Exploring the Interactions between two Ligands, UCB-J and UCB-F, and Synaptic Vesicle Glycoprotein 2 Isoforms.

In silico modeling was applied to study the efficiency of two ligands, namely, UCB-J and UCB-F, to bind to isoforms of the synaptic vesicle glycoprotein 2 (SV2) that are involved in the regulation of synaptic function in the nerve terminals, with the ultimate goal to understand the selectivity of the interaction between UCB-J and UCB-F to different isoforms of SV2. Docking and large-scale molecular dynamics simulations were carried out to unravel various binding patterns, types of interactions, and binding free energies, covering hydrogen bonding and nonspecific hydrophobic interactions, water bridge, π-π, and cation-π interactions. The overall preference for bonding types of UCB-J and UCB-F with particular residues in the protein pockets can be disclosed in detail. A unique interaction fingerprint, namely, hydrogen bonding with additional cation-π interaction with the pyridine moiety of UCB-J, could be established as an explanation for its high selectivity over the SV2 isoform A (SV2A). Other molecular details, primarily referring to the presence of π-π interactions and hydrogen bonding, could also be analyzed as sources of selectivity of the UCB-F tracer for the three isoforms. The simulations provide atomic details to support future development of new selective tracers targeting synaptic vesicle glycoproteins and their associated diseases.

Practical Three-Component Regioselective Synthesis of Drug-Like 3-Aryl(or heteroaryl)-5,6-dihydrobenzo[h]cinnolines as Potential Non-Covalent Multi-Targeting Inhibitors To Combat Neurodegenerative Diseases.

Neurodegenerative diseases (NDs) are one of the prominent health challenges facing contemporary society, and many efforts have been made to overcome and (or) control it. In this research paper, we described a practical one-pot two-step three-component reaction between 3,4-dihydronaphthalen-1(2H)-one (1), aryl(or heteroaryl)glyoxal monohydrates (2a-h), and hydrazine monohydrate (NH2NH2•H2O) for the regioselective preparation of some 3-aryl(or heteroaryl)-5,6-dihydrobenzo[h]cinnoline derivatives (3a-h). After synthesis and characterization of the mentioned cinnolines (3a-h), the in silico multi-targeting inhibitory properties of these heterocyclic scaffolds have been investigated upon various Homo sapiens-type enzymes, including hMAO-A, hMAO-B, hAChE, hBChE, hBACE-1, hBACE-2, hNQO-1, hNQO-2, hnNOS, hiNOS, hPARP-1, hPARP-2, hLRRK-2(G2019S), hGSK-3ß, hp38α MAPK, hJNK-3, hOGA, hNMDA receptor, hnSMase-2, hIDO-1, hCOMT, hLIMK-1, hLIMK-2, hRIPK-1, hUCH-L1, hPARK-7, and hDHODH, which have confirmed their functions and roles in the neurodegenerative diseases (NDs), based on molecular docking studies, and the obtained results were compared with a wide range of approved drugs and well-known (with IC50, EC50, etc.) compounds. In addition, in silico ADMET prediction analysis was performed to examine the prospective drug properties of the synthesized heterocyclic compounds (3a-h). The obtained results from the molecular docking studies and ADMET-related data demonstrated that these series of 3-aryl(or heteroaryl)-5,6-dihydrobenzo[h]cinnolines (3a-h), especially hit ones, can really be turned into the potent core of new drugs for the treatment of neurodegenerative diseases (NDs), and/or due to the having some reactionable locations, they are able to have further organic reactions (such as cross-coupling reactions), and expansion of these compounds (for example, with using other types of aryl(or heteroaryl)glyoxal monohydrates) makes a new avenue for designing novel and efficient drugs for this purpose.

Deep Learning-Based construction of a Drug-Like compound database and its application in virtual screening of HsDHODH inhibitors.

The process of virtual screening relies heavily on the databases, but it is disadvantageous to conduct virtual screening based on commercial databases with patent-protected compounds, high compound toxicity and side effects. Therefore, this paper utilizes generative recurrent neural networks (RNN) containing long short-term memory (LSTM) cells to learn the properties of drug compounds in the DrugBank, aiming to obtain a new and virtual screening compounds database with drug-like properties. Ultimately, a compounds database consisting of 26,316 compounds is obtained by this method. To evaluate the potential of this compounds database, a series of tests are performed, including chemical space, ADME properties, compound fragmentation, and synthesizability analysis. As a result, it is proved that the database is equipped with good drug-like properties and a relatively new backbone, its potential in virtual screening is further tested. Finally, a series of seedling compounds with completely new backbones are obtained through docking and binding free energy calculations.

Protein-Ligand CH-π Interactions: Structural Informatics, Energy Function Development, and Docking Implementation.

Here, we develop an empirical energy function based on quantum mechanical data for the interaction between methane and benzene that captures the contribution from CH-π interactions. Such interactions are frequently observed in protein-ligand crystal structures, particularly for carbohydrate ligands, but have been hard to quantify due to the absence of a model for CH-π interactions in typical molecular mechanical force fields or docking scoring functions. The CH-π term was added to the AutoDock Vina (AD VINA) scoring function enabling its performance to be evaluated against a cohort of more than 1600 occurrences in 496 experimental structures of protein-ligand complexes. By employing a conformational grid search algorithm, inclusion of the CH-π term was shown to improve the prediction of the preferred orientation of flexible ligands in protein-binding sites and to enhance the detection of carbohydrate-binding sites that display CH-π interactions. Last but not least, this term was also shown to improve docking performance for the CASF-2016 benchmark set and a carbohydrate set.

Thermal Titration Molecular Dynamics (TTMD): Not Your Usual Post-Docking Refinement.

Molecular docking is one of the most widely used computational approaches in the field of rational drug design, thanks to its favorable balance between the rapidity of execution and the accuracy of provided results. Although very efficient in exploring the conformational degrees of freedom available to the ligand, docking programs can sometimes suffer from inaccurate scoring and ranking of generated poses. To address this issue, several post-docking filters and refinement protocols have been proposed throughout the years, including pharmacophore models and molecular dynamics simulations. In this work, we present the first application of Thermal Titration Molecular Dynamics (TTMD), a recently developed method for the qualitative estimation of protein-ligand unbinding kinetics, to the refinement of docking results. TTMD evaluates the conservation of the native binding mode throughout a series of molecular dynamics simulations performed at progressively increasing temperatures with a scoring function based on protein-ligand interaction fingerprints. The protocol was successfully applied to retrieve the native-like binding pose among a set of decoy poses of drug-like ligands generated on four different pharmaceutically relevant biological targets, including casein kinase 1δ, casein kinase 2, pyruvate dehydrogenase kinase 2, and SARS-CoV-2 main protease.

Fosfatase Cdc25B: Interações transientes intramoleculares e complexação com pequenos ligantes / Cdc25B phosphatase: Transient intramolecular interactions and small molecules complexation

Proteínas tirosina-fosfatase (PTPs) possuem papel fundamental na regulação da transdução de sinais e estão envolvidas em diversos processos fundamentais do ciclo celular. As Cdc25 (Cell Division Cycle 25) são fosfatases duais encontradas em todos os organismos eucarióticos e atuam em checkpoints do ciclo celular, permitindo ou inibindo o prosseguimento deste. Este grupo de proteínas pertence à classe de PTPs com atividade baseada em cisteína, apresenta domínio catalítico altamente conservado assim como o motivo catalítico, P-loop. Devido sua função, as Cdc25 são consideradas possíveis alvos terapêuticos para tratamento de câncer e sua interação com pequenas moléculas e inibidores tem sido investigada de forma que análises estruturais e de ligação das Cdc25 com inibidores podem elucidar aspectos importantes do mecanismo de ação destes além de direcionar para o desenho racional de fármacos. Interações cátion-π são interações intra ou intermoleculares não-covalentes que ocorrem entre uma espécie química catiônica, como o grupo guanidino de argininas, e uma das faces de um sistema π rico em elétrons, como dos anéis indólicos de triptofanos. Apesar de pouco discutidas na literatura, quando em comparação às interações não-covalentes mais convencionais, do ponto de vista energético as interações cátion-π são tão importantes na estruturação de proteínas quanto às ligações de hidrogênio ou pontes salinas. De fato estas interações são observadas com frequência em estruturas proteicas resolvidas. O domínio catalítico da Cdc25B possui diversas argininas expostas em sua superfície e um único resíduo de triptofano localizado na região C-terminal flexível, muito próximo do sítio catalítico da proteína. A flexibilidade de proteínas ou de regiões proteicas apresenta importante papel no reconhecimento entre biomoléculas participantes de vias de sinalização e tem sido muito estudada atualmente. Aqui, simulações de dinâmica molecular, experimentos de 1H-15N HSQC RMN, ensaios de cinética de inibição e de ancoragem molecular, evidenciam a existência de contatos cátion-π transientes na superfície de um importante membro da família das Cdc25, a Cdc25B, e de sítios de interação entre inibidores testados e a proteína com destaque a sítios na proximidades do P-loop, região próxima ao C-terminal desordenado, onde se demonstra estabilidade da interação com os pequenos ligantes

Protein tyrosine phosphatase (PTPs) play a fundamental role in the regulation of signal transduction and are involved in several fundamental processes of the cell cycle. Cdc25 (Cell Division Cycle 25) are dual phosphatases found in all eukaryotic organisms and act at checkpoints of the cell cycle, allowing or inhibiting its progression. This group of proteins belongs to the class of PTPs with cysteine-based activity, presenting a highly conserved catalytic domain as well as the catalytic motif, P-loop. Due to their function, Cdc25 are considered possible therapeutic targets for cancer treatment and their interaction with small molecules and inhibitors has been investigated so that structural and binding analyzes of Cdc25 with inhibitors can elucidate important aspects of their mechanism of action besides directing to rational drug design. Cation-π interactions are non-covalent intra- or intermolecular interactions that occur between a cationic chemical species, such as the guanidino group of arginines, and one of the faces of an electron-rich system, such as the indole rings of tryptophans. Although little discussed in the literature, when compared to more conventional non-covalent interactions, from the energetic point of view, cation-π interactions are as important in the structuring of proteins as hydrogen bonds or salt bridges. In fact, these interactions are frequently observed in solved protein structures. The catalytic domain of Cdc25B has several arginines exposed on its surface and a single tryptophan residue located in the flexible C-terminal region, very close to the catalytic site of the protein. The flexibility of proteins or protein regions plays an important role in the recognition between biomolecules participating in signaling pathways and has been extensively studied today. Here, molecular dynamics simulations, 1H-15N HSQC NMR experiments, inhibition kinetics and molecular anchoring assays, evidence the existence of transient cation-π contacts on the surface of an important member of the Cdc25 family, Cdc25B, and of sites of interaction between tested inhibitors and the protein, with emphasis on sites in the vicinity of the P-loop, a region close to the disordered C-terminus, where stability of the interaction with the small ligands is demonstrated

Structure-based discovery of nonopioid analgesics acting through the α2A-adrenergic receptor.

Because nonopioid analgesics are much sought after, we computationally docked more than 301 million virtual molecules against a validated pain target, the α2A-adrenergic receptor (α2AAR), seeking new α2AAR agonists chemotypes that lack the sedation conferred by known α2AAR drugs, such as dexmedetomidine. We identified 17 ligands with potencies as low as 12 nanomolar, many with partial agonism and preferential Gi and Go signaling. Experimental structures of α2AAR complexed with two of these agonists confirmed the docking predictions and templated further optimization. Several compounds, including the initial docking hit '9087 [mean effective concentration (EC50) of 52 nanomolar] and two analogs, '7075 and PS75 (EC50 4.1 and 4.8 nanomolar), exerted on-target analgesic activity in multiple in vivo pain models without sedation. These newly discovered agonists are interesting as therapeutic leads that lack the liabilities of opioids and the sedation of dexmedetomidine.

Effects of Vitexin, a Natural Flavonoid Glycoside, on the Proliferation, Invasion, and Apoptosis of Human U251 Glioblastoma Cells.

Glioblastoma is a highly aggressive brain tumor characterized by high recurrence and poor prognosis. Vitexin has shown activities against esophageal, liver, lung, colorectal, and ovarian cancers; however, there is little knowledge on the activity of vitexin against glioblastoma. This study was therefore designed with aims to examine the effects of vitexin on proliferation, invasion, and apoptosis of human U251 glioblastoma cells and explore the underlying molecular mechanisms using mRNA sequencing and molecular docking. Vitexin was found to inhibit cell proliferation, colony formation, and invasion and promote apoptosis in U251 cells. mRNA sequencing identified 499 differentially expressed genes in vitexin-treated U251 cells relative to controls, including 154 upregulated genes and 345 downregulated genes. Gene ontology (GO) term enrichment analysis revealed that the upregulated genes were most significantly enriched in intrinsic apoptotic signaling pathway and the downregulated genes were most significantly enriched in positive regulation of cell development and positive regulation of locomotion relating to biological processes, endoplasmic reticulum lumen and side of membrane relating to cellular components, and receptor ligand activity and receptor regulator activity relating to molecular functions. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis revealed that the upregulated genes were involved in the pathways of transcriptional misregulation in cancer and the downregulated genes were involved in FoxO and JAK/STAT signaling pathways. Western blotting assay revealed that vitexin treatment resulted in reduced p-JAK1, p-JAK3, and p-STAT3 protein expression in U251 cells relative to untreated controls, and molecular docking predicted that vitexin had docking scores of -8.8, -10.8, and -10.5 kJ/mol with STAT3, JAK1, and JAK2, respectively. The results of the present study demonstrate that vitexin inhibits the proliferation and invasion and induces the apoptosis of glioblastoma U251 cells through suppressing the JAK/STAT3 signaling pathway, and vitexin may be a promising potential agent for the chemotherapy of glioblastoma.

Avaliação in vitro e in silico da atividade do S-(-)-Álcool Perílico sobre linhagens celulares do Carcinoma Epidermóide de Língua / In vitro and in silico evaluation of the activity of S-(-)-Peryllic Alcohol on Tongue Squamous Carcinoma cell lines

O carcinoma epidermóide oral (CEO) é a neoplasia maligna mais frequente da cavidade oral e constitui um problema de saúde pública devido a sua alta taxa de incidência e mortalidade devido em muitos casos ao fracasso terapêutico e a resistência tumoral. Assim sendo, destaca-se a busca por novas moléculas biologicamente ativas, como as encontradas nos produtos de origem natural. Este trabalho tem como objetivo avaliar a atividade antineoplásica do S-(-)-álcool perílico (POH) em culturas de células de CEO de língua e predizer sua afinidade através de modelo computacional sobre proteínas que regulam o ciclo celular. Para isso, foram utilizadas duas linhagens celulares de CEO de língua, HSC-3 e SCC-25. Os seguintes grupos foram analisados: G0 (controle; células cultivadas na ausência de POH), G1 (células tratadas com cisplatina a 40 µM), G2 (células tratadas com POH a 0,5 mM), G3 (células tratadas com POH a 1,0 mM), G4 (células tratadas com POH a 1,5 mM) e G5 (células tratadas com POH a 3,0 mM). Diferenças entre estes grupos foram investigadas através dos seguintes ensaios: viabilidade celular (Alamar Blue e Live/Dead assay) e atividade migratória (Wound healing). Foi também realizada a predição de afinidade entre o POH e as moléculas de controle do ciclo celular utilizando a docagem molecular com emprego do software Molegro Virtual Docker, v. 6.0.1. Os dados foram tratados estatisticamente pelo GraphPad Prism 6.0 (GraphPad Software, EUA), análises paramétricas utilizando teste Anova, pós-teste de Tukey e teste estatístico não-paramétricos de Kruskal-Wallis, seguido pelo teste t de estudent foram adotados para determinação de diferenças entre os grupos experimentais. O índice de significância considerado neste trabalho foi de 5%. Para ambas as técnicas de avaliação da viabilidade celular (Alamar Blue e Live/dead assay) analisadas neste trabalho, o POH foi capaz de reduzir a viabilidade celular de linhagens do CEO de língua de maneira dosedependente e tempo-dependente (p<0,05). As concentrações de 1,5 mM e 3 mM do POH obtiveram resultados melhores ou semelhantes aos encontrados na cisplatina 40 µM, para as duas linhagens, na avaliação da viabilidade celular (p<0,05). Os valores de IC50 do POH foram de 1,5 mM para a célula SCC-25 em todos os intervalos de tempo (24 h, 48 h e 72 h), uma vez que, para a linhagem HSC-3, foram de 3 mM para os tempos de 24 h e 48 h e de 1,5 mM para o intervalo de 72 h. O POH foi capaz de inibir a migração das duas linhagens celulares de CEO de maneira dependente da concentração (p≤0,05), comparados ao grupo controle. A habilidade da molécula POH se ligar a proteínas responsáveis pela ativação do ciclo celular foi avaliada usando docking models. Dentre elas, a proteína GTPase Kras mostrou a melhor energia de ligação (-86.70 kcal/mol), apresentando ligações de hidrogênio com os resíduos THR58 (A) e ASP57 (A) e ligações estéricas com os resíduos TRY32 (A) e ALA18 (A). As evidências deste estudo corroboram a ideia de que o POH possui atividade sobre o CEO, sugerindo que essa molécula possa ser uma forte candidata para o desenvolvimento de medicamentos direcionados ao tratamento desta patologia (AU).

Oral squamous cell carcinoma (OSCC) is the most frequent malignant neoplasm of the oral cavity and constitutes a public health problem due to its high incidence and mortality rate caused in many cases by therapeutic failure and tumor resistance. Therefore, the search for new biologically active molecules stands out, such as those found in products of natural origin. This work aims to evaluate the antineoplastic activity of S-(-)-perillyl alcohol (POH) in cell cultures of tongue CEO and to predict its affinity through a computer model on proteins that regulate the cell cycle. For this purpose, two cell lines of tongue CEO were used, HSC-3 and SCC-25. The following groups were analyzed: G0 (control; cells cultured in the absence of POH), G1 (cells treated with 40 µM cisplatin), G2 (cells treated with 0.5 mM POH), G3 (cells treated with 1 .0 mM), G4 (cells treated with 1.5 mM POH) and G5 (cells treated with 3.0 mM POH). Differences between these groups were investigated through the following assays: cell viability (Alamar Blue and Live/Dead assay) and migratory activity (Wound healing). Affinity prediction between POH and cell cycle control molecules were also performed using molecular docking using Molegro Virtual Docker, v. 6.0.1. The data was statistically treated by GraphPad Prism 6.0 (GraphPad Software, USA), parametric analysis using Anova test, Tukey post-test and Kruskal-Wallis non-parametric statistical test, followed by t student test were adopted for determination of differences between the experimental groups. The significance index considered in this work was 5%. For both cell viability assessment techniques (Alamar Blue and Live/dead assay) analyzed in this work, POH was able to reduce the cell viability of tongue CEO lines in a dose-dependent and time-dependent manner (p<0 .05). The concentrations of 1.5 mM and 3 mM of POH obtained better or similar results to those found in 40 µM cisplatin, for the two strains, in the evaluation of cell viability (p<0.05). The IC50 values of POH were 1.5 mM for the SCC-25 cell at all time intervals (24 h, 48 h and 72 h), since for the HSC-3 line they were 3 mM for 24 h and 48 h times and 1.5 mM for the 72 h interval. POH was able to inhibit the migration of the two DSC cell lines in a concentration-dependent manner (p≤0.05), compared to the control group. The ability of the POH molecule to bind to proteins responsible for cell cycle activation was evaluated using docking models. Among them, the protein GTPase Kras showed the best binding energy (-86.70 kcal/mol), featuring hydrogen bonds with residues THR58 (A) and ASP57 (A) and steric bonds with residues TRY32 (A) and ALA18 ( THE). The evidence from this study supports the idea that POH has antineoplastic activity on the CEO, suggesting that this molecule may be a strong candidate for the development of drugs aimed at the treatment of this pathology (AU).

Interaction between miR4749 and Human Serum Albumin as Revealed by Fluorescence, FRET, Atomic Force Spectroscopy and Computational Modelling.

The interaction of Human Serum Albumin (HSA) with the microRNA, miR4749, was investigated by Atomic Force Spectrscopy (AFS), static and time-resolved fluorescence spectroscopy and by computational methods. The formation of a HSA/miR4749 complex with an affinity of about 104 M-1 has been assessed through a Stern-Volmer analysis of steady-state fluorescence quenching of the lone Trp residue (Trp214) emission of HSA. Förster Resonance Energy Transfer (FRET) measurements of fluorescence lifetime of the HSA/miR4749 complex were carried out in the absence and in the presence of an acceptor chromophore linked to miR4749. This allowed us to determine a distance of 4.3 ± 0.5 nm between the lone Trp of HSA and the dye bound to miR4749 5p-end. Such a distance was exploited for a screening of the possible binding sites between HSA and miR4749, as predicted by computational docking. Such an approach, further refined by binding free energy calculations, led us to the identification of a consistent model for the structure of the HSA/miR4749 complex in which a positively charged HSA pocket accommodates the negatively charged miRNA molecule. These results designate native HSA as a suitable miRNA carrier under physiological conditions for delivering to appropriate targets.

A Pre-clinical Trial Study: Anti-human Colon Cancer Effect of Thalassiolin B in vitro with Enzymes Inhibition Effects and Molecular Docking Studies.

In this study, it is recorded the inhibition effect of Thalassiolin B on aldose reductase, alpha-glucosidase and alpha-amylase enzymes. In the next step, the molecular docking method was used to compare the biological activities of the Thalassiolin B molecule against enzymes formed from the assembly of proteins. In these calculations, the enzymes used are Aldose reductase, Alpha-Amylase, and Alpha-Glucosidase, respectively. After the docking method, ADME/T analysis of Thalassiolin B molecule was performed to be used as a drug in the pharmaceutical industry. In the MTT assay, the anti-human colon cancer properties of Thalassiolin B against EB, LS1034, and SW480 cell lines were investigated. The cell viability of Thalassiolin B was very low against human colon cancer cell lines without any cytotoxicity on the human normal (HUVEC) cell line. The IC50 of the Thalassiolin B against EB, LS1034, and SW480 were 483, 252, and 236 µg/mL, respectively. Thereby, the best cytotoxicity results and anti-human colon cancer potentials of our Thalassiolin B were observed in the case of the SW480 cell line. Maybe the anti-human colon cancer properties of Thalassiolin B are related to their antioxidant effects.

Thymus fontanesii attenuates CCl4-induced oxidative stress and inflammation in mild liver fibrosis.

Liver injury is a major public health problem all over the world that raises the demand of developing novel effective and safe remedies. Traditionally, Thyme (Thymus fontanesii) has a therapeutic potential against different organs toxicity due to its antioxidant activity. The present study aimed to evaluate the antioxidant activities in vitro and the possible hepato-protective effects of T. fontanesii aqueous extract (TFAE) against CCl4 induced liver damage (mild fibrosis) in male albino mice and annotate its phytochemical constituents as well. The extract displayed substantial antioxidant activities in vitro and high content of flavonoids and other phenolic compounds. Oral administration of TFAE (especially high dose) significantly suppressed (but with different degrees) the incidence and severity of CCl4 liver toxicity by activating the hepatic antioxidant defense mechanisms, modulating hepatic functions, and decreasing the production of lipid peroxidation, pro-inflammatory mediators, and pro-fibrotic proteins expression including COL1A1, Fn, and TGF-ß1. These activities might be attributed to the presence of 58 secondary metabolites (identified by LC-MS), mainly phenolic acids, flavonoids and diterpenoids that were able, according to molecular docking, to bind to the inhibitor's binding site of three protein targets involved in liver inflammation and fibrosis. These results showcase the antioxidant and anti-inflammatory properties of Thyme (Thymus fontanesii), illustrate the protective and beneficial effects of the plant against CCl4-induced hepatic toxicity in mice, and support its consumption, traditional uses and promotes its valorization as nutraceutical product.

Molecular Docking and Molecular Dynamics Simulations Discover Curcumin Analogue as a Plausible Dual Inhibitor for SARS-CoV-2.

Recently, the world has been witnessing a global pandemic with no effective therapeutics yet, while cancer continues to be a major disease claiming many lives. The natural compound curcumin is bestowed with multiple medicinal applications in addition to demonstrating antiviral and anticancer activities. In order to elucidate the impact of curcumin on COVID-19 and cancer, the current investigation has adapted several computational techniques to unfold its possible inhibitory activity. Accordingly, curcumin and similar compounds and analogues were retrieved and assessed for their binding affinities at the binding pocket of SARS-CoV-2 main protease and DDX3. The best binding pose was escalated to molecular dynamics simulation (MDS) studies to assess the time dependent stability. Our findings have rendered one compound that has demonstrated good molecular dock score complemented by key residue interactions and have shown stable MDS results inferred by root mean square deviation (RMSD), radius of gyration (Rg), binding mode, hydrogen bond interactions, and interaction energy. Essential dynamics results have shown that the systemadapts minimum energy conformation to attain a stable state. The discovered compound (curA) could act as plausible inhibitor against SARS-CoV-2 and DDX3. Furthermore, curA could serve as a chemical scaffold for designing and developing new compounds.

Identification of Potential Antiviral Inhibitors from Hydroxychloroquine and 1,2,4,5-Tetraoxanes Analogues and Investigation of the Mechanism of Action in SARS-CoV-2.

This study aimed to identify potential inhibitors and investigate the mechanism of action on SARS-CoV-2 ACE2 receptors using a molecular modeling study and theoretical determination of biological activity. Hydroxychloroquine was used as a pivot structure and antimalarial analogues of 1,2,4,5 tetraoxanes were used for the construction and evaluation of pharmacophoric models. The pharmacophore-based virtual screening was performed on the Molport® database (~7.9 million compounds) and obtained 313 structures. Additionally, a pharmacokinetic study was developed, obtaining 174 structures with 99% confidence for human intestinal absorption and penetration into the blood-brain barrier (BBB); posteriorly, a study of toxicological properties was realized. Toxicological predictions showed that the selected molecules do not present a risk of hepatotoxicity, carcinogenicity, mutagenicity, and skin irritation. Only 54 structures were selected for molecular docking studies, and five structures showed binding affinity (ΔG) values satisfactory for ACE2 receptors (PDB 6M0J), in which the molecule MolPort-007-913-111 had the best ΔG value of -8.540 Kcal/mol, followed by MolPort-002-693-933 with ΔG = -8.440 Kcal/mol. Theoretical determination of biological activity was realized for 54 structures, and five molecules showed potential protease inhibitors. Additionally, we investigated the Mpro receptor (6M0K) for the five structures via molecular docking, and we confirmed the possible interaction with the target. In parallel, we selected the TopsHits 9 with antiviral potential that evaluated synthetic accessibility for future synthesis studies and in vivo and in vitro tests.

Mutation in the CX3C Motif of G Protein Disrupts Its Interaction with Heparan Sulfate: A Calorimetric, Spectroscopic, and Molecular Docking Study.

Respiratory syncytial virus (RSV) is the leading cause of lower respiratory tract infection in children and infants. To date, there is no effective vaccine available against RSV. Heparan sulfate is a type of glycosaminoglycan that aids in the attachment of the RSV to the host cell membrane via the G protein. In the present study, the effect of amino acid substitution on the structure and stability of the ectodomain G protein was studied. Further, it was investigated whether mutation (K117A) in the CX3C motif of G protein alters the binding with heparan sulfate. The point mutation significantly affects the conformational stability of the G protein. The mutant protein showed a low binding affinity with heparan sulfate as compared to the wild-type G protein, as determined by fluorescence quenching, isothermal titration calorimetry (ITC), and molecular docking studies. The low binding affinity and decreased stability suggested that this mutation may play an important role in prevention of attachment of virion to the host cell receptors. Collectively, this investigation suggests that mutation in the CX3C motif of G protein may likely improve the efficacy and safety of the RSV vaccine.

Neuropsychopharmacology of Emerging Drugs of Abuse: meta- and para-Halogen-Ring-Substituted α-PVP ("flakka") Derivatives.

Changes in the molecular structure of synthetic cathinones has led to an increase in the number of novel emerging drugs in the illicit drug market at an unprecedented rate. Unfortunately, little is known about the neuropsychopharmacology of recently emerged halogen-substituted α-PVP derivatives. Thus, the aim of this study was to investigate the role of para- and meta-halogen (F-, Cl-, and Br-) substitutions on the in vitro, in silico, and in vivo effects of α-pyrrolidinopentiophenone (α-PVP) derivatives. HEK293 cells expressing the human dopamine or serotonin transporter (hDAT and hSERT) were used for the uptake inhibition and transporter affinity assays. Molecular docking was used to model the interaction mechanism against DAT. Swiss CD-1 mice were used for the horizontal locomotor activity, open field test, and conditioned place preference paradigm. All compounds demonstrated potent DA uptake inhibition and higher DAT selectivity than cocaine. Meta-substituted cathinones showed higher DAT/SERT ratios than their para- analogs, which correlates with an increased psychostimulant effect in vivo and with different meta- and para-in silico interactions at DAT. Moreover, all compounds induced rewarding and acute anxiogenic effects in mice. In conclusion, the present study demonstrates the role of meta- and para-halogen substitutions in the mechanism of action and provides the first evidence of the rewarding and anxiety-like properties of halogenated α-PVP derivatives.

Commikuanoids A-C: New cycloartane triterpenoids with exploration of carbonic anhydrase-II inhibition from the resins of Commiphora kua by in vitro and in silico molecular docking.

Three new cycloartane triterpenoids, commikuanoids A-C (1-3), together with four known compounds 4-7, were isolated from the resin of Commiphora kua. Their structures were confirmed by advanced NMR techniques such as 1D (1H and 13C) and 2D (HMBC, HSQC, COSY, NOESY and NOE) and high-resolution mass spectrometry (HRMS). Five compounds (1-5) were screened for in vitro carbonic anhydrase II (CA II) inhibitory activity. All the tested compounds demonstrated significant activity against CA II with IC50 values ranging from 4.9-19.6 µM. Moreover, the binding pattern of each compound in the binding site of CA-II was predicted through in silico molecular docking approach. It was observed that compounds 2, 4, and 5 binds with the Zn ion present in the active site of CA II, while compounds 1 and 3 mediated hydrogen bonding with Thr199 of CA-II, and all the compounds showed good binding score (> - 5 kcal/mol).

Analysis of the active components and mechanism of Shufeng Jiedu capsule against COVID-19 based on network pharmacology and molecular docking.

ABSTRACT: This study investigates the active components and mechanism of Shufeng Jiedu Capsules (SFJDC) against novel coronavirus through network pharmacology and molecular docking.The TCMSP, TCMID, and BATMAN-TCM databases were used to retrieve the components of SFJDC. The active components were screened by ADME (absorption, distribution, metabolism, and excretion) parameters, and identified by Pubchem, Chemical Book, and ChemDraw softwares. The molecular docking ligands were constructed. SARS Coronavirus-2 Major Protease (SARS-CoV-2-Mpro) and angiotension converting enzyme 2 (ACE2) were used as molecular docking receptors. AutoDock software was used for molecular docking. Cytoscape 3.7.1 software was used to generate an herbs-active components-targets network. Gene Ontology gene function and Kyoto Encyclopedia of Genes and Genomes signal pathway analysis were performed by DAVID data.A total of 1244 components were identified from SFJDC, and 210 active components were obtained. Among them, 97 active components were used as docking ligands to dock with SARS-CoV-2-Mpro and ACE2. There were 48 components with good binding activity to SARS-CoV-2-Mpro. Ten active components (including 7-Acetoxy-2-methylisoflavone, Kaempferol, Quercetin, Baicalein, Glabrene, Glucobrassicin, Isoglycyrol, Wogonin, Petunidin, and Luteolin) combined with SARS-CoV-2-Mpro and ACE2 simultaneously. Among them, Kaempferol, Wogonin, and Baicalein showed higher binding activity. The herbs-active components-targets network contained 7 herbs, 10 active components, and 225 targets. The 225 target targets were involved in 653 biological processes of Gene Ontology analysis and 130 signal pathways (false discovery rate ≤ 0.01) of Kyoto Encyclopedia of Genes and Genomes analysis.The active components of SFJDC (such as Kaempferol, Wogonin, and Baicalein) may combine with ACE2 and act on multiple signaling pathways and targets to exert therapeutic effect on novel coronavirus.

Biocompatible silver(I) complexes with heterocyclic thioamide ligands for selective killing of cancer cells and high antimicrobial activity - A combined in vitro and in silico study.

A series of heteroleptic Ag(I) complexes bearing 4,6-dimethyl-2-pyrimidinethiol (dmp2SH), i.e., [AgCl(dmp2SH)(PPh3)2] (1), [Ag(dmp2SH)(PPh3)2]NO3 (2), [Ag(dmp2SΗ)(xantphos)]NO3 (3), [Ag(µ-dmp2S)(PPh3)]2 (4), [Ag(dmp2S)(xantphos)] (5), [Ag(µ-dmp2S)(DPEphos)]2 (6) (xantphos = 4,5-bis(diphenylphosphino)-9,9-dimethylxanthene and DPEPhos = bis[(2-diphenylphosphino)phenyl]ether) were synthesized. The complexes display systematic variation of particular structural characteristics which were proved to have a significant impact on their in vitro cytotoxicity and antimicrobial properties. A moderate-to-high potential for bacteria growth inhibition was observed for all complexes, with 2, 3 and 5 being particularly effective against Gram-(+) bacteria (IC50 = 1.6-4.5 µM). The three complexes exhibit high in vitro cytotoxicity against HeLa and MCF-7 cancer cells (IC50 = 0.32-3.00 µΜ), suggesting the importance of coordination unsaturation and cationic charge for effective bioactivity. A very low cytotoxicity against HDFa normal cells was observed, revealing a high degree of selectivity (selectivity index ~10) and, hence, biocompatibility. Fluorescence microscopy using 2 showed effective targeting on the membrane of the HeLa cancer cells, subsequently inducing cell death. Binding of the complexes to serum albumin proteins is reasonably strong for potential uptake and subsequent release to target sites. A moderate in vitro antioxidant capacity for free radicals scavenging was observed and a low potential to destroy the double-strand structure of calf-thymus DNA by intercalation, suggesting likely implication of these properties in the bioactivity mechanisms of these complexes. Further insight into possible mechanisms of bioactivity was obtained by molecular modeling calculations, by exploring their ability to act as potential inhibitors of DNA-gyrase, human estrogen receptor alpha, human cyclin-dependent kinase 6, and human papillomavirus E6 oncoprotein.

Comprehensive Analysis of Tripterine Anti-Ovarian Cancer Effects Using Weighted Gene Co-Expression Network Analysis and Molecular Docking.

BACKGROUND Ovarian cancer has the highest mortality of gynecological cancers worldwide. The aim of this study was to identify the role of tripterine against ovarian cancer. MATERIAL AND METHODS GSE18520 and GSE12470 data sets were downloaded from the GEO database. WGCNA was used to analyze gene modules and hub genes related to ovarian cancer. These hub genes were intersected with tripterine targets, and GO and KEGG enrichment analyses were performed. HPA and GEPIA determined the expression of tripterine anti-ovarian hub genes in tumor tissues. Kaplan-Meier plotter was used to explore the role of hub genes in ovarian cancer prognosis. AutoDock was used to conduct molecular docking of tripterine and hub genes to observe whether the combination was stable. RESULTS By differential analysis of gene expression and the construction of WGCNA co-expression network, 5 hub genes, ARHGAP11A, MUC1, HBB, RUNX1T1, and FUT8, were screened by module gene screening. Seven biological processes and 20 KEGG-related pathways were obtained by gene enrichment. The expression of tripterine anti-ovarian hub genes ARHGAP11A, MUC1, and FUT8 were obtained by HPA and GEPIA. Using Kaplan-Meier plotter, the survival of ovarian cancer was negatively correlated with ARHGAP11A, MUC1, and FUT8. Molecular docking showed the combination of tripterine and FUT8 was most stable, having the greatest potential role. CONCLUSIONS Tripterine may be involved in megakaryocyte development and platelet production through potential genes ARHGAP11A, MUC1, HBB, RUNX1T1, and FUT8 and may have an anti-ovarian cancer effect in immune factors signaling, transporting and exchanging oxygen pathways, and autophagy pathways, through these 5 key genes.