Docking Program Research Articles

Novel isatin-based complexes of Mn(II) and Cu(II) ions: Characterization, homogeneous catalysts for sulfides oxidation, bioactivity screening and theoretical implementations via DFT and pharmacokinetic studies

Two mononuclear manganese(II) and copper(II) complexes were prepared from the coordination of 3,5-di-tert-butyl isatin hydrazone derivative (HLOEt) with either 2 : 1 or 1 : 1 M ratio for Mn(II) or Cu(II) ion, within octahedral and square planar geometries (Mn(LOEt)2 and CuLOEt), respectively. The catalytic potential of both M(II)-complexes was evaluated in the oxidation of sulfides, i.e. diphenyl sulfide (DPS) and methylphenyl sulfide (MPS), by tert-butyl hydroperoxide (tBuOOH) in acetonitrile. The chemo- and regio-selectivity of the redox system was determined by formation of mono-oxoproducts, diphenyl sufoxide (DPO) and methylphenyl sulfoxide (MPO), with detection of further products of mainly dioxide-product of diphenyl sufone (DPN) and methylphenyl sulfone (MPN). With Mn(LOEt)2, the reaction gave 55 and 54% (ee, 79% of S and 21% of R) yields of DPO and MPO, respectively. The catalytic activity of CuLOEt was slightly more progressed than that of Mn(LOEt)2, which awarded 52 and 56% (ee, 83% of S and 17% of R) percentages of DPO and MPO, respectively. The higher catalytic reactivity of CuLOEt catalyst was based on their geometrical structures to facilitate the approach of the oxidant and substrate in the redox systems. Their reactivity was studied against some common strains of bacteria and fungi. Moreover, their bio-potential was explored as anticancer reagents versus some human cancer cell lines. Both M(II)-complexes exhibited high biological action against the microorganism and cancer growth. The effect of M(II) ion in thier complexes was examined through the interaction of with ctDNA (calf thymus DNA). Such interaction was tested spectroscopically and via changes in ctDNA viscosity. The reactivity was measured by the binding constant values (Kb = 3.19, 13.85 and 15.39 × 108 mol−1 dm3 for HLOEt, Mn(LOEt)2 and CuLOEt, respectively), which reflects high interaction with ctDNA. Furthermore, the Gibbs’ free energy values supported their high potential against ctNDA, with −1.24, −1.36 and −1.37 kJ mol−1, respectively. Furthermore, HLOEt, CuLOEt and Mn(LOEt)2 were optimized by DFT/B3LYP method under either of 6-31G* of SDD basis set to estimate the essential physical characteristics. On the other hand, in silico approaches were utilized through online software as Swiss-ADME and Pharmacophore beside the molecular docking program. Pharmacokinetic, drug-likeness and the interaction with iso-enzymes were investigated for CuLOEt complex versus receptor tyrosine kinase (2a91, 2src) and human oestrogen receptor (2iok, 4rj3), as well as, liver cancer cells via 6jxt and (PCSK9) Proprotein Convertase Subtilisin/Kexin type 9 (4nmx, 4ne9). Only the proteins 4nmx and 4ne9 from liver cancer cells were found to be effectively inhibited by CuLOEt complex.

Studying the Cytotoxic Activity of Newly Designed and Synthesized HDAC Inhibitors Derivatives of Pentanoyl Anilide‐5‐Biguanide

AbstractHistone deacetylase inhibitors (HDAC‐Is) have suggested to be a promising class of anticancer agents that are used for many types of cancer and they are proposed to be new treatment for breast cancer (BC) management. Histone deacetylase enzymes (HDAC) play an important role in BC development and progression where found to be overexpressed in the cancer cells, therefore the inhibition of these enzymes may be the key to develop new anticancer agents against BC. The study aims to synthesize three newly designed molecules derived from fusion of acylanilide part of well‐known HDAC inhibitor vorinostat with the biguanide part of metformin to get molecules are synthesized successfully as follows: pentanoyl anilide‐5‐biguanide (12), pentanoyl para‐fluoroanilide‐5‐biguanide (13), and pentanoyl para‐chloroanilide‐5‐biguanide (14). The in silico study using docking programs, SeeSAR and Chimera programs, to find and assess the inhibitory effect of these analogues against HDAC enzymes (HDAC1, 2, and 3) is deducted. Then, the practical synthesis, purification, and identification are performed. The determination of cytotoxicity for these newly synthesized analogues against MCF‐7 cell line of BC is done through MTT stain method. The results obtained reveal considerable inhibition of cancer growth with IC50 range 78.95–99.18 µM. These newly synthesized analogues may be represented as promising line for the discovery of new agents fighting BC in addition to other types of cancer.

A Comparative Computational Analysis Approach to Predict Significant Protein-Protein Interactions of Human and Vancomycin Resistant Enterococcus faecalis (VRE) to Prioritize Potential Drug Targets

Background: Various challenges exist in the treatment of infectious diseases due to the significant rise in drug resistance, resulting in the failure of antibiotic treatment. As a consequence, a dire need has arisen for the rethinking of the drug discovery cycle because of the challenge of drug resistance. The underlying cause of the infectious diseases depends upon associations within the Host-pathogen Protein- Protein Interactions (HP-PPIs) network, which represents a key to unlock new pathogenesis mechanisms. Hence, the elucidation of significant PPIs is a promising approach for the identification of potential drug targets. Objective: Identification of the most significant HP-PPIs and their partners, and targeting them to prioritize potential new drug targets against Vancomycin-resistant Enterococcus faecalis (VRE). Methods: We applied a computational approach based on one of the emerging techniques i.e. Interolog methodology to predict the significant Host-Pathogen PPIs. Structure-Based Studies were applied to model shortlisted protein structures and validate them through PSIPRED, PROCHECK, VERIFY3D, and ERRAT tools. Furthermore, 18,000 drug-like compounds from the ZINC library were docked against these proteins to study protein-chemical interactions using the AutoDock based molecular docking method. Results: The study resulted in the identification of 118 PPIs for Enterococcus faecalis, and prioritized two novel drug targets i.e. Exodeoxyribonuclease (ExoA) and ATP-dependent Clp protease proteolytic subunit (ClpP). Consequently, the docking program ranked 2,670 and 3,154 compounds as potential binders against Exodeoxyribonuclease and ATP-dependent Clp protease proteolytic subunit, respectively. Conclusion: Thereby, the current study enabled us to identify and prioritize potential PPIs in VRE and their interacting proteins in human hosts along with the pool of novel drug candidates.

Re-Exploring the Ability of Common Docking Programs to Correctly Reproduce the Binding Modes of Non-Covalent Inhibitors of SARS-CoV-2 Protease Mpro.

In the latest few decades, molecular docking has imposed itself as one of the most used approaches for computational drug discovery. Several docking benchmarks have been published, comparing the performance of different algorithms in respect to a molecular target of interest, usually evaluating their ability in reproducing the experimental data, which, in most cases, comes from X-ray structures. In this study, we elucidated the variation of the performance of three docking algorithms, namely GOLD, Glide, and PLANTS, in replicating the coordinates of the crystallographic ligands of SARS-CoV-2 main protease (Mpro). Through the comparison of the data coming from docking experiments and the values derived from the calculation of the solvent exposure of the crystallographic ligands, we highlighted the importance of this last variable for docking performance. Indeed, we underlined how an increase in the percentage of the ligand surface exposed to the solvent in a crystallographic complex makes it harder for the docking algorithms to reproduce its conformation. We further validated our hypothesis through molecular dynamics simulations, showing that the less stable protein–ligand complexes (in terms of root-mean-square deviation and root-mean-square fluctuation) tend to be derived from the cases in which the solvent exposure of the ligand in the starting system is higher.

Esculentoside A alleviates cognitive deficits and amyloid pathology through peroxisome proliferator-activated receptor γ-dependent mechanism in an Alzheimer's disease model

BackgroundAlzheimer's disease (AD) is characterized clinically by cognitive deficits and pathologically by amyloid-β (Aβ) deposition and tau aggregation, as well as the brain atrophy. Esculentoside A (EsA), a neuroprotective saponin, is isolated from Phytolacca esculenta and shows potent health-promoting effects in a variety of experimental models. However, there are minimal reports on the effects of EsA on triple transgenic AD mice. PurposeThe current research aimed at investigating the protective effects and underlying mechanisms of EsA on the mitigation of cognitive deficits and pathology in triple transgenic AD mice. MethodsTriple transgenic AD mice (3 × Tg-AD) of 8 months old received intraperitoneal treatment of 5 or 10 mg/kg EsA for 8 consecutive weeks. Morris water maze test and open field test were made to evaluate the cognitive function and degree of anxiety of the mice. Liquid chromatography with tandem mass spectrometry analysis was performed to characterize and to quantify EsA in the blood and brain of mice. Immunofluorescence assay and Western blot were adopted to measure the levels of peroxisome proliferator-activated receptor gamma (PPARγ) and key proteins in Aβ pathology, ER stress- and apoptosis-associated pathways. The combination of EsA with PPARγ were theoretically calculated by molecular docking programs and experimentally confirmed by the bio-layer interferometry technology. ResultsSupplemental EsA could improve the cognitive deficits of 3 × Tg-AD mice. EsA penetrated the brain-blood barrier to exert a strong effect on AD mice, evidenced as decreasing Aβ generation, reducing the degrees of oxidative and ER stress, and mitigating neuronal apoptosis through the increase of PPARγ expression. In the culture of primary neurons, addition of PPARγ inhibitor GW9662 eliminated the effects of EsA on AD pathologies. Direct combination of EsA with PPARγ were demonstrated by molecular docking programs and bio-layer interferometry technology. ConclusionsFor the first time, these outcomes revealed that EsA could penetrate the brain-blood barrier to exert a strong effect on ameliorating cognitive deficits in 3 × Tg-AD mice and exert neuroprotective effects toward AD pathology via PPARγ-dependent mechanism.

Molecular Docking and Dynamics Studies to Explore Effective Inhibitory Peptides Against the Spike Receptor Binding Domain of SARS-CoV-2.

The spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has become a pandemic due to the high transmission and mortality rate of this virus. The world health and economic sectors have been severely affected by this deadly virus, exacerbated by the lack of sufficient efficient vaccines. The design of effective drug candidates and their rapid development is necessary to combat this virus. In this study, we selected 23 antimicrobial peptides from the literature and predicted their structure using PEP-FOLD 3.5. In addition, we docked them to the SARS-CoV-2 spike protein receptor-binding domain (RBD) to study their capability to inhibit the RBD, which plays a significant role in virus binding, fusion and entry into the host cell. We used several docking programs including HDOCK, HPEPDOCK, ClusPro, and HawkDock to calculate the binding energy of the protein-peptide complexes. We identified four peptides with high binding free energy and docking scores. The docking results were further verified by molecular dynamics (MD) simulations to characterize the protein-peptide complexes in terms of their root-mean-square fluctuation (RMSF), root-mean-square deviation (RMSD), radius of gyration (Rg), solvent-accessible surface area (SASA), and hydrogen bond formation. Allergenicity and toxicity predictions suggested that the peptides we identified were non-allergenic and non-toxic. This study suggests that these four antimicrobial peptides could inhibit the RBD of SARS-CoV-2. Future in vitro and in vivo studies are necessary to confirm this.

LRET-derived HADDOCK structural models describe the conformational heterogeneity required for DNA cleavage by the Mre11-Rad50 DNA damage repair complex.

The Mre11-Rad50-Nbs1 protein complex is one of the first responders to DNA double-strand breaks. Studies have shown that the catalytic activities of the evolutionarily conserved Mre11-Rad50 (MR) core complex depend on an ATP-dependent global conformational change that takes the macromolecule from an open, extended structure in the absence of ATP to a closed, globular structure when ATP is bound. We have previously identified an additional 'partially open' conformation using luminescence resonance energy transfer (LRET) experiments. Here, a combination of LRET and the molecular docking program HADDOCK was used to further investigate this partially open state and identify three conformations of MR in solution: closed, partially open, and open, which are in addition to the extended, apo conformation. Mutants disrupting specific Mre11-Rad50 interactions within each conformation were used in nuclease activity assays on a variety of DNA substrates to help put the three states into a functional perspective. LRET data collected on MR bound to DNA demonstrate that the three conformations also exist when nuclease substrates are bound. These models were further supported with small-angle X-ray scattering data, which corroborate the presence of multiple states in solution. Together, the data suggest a mechanism for the nuclease activity of the MR complex along the DNA.

Assessing the therapeutic potential of agomelatine, ramelteon, and melatonin against SARS-CoV-2

BackgroundThe SARS-Cov-2(severe acute respiratory syndrome coronavirus 2) infection affecting human populations worldwide is now a very concerning issue considering the morbidity and mortality rates. Despite several measures followed by the medical fraternity and general public, there is no resolution. Therapeutic measures to tackle the infection have been based on researching new designer drug molecules that could prevent viral entry into the human host. Melatonin has been tried as an adjuvant in the management of COVID 19(coronavirus disease) illness but its specific antiviral role has not been investigated. Objectives: The objectives of the present study were to conduct an in-silico analysis to investigate if melatonin and related drugs namely ramelteon and agomelatine could be used as antiviral agents in SARS-CoV-2 infection based on their binding to the SARS-CoV-2 receptor binding site (RBD) and Angiotensin-converting enzyme 2 (ACE 2). MethodsFor docking studies (Pdb Id 1M0J), the SARS-CoV-2 spike protein receptor-binding domain (RBD) crystal structure which was ACE2 cell receptor bounded was employed. From the PubChem database, the three-dimensional configuration of the ligands melatonin, ramelteon, and agomelatine was retrieved, and conceptual density functional theory (CDFT) was performed to determine molecular descriptors. Charges were added and optimized with the universal force field to prepare the ligands for the process of docking. For facilitation of readability by the AutoDock software conversion to PDBQT(Protein Data Bank, Partial Charge (Q), & Atom Type (T)) format was performed. AutoDock version 4.2.6 docking program and AutoDock Tools (ADT) version 1.5.6 were used for molecular docking. Desmond, a Package of Schrödinger LLC was used to simulate molecular dynamics for hundred nanoseconds using. ResultsData from the present study reveal that melatonin, ramelteon, and agomelatine demonstrate significant binding with SARS-CoV-2 RBD and ACE 2 demonstrating the fact that they can strongly prevent viral entry into the host cells through dual binding effects. However, Ramelteon was found to be the most superior amongst the 3 drugs analyzed in its antiviral properties against SARS-CoV-2. ConclusionResults advocate further research in exploring the potential therapeutic applications of melatonin, ramelteon, and agomelatine for the management of SARS-CoV-2 infection.

Inclusion of Desolvation Energy into Protein-Protein Docking through Atomic Contact Potentials.

Protein-protein interactions are crucial in many biological processes. Therefore, determining the structure of a protein-protein complex is valuable for understanding its molecular mechanisms and developing drugs. Molecular docking is a powerful computational tool in the prediction of protein-protein complex structures, in which a scoring function with good performance is very important. In this study, we have proposed a hybrid scoring function of atomic contact-based desolvation energies and distance-dependent interatomic potentials for protein-protein interactions, named HITScorePP, where the atomic contact desolvation energies were derived using an iterative method and the distance-dependent potentials were directly taken from our ITScorePP scoring function. Integrating the hybrid scoring function into our fast Fourier transform (FFT) based HDOCK docking scheme, the updated docking program, named HDOCK2.0, significantly improved the docking performance on the 55 newly added complexes in the protein docking benchmark 5.0 and a data set of 19 antibacterial protein complexes. HDOCK2.0 was also compared with four other state-of-the-art docking programs including Rosetta, ZDOCK3.0.2, FRODOCK3.0, ATTRACT, and PatchDock and obtained the overall best performance in binding mode predictions. These results demonstrated the accuracy of our hybrid scoring function and the necessity of included desolvation effects in protein-protein docking.

Identification of selective mtbDHFR inhibitors by virtual screening and experimental approaches.

mtbDHFR-targeting inhibition has become a promising approach for tuberculosis treatment. In the current research, a multi-step virtual screening effort toward ZINC and MCE databases was devoted to discover novel mtbDHFR inhibitors. Based on binding affinity of small molecules through molecular docking study in AutoDock Vina, the number of compounds was reduced to 952,688. Further, these compounds were employed by a step-by-step multiple docking programs of Schrödinger suite and filtered by pharmacokinetics and PAINS parameters. Finally, nine ZINC compounds and 400MCE compounds were obtained. These compounds of binding ability were tested with mtbDHFR by FluoPol-ABPP approach established in this work. Finally, AF-353 compound was found to have strong binding effect to mtbDHFR. AF-353 was further tested for mtb and hDHFR enzymatic activities, and it was proved to possess 50-fold selectivity toward mtbDHFR over hDHFR. In silico MD simulation results supported this selectivity.

Aspirin-aromatic amino acid conjugates as selective Cox-2 inhibitors: A docking study


 
 
 
 Purpose: To examine eight compounds in which aspirin was conjugated with aromatic amino acids virtually using docking studies for their ability to inhibit cyclooxygenase 2 (Cox-2) enzyme.
 Methods: The compounds were drawn, energy minimised and then docked into the active site of Cox-2 along with celecoxib for comparison using GOLD docking program.
 Results: Five of the designed compounds docked into the active site with a bent conformation producing a pose similar to that of celecoxib, with the aromatic amino acid moiety facing the outside of the active site. The interactions were mainly hydrophobic with some hydrogen bonds formed between the compounds and the key residues in the active site. Although the obtained scores were less than that of celecoxib, they were the top ranked poses in the solutions generated for each compound.
 Conclusion: The conjugation of aspirin with amino acids may offer a potential for the development of selective, but safe, Cox-2 inhibitors.
 
 
 

Insect protease inhibitors; promising inhibitory compounds against SARS-CoV-2 main protease

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19), has adversely affected global health since its emergence in 2019. The lack of effective treatments prompted worldwide efforts to immediately develop therapeutic strategies against COVID-19. The main protease (Mpro) of SARS-CoV-2 plays a crucial role in viral replication, and therefore it serves as an attractive target for COVID-19-specific drug development. Due to the richness and diversity of insect protease inhibitors, we docked SARS-CoV-2 Mpro onto 25 publicly accessible insect-derived protease inhibitors using the ClusPro server, and the regions with high inhibitory potentials against Mpro were used to design peptides. Interactions of these inhibitory peptides with Mpro were further assessed by two directed docking programs, AutoDock and Haddock. AutoDock analysis predicted the highest binding energy (−9.39 kcal/mol) and the lowest inhibition constant (130 nM) for the peptide 1KJ0-7 derived from SGCI (Schistocerca gregaria chymotrypsin inhibitor). On the other hand, Haddock analysis resulted in the discovery of a different peptide designated 2ERW-9 from infestin, a serine protease inhibitor of Triatoma infestans, with the best docking score (−131), binding energy (−11.7 kcal/mol), and dissociation constant (2.6E-09 M) for Mpro. Furthermore, using molecular dynamic simulations, 1KJ0-7 and 2ERW-9 were demonstrated to form stable complexes with Mpro. The peptides also showed suitable drug-likeness properties compared to commercially available drugs based on Lipinski's rule. Our findings present two peptides with possible protease inhibitor activities against Mpro and further demonstrate the potential of insect-derived peptides and computer-aided methods for drug discovery.

Consensus combining outcomes of multiple ensemble dockings: examples using dDAT crystalized complexes

Docking using different programs provides more reliable information about the interaction of molecules than data obtained in a single program. An exponential consensus ranking (ECR) was developed to combine scoring functions across docking programs differing in efficiencies and scales of measurements. The ECR method was adapted to merge results of re- and cross-dockings (i.e., ensemble docking) made in multiple docking programs. Adapted ECR consisted of four consecutive steps: 1- determination of scoring functions for a ligand with a series of macromolecules in multiple docking programs; 2- ranking of the scoring functions per macromolecule in each program; 3- combining the ranking across the programs creating a ranking per macromolecule; 4- averaging the ranking per macromolecule creating a final ranking. This last step incorporated the heterogeneity of the macromolecule conformations in the consensual score. The final ranking based on the adapted ECR represents relative affinity of a series of ligands to a macromolecule on average. As an example, a ranking of the average affinity of antidepressants and other ligands to the Drosophila melanogaster dopamine transporter (dDAT) was presented. Adapted ECR generated a ranking similar to that based on the affinity constant of each ligand obtained from the literature.• A final ranking of the average relative affinity of different ligands to the dDAT.• A consensus method combining multiple ensemble dockings.• A complete protocol to make re-docking and cross-docking using Autodock Vina, Gold and DockThor.

Design and synthesis of antivirals benzimidazoles and quinoxalines

Background Chronic hepatitis C can cause serious, even deadly, health problems like cirrhosis and liver cancer. There is no vaccine for hepatitis C. The hepatitis C virus (HCV) NS5B gene encodes RNA-dependent RNA polymerase, which is a key player in viral replication and is a promising target for the development of antiviral drugs. Drugs having benzimidazole and quinoxaline scaffolds were described to selectively block the activity of NS5B polymerase. New antiviral drugs have to be developed to overcome drug resistance.Objective The main goal of this work was to develop new effective anti-bovine viral diarrhea virus (BVDV) and anti-HCV agents by designing and synthesizing benzimidazole and quinoxaline derivatives.Materials and methods Synthesis of target compounds based on benzimidazole and quinoxaline scaffolds according to reported methods was done. Antiviral activity against BVDV was studied. BVDV and Madin-Darby bovine kidney cells were obtained from the American Type Culture Collection. Antiviral activity against HCV infectious system was evaluated. Huh7.5.1 cells were cultured and treated with different concentrations of studied compounds. GOLD molecular docking study was evaluated. The crystal structures of the HCV polymerases in complex with its co-crystalized native ligand were retrieved from the Protein Data Bank. Acute toxicity studies were carried out on animals. Results and conclusion A rational design based on the previous work was performed to indicate new promising benzimidazole and quinoxaline derivatives to be synthesized and tested as anti-HCV compounds. New benzimidazole and quinoxaline derivatives were synthesized and tested for anti-BVDV activity. All of the compounds showed strong activity against BVDV, except 17, which exhibited moderate antiviral activity. Compounds 12 and 13 were the most promising. The anti-HCV activity of 12 and 13 was investigated after infection of Huh 7.5.1 cells with HCV (JFH1). The IC50 values of 12 and 13 were found to be 19.1 and 49.4 μM, respectively; their CC50 values were 752.25 and 1480 μM, respectively; and their SI were calculated to be 39.3 for 12 and 30.03 for 13. The assigned compounds were docked into the hepatitis-C virus polymerase enzyme (pdb: 3FRZ) using GOLD 5.2.2 docking program. They revealed GoldScore fitness activities of 69.78–80.71, which is comparable to the native ‘PF-00868554’ ligand as a potent HCV polymerase inhibitor. They are bound by up to three hydrogen bonds, mainly with aminoacids R422 and S476, as well as they were embedded into the two small hydrophobic pockets formed by amino acid residues including L419, M423, L482,and L497. The acute toxicity of compound 12 on rats was tested. No signs of toxicity, no deaths, and no significant changes were observed in the biochemical parameters of liver and kidneys.

Fenofibrate-Nicotinamide Cocrystals: Molecular Docking Studies and Evaluation in Tablet Dosage Form

The objectives of present investigation were to evaluate prepared cocrystals of fenofibrate and nicotinamide for pre-compression characteristics, docking studies for target peroxisome proliferator-activated receptor alpha, evaluate performance of cocrystals in tablet dosage form and to carry out in vivo antihyperlipidemic activity. The cocrystals were prepared by antisolvent addition method. Docking studies of cocrystals and pure fenofibrate against of target peroxisome proliferator-activated receptor alpha were carried out by using PyRx (version 0.8) docking tool, AutoDock Vina as docking program. The prepared cocrystals were evaluated for pre-compression properties like angle of repose, bulk density and Carr’s index. Cocrystals were formulated in tablet dosage form and evaluated for official and unofficial quality control tests. The antihyperlipidemic activity carried out in rats by using Triton X-100 induced hyperlipidemia model. Cocrystals binds with peroxisome proliferator-activated receptor alpha with more binding affinity as compared with fenofibrate. Cocrystal shows binding energy of -9.3 kcal/mol while fenofibrate shows -8.5 kcal/mol. The pre-compression properties were within the limits of United States Pharmacopeia guidelines. The pure fenofibrate tablet showed 24.7 % drug release at the end of 90 min and cocrystal based tablet showed 100 % at 45 min. There was no statistically significant difference in values for all biochemical parameters in case of in vivo activity for cocrystals in comparison with pure fenofibrate. From the docking studies we can conclude that cocrystals showed stronger more substantial formed stable complexes with target peroxisome proliferator-activated receptor alpha, but no statistically significant difference in pharmacodynamic studies.

Experimental, insilico, DFT studies of novel compound 2-{2-[(3,4-dimethoxyphenyl)methylidene]hydrazinecarbonothioyl}-N-methyl-N- phenylhydrazine-1-carbothioamide

In the current investigation, we have obtained single crystals 2-{2-[(3,4-dimethoxyphenyl)methylidene]hydrazinecarbonothioyl}-N-methyl-N-phenylhydrazine-1-carbothioamide (H2L) by refluxing 3,4 dimethoxybenzaldehyde and N(4)- methyl-N(4)-phenyl thiosemicarbazide. Here we discuss the experimental as well as theoretical studies of the selected molecule. Computational studies were made by Gaussian 09 program. X-ray refinement data of the molecule is used for geometry optimization process using DFT (B3LYP) method with the 6–31 + G (d,p) basis sets. The optimised molecular structure, MEP, NBO, HOMO-LUMO analysis, and NLO effects of 2-{2-[(3,4-dimethoxyphenyl)methylidene]hydrazinecarbonothioyl}-N-methyl-N-phenylhydrazine-1-carbothioamide have been communicated in this paper. NBO analysis gave insight into the strongly delocalized structure, responsible for the nonlinearity and hence the stability of the molecule. H2L obeys Lipinski’s rule, and further in silico assessment of oral bioavailability, ADME, drug-likeness, and medicinal chemistry friendliness proposes that this molecule is a promising candidate for the cancer drug discovery process. Simultaneously, molecular docking of the compound into the 3D crystal structure of ribonucleotide reductase M−2 subunit (PDB ID: 2UW2) and Histone deacetylase 8 (PDB ID 1 T69) have been performed using GLIDE Dock Program. The study has shown that the ligand could be a potential inhibitor for the ribonucleotide reductase M−2 subunit protein.

Spectroscopic Identification, Structural Features and Molecular Docking Studies on 5-(4-Propoxybenzylidene)-2-[3-(4-chlorophenyl)-5-[4(propan-2-yl) phenyl-4,5-dihydro- 1H-pyrazol-1-yl]-1,3-thiazol-4(5H)-one using Pim-1 Kinase Cancer Protein

A comprehensive investigation of the molecular structure, electronic properties and vibrational spectra of 5-(4-propoxybenzylidene)-2-[3-(4-chlorophenyl)-5-[4-(propan-2-yl)phenyl]-4,5-dihydro-1Hpyrazol- 1-yl]-1,3-thiazol-4(5H)-one have been studied. Many natural and/or synthetic compounds contain, thiazole which are attractive compounds found in the building of numerous natural products and certain pharmaceutical agents. To understand the molecular-orbital interaction and structural investigation of the title compound, the density functional theory (DFT) calculation has been carried out using B3LYP/6-31G and 6-311G basis sets combination. The experimental FT-IR, FT-Raman spectral data along with theoretical quantum chemical calculation were investigated. For potential energy distributions (PED) analysis, the VEDA 4 program is utilized to do comparative frequency assignments. With the optimized structures, the highest occupied molecular orbital (HOMO), the lowest unoccupied molecular orbital (LUMO) energies, molecular electrostatic potential (MEP) and natural bond orbital (NBO) were applied to describe the chemical reactivity.The electron density interactions distributed in space, which exist within these compounds are analyzed by different topological methods namely, atom in molecule (AIM), localized orbital locator (LOL), electron localization function (ELF) and the reduced density gradient (RDG). Finally, the molecular docking studies of the title compound for potent Pim-1 kinase cancer PDB ID: 3A99, 1GJ8, 1XQZ was investigated using theAuto Dock program

Benzoyl-xanthone derivative induces apoptosis in MCF-7 cells by binding TRAF6.

TNF receptor-associated factor 6 (TRAF6) has been reported to be associated with the development of cancer. Nevertheless, the exact role of TRAF6 in cancer remains unclear. The purpose of the present study was to explore the mechanism of 2-benzoyl-3-hydroxy-4-methyl-9H-xanthen-9-one leading to the inhibition of the activation of AKT and TGF-β-activated kinase 1 (TAK1), and to the apoptosis of MCF-7 cells. Using a computational docking program and examination of AKT and TAK1 level changes, a new small molecule was identified, 2-benzoyl-3-hydroxy-4-methyl-9H-xanthen-9-one, which competitively bound to TRAF6. Next, the effect of this new compound on MCF-7 cells' biological behavior was studied in vitro. MTT assays were used to investigate cell viability; flow cytometry and invasion assays were performed to detect early apoptosis and invasion in MCF-7 cells, respectively. Immunoprecipitation, western blotting and caspase-3/9 activity assays were carried out to explore changes in protein expression. Briefly, the present data indicated that 2-benzoyl-3-hydroxy-4-methyl-9H-xanthen-9-one could suppress proliferation, induce early apoptosis and inhibit invasion in MCF-7 cells by suppressing the expression of Bcl-2 and promoting the expression of Bax, caspase-9, and caspase-3. These findings indicated that 2-benzoyl-3-hydroxy-4-methyl-9H-xanthen-9-one could induce apoptosis by inhibiting the activation of AKT and TAK1, and affecting the Bcl-2/Bax-caspase-9-caspase-3 pathway by competitively binding with TRAF6.

Identification of African Swine Fever Virus Inhibitors through High Performance Virtual Screening Using Machine Learning

African swine fever virus (ASFV) is a highly contagious virus that causes severe hemorrhagic viral disease resulting in high mortality in domestic and wild pigs, until few antiviral agents can inhibit ASFV infections. Thus, new anti-ASFV drugs need to be urgently identified. Recently, we identified pentagastrin as a potential antiviral drug against ASFVs using molecular docking and machine learning models. However, the scoring functions are easily influenced by properties of protein pockets, resulting in a scoring bias. Here, we employed the 5′-P binding pocket of AsfvPolX as a potential binding site to identify antiviral drugs and classified 13 AsfvPolX structures into three classes based on pocket parameters calculated by the SiteMap module. We then applied principal component analysis to eliminate this scoring bias, which was effective in making the SP Glide score more balanced between 13 AsfvPolX structures in the dataset. As a result, we identified cangrelor and fostamatinib as potential antiviral drugs against ASFVs. Furthermore, the classification of the pocket properties of AsfvPolX protein can provide an alternative approach to identify novel antiviral drugs by optimizing the scoring function of the docking programs. Here, we report a machine learning-based novel approach to generate high binding affinity compounds that are individually matched to the available classification of the pocket properties of AsfvPolX protein.

A random forest classifier for protein-protein docking models.

Herein, we present the results of a machine learning approach we developed to single out correct 3D docking models of protein-protein complexes obtained by popular docking software. To this aim, we generated docking models for each of the 230 complexes in the protein-protein benchmark, version 5, using three different docking programs (HADDOCK, FTDock and ZDOCK), for a cumulative set of docking models. Three different machine learning approaches (Random Forest, Supported Vector Machine and Perceptron) were used to train classifiers with 158 different scoring functions (features). The Random Forest algorithm outperformed the other two algorithms and was selected for further optimization. Using a features selection algorithm, and optimizing the random forest hyperparameters, allowed us to train and validate a random forest classifier, named COnservation Driven Expert System (CoDES). Testing of CoDES on independent datasets, as well as results of its comparative performance with machine learning methods recently developed in the field for the scoring of docking decoys, confirm its state-of-the-art ability to discriminate correct from incorrect decoys both in terms of global parameters and in terms of decoys ranked at the top positions. Supplementary data are available at Bioinformatics Advances online. The docking models are available at https://doi.org/10.5281/zenodo.4012018. The programs underlying this article will be shared on request to the corresponding authors.