Investigation of a set of flavonoid compounds as Helicobacter pylori urease inhibitors: insights from in silico studies.

Helicobacter pylori (H. pylori) is a spiral, microaerophilic gram-negative bacterium, which is associated with the destruction of the lining of the stomach, leads to chronic inflammation of the stomach, which can cause stomach and duodenal ulcers. The problems caused by the treatment with antibiotics have caused researchers to use new approaches to treat infections caused by H. pylori, among them specific treatments with flavonoids. Urease enzyme, as one of the most important pathogenic and antigenic factors of this bacterium, is a suitable target for this purpose. In this study, the inhibitory effect of flavonoid compounds compared to acetohydroxamic acid on H. pylori urease enzyme was evaluated using molecular modeling methods. First, the interaction of flavonoids with urease enzyme compared with acetohydroxamic acid was investigated by molecular docking method to produce efficient docking poses. Then the physicochemical properties and toxicity of the best flavonoid compounds were analyzed using the swissadme server. Also, molecular dynamics calculations were performed to precisely understand the interactions between ligands and protein. The results of this study show that all the investigated flavonoid compounds are capable of inhibiting H. pylori urease. Among these compounds, six compounds chrysin, galangin, kaempferol, luteolin, morin and quercetin showed a greater tendency to bind to urease, compared to the acetohydroxamic acid inhibitor. These compounds are desirable in terms of physicochemical properties. This study also revealed that the flavonoids with their hydroxyl groups (-OH) play an important role during bond formation with amino acids Ala278, Ala169, His314, Asp362 and Asn168. Therefore, flavonoid compounds, due to their suitable location in the active site of the urease, create a more effective inhibition than the chemical drug acetohydroxamic acid and can be suitable candidates for the treatment of Helicobacter pylori under in vitro and in vivo investigations.Communicated by Ramaswamy H. Sarma.

Identification of novel potential inhibitors of monkeypox virus thymidine kinase using molecular docking, molecular dynamics simulation and MM/PBSA methods.

The monkeypox spread has been announced a public health emergency of international concern (PHEIC) by the World Health Organization (WHO). Both monkeypox and smallpox viruses are placed in the genus Orthopoxvirus. Despite recommendations for the administration of smallpox drugs versus monkeypox, no specific drug for monkeypox has yet been introduced. A reliable and effective method against this outbreak can be the use of natural products. This study aimed for identification of natural flavonoid derivatives as potential thymidine kinase inhibitors, the main drug target of monkeypox virus. Thymidine kinase protein structure was predicted by homology modeling and the quality of generated model was evaluated. Then, the interaction between natural flavonoids and the modeled thymidine kinase was explored by molecular docking. Based on docking results, more than half of the flavonoids with higher docking scores compared to reference drug (ganciclovir) were exhibited better binding affinities toward the protein. In addition, stability of the top flavonoids including eupatorin, fisetin, rhamnetin and scutellarein, was confirmed by MD simulations and binding free energy calculations using MM/PBSA analysis. These selected compounds were also shown acceptable results for drug likeness and ADMET analysis. Therefore, the results of the study showed that these flavonoids could be considered as potential thymidine kinase inhibitors for use against monkeypox virus.

In silico study of potential immunonutrient-based sports supplements against COVID-19 via targeting ACE2 inhibition using molecular docking and molecular dynamics simulations.

Use of some sports supplements can inhibit angiotensin-converting enzyme II (ACE2), a receptor for the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), as reviewed through molecular docking and sequent molecular dynamics (MD) simulations against this condition. The crystal structures of ACE2 receptors of SARS-CoV-2 and SARS-CoV, applied in docking analysis, were taken from the Protein Data Bank (PDB). The receptors were then prepared using the Molecular Operating Environment (MOE), as a drug-discovery software platform for docking. Supplements such as quercetin and beta glucan (ß-glucan) were the top docked compounds to ACE2 receptor though they strongly interacted with CoV target protein. The study data showed that immune responses to immunonutrient-based sports compounds (viz. quercetin and ß-glucan) in Coronavirus disease 2019 (COVID-19) were essential in mounting successful immune responses by athletes. While awaiting the development of an effective vaccine, there is a need to focus on immunonutrient-based sports supplements as preventive and therapeutic options that can be implemented in a safe and quick manner to bolster immune responses in athletes.Communicated by Ramaswamy H. Sarma.

Evaluation of apigenin-based biflavonoid derivatives as potential therapeutic agents against viral protease (3CLpro) of SARS-CoV-2 via molecular docking, molecular dynamics and quantum mechanics studies.

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is the causative agent of the pandemic COVID-19 disease that affects human respiratory function. Despite the scientific progression made in the development of the vaccine, there is an urgent need for the discovery of antiviral drugs for better performance at different stages of SARS-CoV-2 reproduction. The main protease (Mpro or 3CLpro) plays a pivotal role in the life cycle of the virus, making it an attractive target for the development of antiviral agents effective against the new strains of coronaviruses (CoVs). In this study, a series of apigenin-based natural biflavonoid derivatives as potential inhibitors of coronaviruses 3CLpro was investigated by in silico approaches. For this purpose, the molecular docking was performed to analyze the interaction of the natural biflavonoids with SARS-Cov-2 main protease and for further investigation, docking to the 3CLpro of SARS-CoV and MERS-CoV. Based on docking scores and comparison with the reference inhibitors (ritonavir and lopinavir), more than half of the biflavonoids had strong interactions with the residues of the binding pocket of the coronaviruses 3CLpro and exhibited better binding affinities toward the main protease than ritonavir and lopinavir. The top biflavonoids were further explored through molecular dynamics simulation, binding free energy calculation and residual energy contributions estimated by the MM-PBSA. Also, drug likeness property investigation by Swiss ADME tools and density functional theory (DFT) calculations were performed. The results confirmed that the 3CLpro-amentoflavone, 3CLpro-bilobetin, 3CLpro-ginkgetin, and 3CLpro-sotetsuflavone complexes possess a large amount of dynamic properties such as high stability, significant binding energy and fewer conformation fluctuations. Also, the pharmacokinetics and drug-likeness studies and HOMO-LUMO and DFT descriptor values indicated a promising result of the selected natural biflavonoids. Overall findings indicate that the apigenin-based biflavonoids may inhibit COVID-19 by significant interactions in the binding pocket and those results can pave the way in drug discovery although the effectiveness of these bioactive compounds should be further validated by in-vitro and in-vivo investigations.Communicated by Ramaswamy H. Sarma.

Molecular docking and mouse modeling suggest CMKLR1 and INSR as targets for improving PCOS phenotypes by minocycline.

Polycystic ovary syndrome (PCOS) is the most common cause of women's infertility. Some inflammatory pathways play a pivotal role in the pathogenesis of PCOS. This study aimed to investigate the possible beneficial effects of minocycline on chemokine-like receptor 1 (CMKLR1) and Insulin Receptor (INSR) in a PCOS model. A molecular docking study was implemented using Molecular Operating Environment (MOE) software. The PCOS was induced in NMRI mice (mean body weight 14.47±0.23) by 28 days estradiol valerate injection (2 mg/kg/day). The mice were then divided into six groups (n=8 per group, mean body weight 17.77± 0.26): control (received normal saline), PCOS model, control for minocycline, minocycline treated PCOS (50 mg/kg), letrozole treated PCOS (0.5 mg/kg), and metformin-treated PCOS (300 mg/kg). Serum FSH, LH, estradiol (E2), and testosterone were detected by ELISA. The ovarian tissues were stained by hematoxylin and eosin. The CMKLR1 and INSR expression levels were determined by Real-time-PCR. The molecular docking studies showed scores of -10.92 and -9.30 kcal/mol, respectively, for minocycline with CMKLR1 and INSR. Estradiol valerate treatment led to a significant increase in E2, graffian follicle, and decrease in corpus luteum (CL) numbers (P<0.05), while minocycline treatment improved these PCOS features. The minocycline treatment significantly decreased the CMKLR1 expression and increased the INSR expression (P<0.05) while the CMKLR1 expression was increased in PCOS model. Minocycline may improve ovulation in PCOS model by returning E2 to a normal level and increasing CL number (ovulation signs). These beneficial outcomes may be related to the changes in CMKLR1 and INSR gene expression involved in glucose metabolism and inflammation.

In silico analysis and identification of antiviral coumarin derivatives against 3-chymotrypsin-like main protease of the novel coronavirus SARS-CoV-2.

Coronavirus disease 2019 (COVID-19) is a pandemic viral disease caused by SARS-CoV-2 that generated serious damages for both the human population and the global economy. Therefore, it is currently considered as one of the most important global health problems of human societies and there is an urgent need for potent drugs or vaccines which can effectively combat this virus. The chymotrypsin-like protease (3CLpro) of SARS-CoV-2 plays a key role in the viral replication inside the host and thus is a promising drug target to design and develop effective antiviral drugs against SARS and other coronaviruses. This study evaluated some antiviral coumarin phytochemicals as potential inhibitors of coronaviruses 3CLpro by in silico approaches such as molecular docking, ADMET prediction, molecular dynamics simulation, and MM-PBSA binding energy calculation. Natural coumarin derivatives were docked to the 3CLpro of SARS-CoV-2 and for further investigation, docked to the 3CLpro of SARS-CoV and MERS-CoV. The docking scores of these natural compounds were compared with 3CLpro referenced inhibitors (ritonavir and lopinavir) and co-crystal inhibitor N3. Molecular docking studies suggested more than half of the coumarin phytochemicals had favorable interaction at the binding pocket of the coronaviruses 3CLpro and exhibited better binding affinities toward 3CLpro than ritonavir and lopinavir. Most antiviral phytochemicals interact strongly with one or both the catalytic dyad residues (His41 and Cys145) and the other key residues of SARS-CoV-2 main protease. Further, MD simulation and binding free energy calculations using MM-PBSA were carried out for three 3CLpro-coumarin complexes and 3CLpro-N3/lopinavir. The results confirmed that the 3CLpro-glycycoumarin, 3CLpro-oxypeucedanin hydrate, and 3CLpro-inophyllum P complexes were highly stable, experience fewer conformation fluctuations and share a similar degree of compactness. Also, the pharmacokinetics and drug-likeness studies showed good results for the selected coumarin phytochemicals.Therefore, the coumarin phytochemicals could be used as antiviral agents in the treatment of COVID-19 after further studies.

Beneficial effects of minocycline on the ovary of polycystic ovary syndrome mouse model: Molecular docking analysis and evaluation of TNF-α, TNFR2, TLR-4 gene expression.

Polycystic ovary syndrome (PCOS) is the most common cause of ovulatory infertility. Inflammation may be involved in the pathogenesis and development of PCOS. We investigated the anti-inflammatory effect of minocycline on TNF-α, TNFR2, and TLR4 expression levels and the key features of PCOS in a mouse model. Molecular docking was performed by Molecular Operating Environment software. PCOS was induced by estradiol valerate injection (EV) (2 mg/kg/day) in 40 mice. After 28 days, the mice were divided into five groups, including control, PCOS, minocycline control, minocycline PCOS model (50 mg/kg), and letrozole PCOS (0.5 mg/kg). The Levels of FSH, LH, E2, and testosterone were determined by ELISA. H&E staining was used for histological analysis in the ovarian tissues. Docking scores were -10.35, -10.57, and -12.45 kcal/mol for TNFα, TLR-4, and TNFR2, respectively. The expression levels of TNF-α, TNFR2, and TLR4 were detected by Real-Time PCR. PCOS models exhibited acyclicity, a significant increase in E2 levels (P < 0.01), and no difference in FSH, LH, and testosterone. The expression levels of TNF-α, TNFR2, and TLR-4 significantly increased in PCOS (2.70, 7.90, and 14.83-fold, respectively). EV treatment significantly increased graafian follicles (P < 0.001) and decreased corpus luteum (CL) (P < 0.01). Minocycline treatment in PCOS led to a significant decrease in E2 (P < 0.01) and graafian follicles (P < 0.001) and a significant increase in the CL numbers (P < 0.05). Our findings showed the positive effects of minocycline on estradiol level, CL and graafian follicles counts, suggesting that minocycline might inhibit these proteins and improve ovulation in our mouse model of PCOS.

QSAR Modeling, Molecular Docking and Molecular Dynamics Simulations Studies of Lysine-Specific Demethylase 1 (LSD1) Inhibitors as Anticancer Agents.

BACKGROUND: Histone Lysine Demetylases1 (LSD1) is a promising medication to treat cancer, which plays a crucial role in epigenetic modulation of gene expression. Inhibition of LSD1with small molecules has emerged as a vital mechanism to treat cancer. OBJECTIVE: In the present research, molecular modeling investigations, such as CoMFA, CoMFA-RF, CoMSIA and HQSAR, molecular docking and Molecular Dynamics (MD) simulations were carried out on some tranylcypromine derivatives as LSD1 inhibitors. METHODS: The QSAR models were carried out on a series of Tranylcypromine derivatives as data set via the SYBYL-X2.1.1 program. Molecular docking and MD simulations were carried out by the MOE software and the SYBYL program, respectively. The internal and external predictability performances related to the generated models for these LSD1 inhibitors were justified by evaluating cross-validated correlation coefficient (q2), noncross- validated correlation coefficient (r2ncv) and predicted correlation coefficient (r2pred) of the training and test set molecules, respectively. RESULTS: The CoMFA (q2, 0.670; r2ncv, 0.930; r2pred, 0.968), CoMFA-RF (q2, 0.694; r2ncr, 0.926; r2pred, 0.927), CoMSIA (q2, 0.834; r2ncv, 0.956; r2pred, 0.958) and HQSAR models (q2, 0.854; r2ncv, 0.900; r2pred, 0.728) for training as well as the test set of LSD1 inhibition resulted in significant findings. CONCLUSION: These QSAR models were found to be perfect and strong with better predictability. Contour maps of all models were generated and it was proven by molecular docking studies and molecular dynamics simulation that the hydrophobic, electrostatic and hydrogen bonding fields are crucial in these models for improving the binding affinity and determining the structure-activity relationship. These theoretical results are possibly beneficial to design new strong LSD1 inhibitors with enhanced activity to treat cancer.

Molecular Modeling Studies of Anti-Alzheimer Agents by QSAR, Molecular Docking and Molecular Dynamics Simulations Techniques.

BACKGROUND: Acetylcholinesterase (AChE), a serine hydrolase, is an important drug target in the treatment of Alzheimer's disease (AD). Thus, novel AChE inhibitors were designed and developed as potential drug candidates, for significant therapy of AD. OBJECTIVE: In this work, molecular modeling studies, including CoMFA, CoMFA-RF, CoMSIA, HQSAR and molecular docking and molecular dynamics simulations were performed on a series of AChE inhibitors to get more potent anti-Alzheimer drugs. METHODS: 2D/3D-QSAR models including CoMFA, CoMFA-RF, CoMSIA, and HQSAR methods were carried out on 40 pyrimidinylthiourea derivatives as data set by the Sybylx1.2 program. Molecular docking and molecular dynamics simulations were performed using the MOE software and the Sybyl program, respectively. Partial least squares (PLS) model as descriptors was used for QSAR model generation. RESULTS: The CoMFA (q2, 0.629; r2ncv, 0.901; r2pred, 0.773), CoMFA-RF (q2, 0.775; r2ncv, 0.910; r2pred, 0.824), CoMSIA (q2, 0.754; r2ncv, 0.919; r2pred, 0.874) and HQSAR models (q2, 0.823; r2ncv, 0.976; r2pred, 0.854) for training and test set yielded significant statistical results. CONCLUSION: These QSAR models were excellent, robust and had good predictive capability. Contour maps obtained from the QSAR models were validated by molecular dynamics simulationassisted molecular docking study. The resulted QSAR models could be useful for the rational design of novel potent AChE inhibitors in Alzheimer's treatment.

3D-QSAR (CoMFA, CoMSIA) and Molecular Docking Studies on Histone Deacetylase 1 Selective Inhibitors.

BACKGROUND: Histone deacetylases (HDACs) are attractive therapeutic targets for the treatment of cancer and other diseases. There are numerous published patent applications till 2017. It was claimed that novel HDACIs were optimized as potential drug candidates, designed for regional or systemic release, and created as significant inhibitors. OBJECTIVE: In the present study, 3D-QSAR and molecular docking were used to provide a theoretical basis for finding highly potent anti-tumor drugs. METHODS: QSAR was used to generate models and predict the HDAC1 inhibitory activity using the Sybyl program (x1.2 version). Biaryl benzamides (n=73) as selective HDAC1 inhibitors were selected as our data set, which was split randomly into training (n=63) and test sets (n=10). Docking was carried out using the MOE software. Partial least square was used as QSAR model-generation method. External validation and cross-validation (leave-one-out and leave-10-out) were used as validation methods. RESULTS: Both CoMFA (q2, 0.663; rncv 2 , 0.909) and CoMSIA models (q2, 0.628; rncv 2 , 0.877) for training set yielded significant statistical results. The predictive ability of the derived models was examined by a test set of 10 compounds and external validation results displayed rpred 2 and rm 2 values of 0.767 and 0.664 for CoMFA and 0.722 and 0.750 for CoMSIA, respectively. CONCLUSION: The obtained models showed a good predictive ability in both internal and external validation and could be used for designing new biaryl benzamides as potent HDAC1 inhibitors in cancer treatment. The amido and amine groups of benzamide part as scaffold and the bulk groups as a hydrophobic part were key factors to improve inhibitory activity of HDACIs.

Design, synthesis and biological evaluation of novel coumarin-based benzamides as potent histone deacetylase inhibitors and anticancer agents.

Histone deacetylases (HDACs) are attractive therapeutic targets for the treatment of cancer and other diseases. It has four classes (I-IV), among them especially class I isozyme are involved in promoting tumor cells proliferation, angiogenesis, differentiation, invasion and metastasis and also viable targets for cancer therapeutics. A novel series of coumarin-based benzamides was designed and synthesized as HDAC inhibitors. The cytotoxic activity of the synthesized compounds (8a-u) was evaluated against six human cancer cell lines including HCT116, A2780, MCF7, PC3, HL60 and A549 and a single normal cell line (Huvec). We evaluated their inhibitory activities against pan HDAC and HDAC1 isoform. Four compounds (8f, 8q, 8r and 8u) showed significant cytotoxicity with IC50 in the range of 0.53-57.59 µM on cancer cells and potent pan-HDAC inhibitory activity (consists of HDAC isoenzymes) (IC50 = 0.80-14.81 µM) and HDAC1 inhibitory activity (IC50 = 0.47-0.87 µM and also, had no effect on Huvec (human normal cell line) viability (IC50 > 100 µM). Among them, 8u displayed a higher potency for HDAC1 inhibition with IC50 value of 0.47 ± 0.02 µM near equal to the reference drug Entinostat (IC50 = 0.41 ± 0.06 µM). Molecular docking studies and Molecular dynamics simulation of compound 8a displayed possible mode of interaction between this compound and HDAC1enzyme.

Nanorod vanadatesulfuric acid as a novel, recyclable and heterogeneous catalyst for the one-pot synthesis of tetrahydrobenzopyrans.

Vanadatesulfuric acid (VSA), as a novel and heterogeneous nanorod catalyst, was used for an efficient synthesis of tetrahydrobenzo[b]pyrans using an aldehydes, 1,3-cyclohexanediones or beta-ketoester and malononitrile in C2H5OH/H2O mixture under reflux conditions. VSA is prepared via the reaction of sodium metavanadate and chlorosulfonic acid in high purity. The catalyst was characterized by FT-IR, XRD, TEM and EDAX analysis. Compared to the conventional method, this method consistently has the advantage of high yields, simple workup, short reaction times and reusability of the catalyst.