside) and (-)-Maackiain-3-O-glucosyl-6″-O-malonate could be the potent inhibitors of SARS-CoV-2 targets.

Identification of novel PI3Kδ inhibitors by docking, ADMET prediction and molecular dynamics simulations

BACKGROUND

Phosphoinositide-3-kinase Delta (PI3Kδ) plays a key role in B-cell signal transduction and inhibition of PI3Kδ is confirmed to have clinical benefit in certain types of activation of B-cell malignancies. Virtual screening techniques have been used to discover new molecules for developing novel PI3Kδ inhibitors with little side effects.

METHOD

Computer aided drug design method were used to rapidly screen optimal PI3Kδ inhibitors from the Asinex database. Virtual screening based molecular docking was performed to find novel and potential lead compound targeting PI3Kδ, at first. Subsequently, drug likeness studies were carried out on the retrieved hits to evaluate and analyze their drug like properties such as absorption, distribution, metabolism, excretion, and toxicity (ADMET) for toxicity prediction. Three least toxic compounds were selected for the molecular dynamics (MD) simulations for 30 ns in order to validate its stability inside the active site of PI3Kδ receptor.

RESULTS

Based on the present in silico analysis, two molecules have been identified which occupied the same binding pocket confirming the selection of active site. ASN 16296138 (Glide score: -12.175 kcal/mol, cdocker binding energy: -42.975 kcal/mol and ΔG_bind value: -90.457 kcal/mol) and BAS 00227397 (Glide score: -10.988 kcal/mol, cdocker binding energy: -39.3376 kcal/mol and ΔG_bind value: -81.953 kcal/mol) showed docking affinities comparatively much stronger than those of already reported known inhibitors against PI3Kδ. These two ligand's behaviors also showed consistency during the simulation of protein-ligand complexes for 30000 ps respectively, which is indicative of its stability in the receptor pocket.

CONCLUSION

Compound ASN 16296138 and BAS 00227397 are potential candidates for experimental validation of biological activity against PI3Kδ in future drug discovery studies. This study smoothes the path for the development of novel leads with improved binding properties, high drug likeness, and low toxicity to humans for the treatment of cancer.

In silico insights into the identification of potential novel angiogenic inhibitors against human VEGFR-2: a new SAR-based hierarchical clustering approach

In this study, binding efficiency of new pyrrolopyrimidine structural analogs against human vascular endothelial growth factor receptor-2 (VEGFR-2) were elucidated using integrated in silico methods. Optimized high-resolution model of VEGFR-2 was generated and adopted for structure-based virtual screening approaches. Pyrrolopyrimidine inhibitor (CP15) associated compounds were screened from PubChem database and subjected to virtual screening and comparative docking methods against the receptor ligand-binding domain. Accordingly, high efficient compounds were clustered with similarity indices through PubChem structure cluster module using single-linkage algorithm. Moreover, pharmacokinetics including drug metabolism activities of high-binding leads under investigation was portrayed using ADMET and similarity ensemble analysis. Optimal energy orientations of the selected protein model have been shown to be reliable, and highly recommended for screening and docking studies. Docking and clustering strategies were shown that nineteen candidates as most effective binders for VEGFR-2 than CP15, and are grouped as three classes. Lys⁸⁶⁸, Glu⁸⁸⁵, Cys⁹¹⁹, His¹⁰²⁶, Arg¹⁰²⁷, Asp¹⁰⁴⁶, and Gly¹⁰⁴⁸ residues were predicted as novel hotspot residues, and participate in H-bonds, π-cation, π-stacking, halogen bonds, and salt-bridges formation with ligands. These additional bonds are contributing extent stability that holds the receptor structure at flexible state, this make difficult to any further conformational changes for evoking angiogenic signals. The ADMET and similarity ensemble analysis results were strongly indicated that thirteen candidates as best ligands for angiogenesis targets. Altogether, these findings indicate potential angiogenic templates and their binding levels with VEGFR-2; sorted viewpoints could be useful as a promising way to describe potential angiogenesis inhibitors with related molecular targets.

In silico insights into prediction and analysis of potential novel pyrrolopyridine analogs against human MAPKAPK-2: a new SAR-based hierarchical clustering approach

In the present study, we have focused on to elucidate potential bioactive pyrrolopyridine (PYP23) analogs against human mitogen-activated protein kinase-activated protein kinase-2 (MK-2). Here, in silico methods and computational systems biology tools were used as rational strategies to predict novel PYP23 analogs against the MK-2. Initially, crystal structure (PDB-ID: 2P3G) consists steriochemical conflicts were rectified by structure-optimization approaches using the Modeller program, and a new optimized-high resolution model was generated. The stereochemical qualities of the predicted MK-2 model were judged; these showed that the model was reliable for docking assessments. SAR-based bioactivity analysis showed that among the 197 datasets only 15 candidates contained bioactivity data and were accepted as probable MK-2 inhibitors. Virtual screening and docking strategies of dataset compounds against the ligand-binding domain of MK-2 recognized 13 composites containing high binding affinity than known compounds. Furthermore, the comparative structure clustering, in silico toxicogenomics and QSAR-based anticancer properties prediction approaches were successful in the recognition of five best potential compounds such as 60118340, 60118338, 60117736, 60118473 and 60118322, which have great anticancer and drug-likeness with non-toxicity class indices. Leu⁷⁰, Glu¹³⁹, Leu¹⁴¹, Glu¹⁴⁵, Glu¹⁹⁰, Thr²⁰⁶ and Asp²⁰⁷ were found to be novel hotspot residues prominently involved in H-bonds framing with ligands. Interestingly, they have shown better molecular similarity with known bioactive PYP inhibitors. Thus, predicted five compounds can useful as possible chemotherapeutic agents for MK-2 and show similar molecular actions like known PYP inhibitors. Overall, these streamlined new methods may have great potential to reveal possible ligands toward other molecular targets and biomarkers.

Exploration of the binding pocket of histone deacetylases: the design of potent and isoform-selective inhibitors

Histone deacetylases (HDACs) are enzymes that act on histone proteins to remove the acetyl group and thereby regulate the chromatin state. HDACs act not only on histone protein but also nonhistone proteins that are key players in cellular processes such as the cell cycle, signal transduction, apoptosis, and more. "Classical" HDACs have been shown to be promising targets for anticancer drug design and development. However, the selectivity of HDAC inhibitors for HDAC isoforms remains the motivation of current research in this field. Here, we explored Class I HDACs and HDAC6 by sequence alignment and structural superimposition, catalytic channel extraction, and identification of critical residues involved in HDAC catalysis. Based on the general pharmacophore features of known HDAC inhibitors, we developed a library of compounds by scaffold hopping on a fragment hit identified via structurebased virtual screening of the molecular fragment library retrieved from the Otava database. Molecular docking assay revealed five of these compounds to have increased potency and selectivity for HDACs 1 and 2. Furthermore, their predicted absorption, distribution, metabolism, elimination, and toxicity (ADMET) properties were consistent with those of drug-like compounds. With further modelingbased and experimental investigations, we believe that these findings may offer additional potential HDAC inhibitors with improved selectivity.

Identification of potential isoform-selective histone deacetylase inhibitors for cancer therapy: a combined approach of structure-based virtual screening, ADMET prediction and molecular dynamics simulation assay

Histone deacetylases (HDACs) have gained increased attention as targets for anticancer drug design and development. HDAC inhibitors have proven to be effective for reversing the malignant phenotype in HDAC-dependent cancer cases. However, lack of selectivity of the many HDAC inhibitors in clinical use and trials contributes to toxicities to healthy cells. It is believed that, the continued identification of isoform-selective inhibitors will eliminate these undesirable adverse effects - a task that remains a major challenge to HDAC inhibitor designs. Here, in an attempt to identify isoform-selective inhibitors, a large compound library containing 2,703,000 compounds retrieved from Otava database was screened against class I HDACs by exhaustive approach of structure-based virtual screening using rDOCK and Autodock Vina. A total of 41 compounds were found to show high-isoform selectivity and were further redocked into their respective targets using Autodock4. Thirty-six compounds showed remarkable isoform selectivity and passed drug-likeness and absorption, distribution, metabolism, elimination and toxicity prediction tests using ADMET Predictor™ and admetSAR. Furthermore, to study the stability of ligand binding modes, 10 ns-molecular dynamics (MD) simulations of the free HDAC isoforms and their complexes with respective best-ranked ligands were performed using nanoscale MD software. The inhibitors remained bound to their respective targets over time of the simulation and the overall potential energy, root-mean-square deviation, root-mean-square fluctuation profiles suggested that the detected compounds may be potential isoform-selective HDAC inhibitors or serve as promising scaffolds for further optimization towards the design of selective inhibitors for cancer therapy.

Antileishmanial potential of fused 5-(pyrazin-2-yl)-4H-1,2,4-triazole-3-thiols: Synthesis, biological evaluations and computational studies

A series of newer 1,2,4-triazole-3-thiol derivatives 5(a-m) and 6(a-i) containing a triazole fused with pyrazine moiety of pharmacological significance have been synthesized. All the synthesized compounds were screened for their in vitro antileishmanial and antioxidant activities. Compounds 5f (IC₅₀=79.0µM) and 6f (IC₅₀=79.0µM) were shown significant antileishmanial activity when compared with standard sodium stibogluconate (IC₅₀=490.0µM). Compounds 5b (IC₅₀=13.96µM) and 6b (IC₅₀=13.96µM) showed significant antioxidant activity. After performing molecular docking study and analyzing overall binding modes it was found that the synthesized compounds had potential to inhibit L. donovani pteridine reductase 1 enzyme. In silico ADME and metabolic site prediction studies were also held out to set an effective lead candidate for the future antileishmanial and antibacterial drug discovery initiatives.

In silico identification of potential drug compound against Peroxisome proliferator-activated receptor-gamma by virtual screening and toxicity studies for the treatment of Diabetic Nephropathy

Diabetic Nephropathy is a serious complication of diabetes mellitus. Current therapeutic strategies of Diabetic Nephropathy are based on control of modifiable risks like hypertension, glucose levels, and dyslipidemia. Peroxisome proliferator activated receptor-gamma (PPAR-γ) is implicated in several metabolic syndromes including Diabetic Nephropathy, besides obesity, insulin insensitivity, dislipidemia, inflammation, and hypertension. In the present study, virtual screening of 617 compounds from two different public databases was done against PPAR-γ with an objective to find a possible lead compound. Two softwares, PyRx and iGEMDOCK, were used to achieve the docking accuracy in order to avoid loss of candidate compounds. Rosiglitazone (used to treat Diabetic Nephropathy) was taken as the standard compound. A total of 30 compounds with good binding affinity with PPAR-γ were selected for further filtering, on the basis of absorption, distribution, metabolism, excretion, and toxicity (ADMET). The interaction profiling of these 30 compounds, showed a minimum of one and maximum of three interactions with reference to rosiglitazone (SER-289, HIS-449, HIS-323, TYR-473). The fulfilling of ADMET analysis criteria of 30 compounds led to the selection of four compounds (ZINC ID 00181552, 00276456, 00298314, 00448009). Molecular dynamics simulation of these lead compounds in complex with PPAR-γ revealed that three of the four compounds formed a stable complex in the ligand-binding pocket of PPAR-γ during 20-ns simulation. Hence, these three (ZINC ID 00181552, 00276456, 00298314) of the four compounds are potential candidates for experimental validation of biological activity against PPAR-γ in future drug discovery studies.

In silico high-throughput virtual screening and molecular dynamics simulation study to identify inhibitor for AdeABC efflux pump of Acinetobacter baumannii

Emergence of multi-drug resistant strains of Acinetobacter baumannii has caused significant health problems and is responsible for high morbidity and mortality. Overexpression of AdeABC efflux system is one of the major mechanisms. In this study, we have focused on overcoming the drug resistance by identifying inhibitors that can effectively bind and inhibit integral membrane protein, AdeB of this efflux pump. We performed homology modeling to generate structure of AdeB using MODELLER v9.16 followed by model refinement using 3D-Refine tool and validated using PSVS, ProsaWeb, ERRAT, etc. The energy minimization of modeled protein was done using Protein preparation wizard application included in Schrodinger suite. High-throughput virtual screening of 159,868 medicinal compounds against AdeB was performed using three sequential docking modes (i.e. HTVS, SP and XP). Furthermore, absorption, distribution, metabolism, excretion, and toxicity (ADMET) analysis was done using QIKPROP. The selected 123 compounds were further analyzed for binding free energy by molecular mechanics (using prime MM-GBSA). We have also performed enrichment study (ROC curve analysis) to validate our docking results. The selected molecule and its interaction with AdeB were validated by molecular dynamics simulation (MDS) using GROMACS v5.1.4. In silico high-throughput virtual screening and MDS validation identified ZINC01155930 ((4R)-3-(cycloheptoxycarbonyl)-4-(4-etochromen-3-yl)-2-methyl-4,6,7,8-tetrahydroquinolin-5-olate) as a possible inhibitor for AdeB. Hence, it might be a suitable efflux pump inhibitor worthy of further investigation in order to be used for controlling infections caused by Acinetobacter baumannii.

Modeling, molecular dynamics, and docking assessment of transcription factor rho: a potential drug target in Brucella melitensis 16M

The zoonotic disease brucellosis, a chronic condition in humans affecting renal and cardiac systems and causing osteoarthritis, is caused by Brucella, a genus of Gram-negative, facultative, intracellular pathogens. The mode of transmission and the virulence of the pathogens are still enigmatic. Transcription regulatory elements, such as rho proteins, play an important role in the termination of transcription and/or the selection of genes in Brucella. Adverse effects of the transcription inhibitors play a key role in the non-successive transcription challenges faced by the pathogens. In the investigation presented here, we computationally predicted the transcription termination factor rho (TtFRho) inhibitors against Brucella melitensis 16M via a structure-based method. In view the unknown nature of its crystal structure, we constructed a robust three-dimensional homology model of TtFRho’s structure by comparative modeling with the crystal structure of the Escherichia coli TtFRho (Protein Data Bank ID: 1PVO) as a template in MODELLER (v 9.10). The modeled structure was optimized by applying a molecular dynamics simulation for 2 ns with the CHARMM (Chemistry at HARvard Macromolecular Mechanics) 27 force field in NAMD (NAnoscale Molecular Dynamics program; v 2.9) and then evaluated by calculating the stereochemical quality of the protein. The flexible docking for the interaction phenomenon of the template consists of ligand-related inhibitor molecules from the ZINC (ZINC Is Not Commercial) database using a structure-based virtual screening strategy against minimized TtFRho. Docking simulations revealed two inhibitors compounds – ZINC24934545 and ZINC72319544 – that showed high binding affinity among 2,829 drug analogs that bind with key active-site residues; these residues are considered for protein-ligand binding and unbinding pathways via steered molecular dynamics simulations. Arg215 in the model plays an important role in the stability of the protein-ligand complex via a hydrogen bonding interaction by aromatic-π contacts, and the ADMET (absorption, distribution, metabolism, and excretion) analysis of best leads indicate nontoxic in nature with good potential for drug development.