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Background: Diabetes is a significant health problem that has reached worrisome proportions: almost half of the world's population now has diabetes. Diabetes mellitus, or diabetes, is a severe, long-term disease in which a person's blood glucose levels are elevated due to their body's inability to make any or enough insulin, or to properly utilise the insulin that it does produce. The chemicals extracted from medicinal plants were shown to be both safer and more bioactive than manufactured medicines. Objective: The goal of this research was to use molecular docking to find possible binding affinities of luteolin, a phytocompound from Rumex vesicarius L, to five target proteins, in order to find the lead molecule against diabetes. Methodology: One chemical was isolated from Rumex vesicarius L. leaves in this research. The binding affinity of the complexes was calculated using molecular docking studies. The docking procedure was carried out using AutoDock Tools 1.5.6, which brought the ligand together with the target proteins. Results: The binding energies of Luteolin with major Glutamine-fructose-6-phosphate amido transferase (GFAT1), Pancreatic α-Amylase, Forkhead box protein O1(FOX01), α--glucosidase, and Dipeptidyl peptidase-4 (DPP-4) were determined to be -6.89, -6.80, -6.36, -9.35, and -7.72 kcal. Conclusion: Our findings suggest that luteolin can target not only α--glucosidase but also DPP4 and other targets, suggesting that they may be used as type 2 diabetes mellitus inhibitors. We believe that this phytochemical, luteolin, may be utilised in preclinical studies as an anti-diabetic drug to combat diabetes mellitus.

Introoduction: Inhibition of the reverse transcriptase (RT) enzyme of the human immunodeficiency virus (HIV) by low molecular weight inhibitors is still an active area of research. Here, protein-ligand interactions and possible binding modes of novel compounds with the HIV-1 RT binding pocket (the wild-type as well as Y181C and K103N mutants) were obtained and discussed. Methods: A molecular fragment-based approach using FDA-approved drugs were followed to design novel chemical derivatives using delavirdine, efavirenz, etravirine and rilpivirine as the scaffolds. The drug-likeliness of the derivatives was evaluated using Swiss-ADME. The parent molecule and derivatives were then docked into the binding pocket of related crystal structures (PDB ID: 4G1Q, 1IKW, 1KLM and 3MEC). Genetic Optimization for Ligand Docking (GOLD) Suite 5.2.2 software was used for docking and the results analyzed in the Discovery Studio Visualizer 4. A derivative was chosen for further analysis, if it passed drug-likeliness and the docked energy was more favorable than that of its parent molecule. Out of the fifty-seven derivatives, forty-eight failed in drug-likeness screening by Swiss-ADME or at the docking stage. Results: The final results showed that the selected compounds had higher predicted binding affinities than their parent scaffolds in both wild-type and the mutants. Binding energy improvement was higher for the structures designed based on second-generation NNRTIs (etravirine and rilpivirine) than the first-generation NNRTIs (delavirdine and efavirenz). For example, while the docked energy for rilpivirine was -51 KJ/mol, it was improved for its derivatives RPV01 and RPV15 up to - 58.3 and -54.5 KJ/mol, respectively. Conclusion: In this study, we have identified and proposed some novel molecules with improved binding capacity for HIV RT using fragment-based approach.

Introduction: Lactoperoxidase (LPO) is a member of the mammalian heme peroxidase family and is an enzyme of the innate immune system. It possesses a covalently linked heme prosthetic group (a derivative of protoporphyrin IX) in its active site. LPO catalyzes the oxidation of halides and pseudohalides in the presence of hydrogen peroxide (H2O2) and shows a broad range of the antimicrobial activity. Methods: In this study, we have used two pharmaceutically important drug molecules, namely dapsone and propofol, which were earlier reported as potent inhibitors of LPO. At the same time, the stereochemistry and mode of binding of dapsone and propofol to LPO are still not known because of the lack of the crystal structures of LPO with these two drugs. In order to fill this gap, we utilized molecular docking and molecular dynamics (MD) simulation studies of LPO in its native and complex forms with dapsone and propofol. Results: From the docking results, the estimated binding free energies (ΔG) of -9.25 kcal/mol (Ki = 0.16 μM) and -7.05 kcal/mol (Ki = 6.79 μM) were observed for dapsone, and propofol, respectively. The standard error of the Auto Dock program is 2.5 kcal/mol; therefore, molecular docking results alone were inconclusive. Conclusion: To further validate the docking results, we performed MD simulation on unbound, and two drugs bounded LPO structures. Interestingly, MD simulations results explained that the structural stability of LPO-Propofol complex was higher than LPO-Dapsone complex. The results obtained from this study establish the mode of binding and interaction pattern of the dapsone and propofol to LPO as inhibitors.

Aims: Glucokinase (GK) is a cytoplasmic enzyme that metabolizes the glucose to glucose- 6-phosphate and supports the adjusting of blood glucose levels within the normal range in humans. In pancreatic β-cells, it plays a leading role by governing the glucose-stimulated secretion of insulin and in liver hepatocyte cells, it controls the metabolism of carbohydrates. GK acts as a promising drug target for the treatment of patients with type 2 diabetes mellitus (T2DM). Study Design: In the current study, the goal is to identify new substituted benzamide derivatives and test them via molecular docking as possible anti-diabetic drugs. Place and Duration of Study: The present work has been carried out at S.N.J.B’s S.S.D.J. College of Pharmacy, Neminagar, Chandwad, Nashik, Maharashtra, India during the time period of December-2020 to February-2021. Methodology: This work involved designing novel methyl 2-((4-(benzamido)phenyl)sulfanyl)-1,2,3,4-tetrahydro-6-methylpyrimidine-5-carboxylate derivatives and their screening by molecular docking studies to determine the binding interactions for the best-fit conformations in the binding site of the GK enzyme. Autodockvina 1.1.2 in PyRx 0.8 was used to perform the docking studies of all the designed novel derivatives and native ligand against the crystal structure of GK. Based on the results of docking studies, the selected molecules will be tested for their antidiabetic activity in the animal models. Results: Amongst the designed derivatives, compounds A2, A3, A8, A10, A11, A13, A14, A16, A17, and A18 have shown better binding free energy (between -8.7 to -10.3 kcal/mol) than the native ligand present in the enzyme structure. In present investigation, many molecules had formed strong hydrogen bond with Arg-63 which indicate the potential to activate GK. Conclusion: From above results it has been observed that these designed benzamide derivatives have potential to activate the human GK which enables us to proceed for the syntheses of these derivatives.

In the present communication, a simple and facile method was adopted to synthesize a series of novel 2-[(2-{[5-(pyridin-4-yl)-1,3,4-oxadiazol-2-yl]sulfanyl}ethyl)sulfanyl]-1,3-benzoxazole by fusing 5-(pyridin-4-yl)-1,3,4-oxadiazole-2-thiol with substituted 2-[(2-bromoethyl)sulfanyl]-1,3-benzoxazole and 2-[(2-chloroethyl)sulfanyl]-1,3-benzoxazole to obtain heterocyclic ring systems of 1,3,4 oxadiazole linked benzoxazole moiety. The synthesized compounds were characterized by the aid of LCMS, IR, 1H NMR, 13CNMR, and C, H, N analysis technique. All the newly synthesized compounds were assessed for antimicrobial, antioxidant and antitubercular activities against standard strains. Microbiological results showed that the compounds showcased a wide range of activities and further the results of antimicrobial, antioxidant and molecular docking studies revealed that the compounds 6c, 6d and 6e are more potent and displays excellent docking scores with various amino acids interaction like alkyl-alkyl, pi-alkyl and hydrogen bonding of antitubercular receptor H37R with benzoxazole moieties and displayed encouraging antitubercular results to 6c, 6d and 6e molecules. The structural activity relationship studies illuminated the obtained results.

The pivotal role of the myeloid ecotropic viral integration site 1 (MEIS1) transcriptional factor was reported in cardiac regeneration and hematopoietic stem-cell (HSC) regulation with our previous findings. MEIS1 as a promising target in the context of pharmacological inhibition, we identified a potent myeloid ecotropic viral integration site (MEIS) inhibitor, MEISi-1, to induce murine and human HSC expansion ex vivo and in vivo. In this work, we performed lead optimization on MEISi-1 by synthesizing 45 novel analogues. Structure-activity relationship studies revealed the significance of a para-methoxy group on ring A and a hydrophobic moiety at the meta position of ring B. Obtained biological data were supported by inhibitor docking and molecular dynamics simulation studies. Eleven compounds were depicted as potent inhibitors demonstrating a better inhibitory profile on MEIS1 and target genes Meis1, Hif-1 alpha, and p21. Among those, 4h, 4f, and 4b were the most potent inhibitors. The predicted pharmacokinetics properties fulfill drug-likeness criteria. In addition, compounds exerted neither cytotoxicity on human dermal fibroblasts nor mutagenicity.

Based on tyrosinase inhibition science, two pyrimidine derivatives were designed and studied. Docking of 2-dibenzylamine-5-hydroxy pyrimidine (dba5HP) and 2-benzylamino-5-hydroxy pyrimidine (ba5HP) on mushroom tyrosinase (MT) showed that the former could not occupy MT active site pocket, while ba5HP could do so (Moldock score = − 63.95). MD simulation revealed that the complex of ba5HP-MT reached stability

The development of new, more selective, environmental-friendly insecticide alternatives is in high demand for the control of Spodoptera frugiperda (S. frugiperda). The major objective of this work was to search for new potential S. frugiperda acetylcholinesterase (AChE) inhibitors. A ligand-based virtual screening was initially carried out considering six scaffolds derived from eugenol and the ZINC15, PubChem, and MolPort databases. Subsequently, molecular docking analysis of the selected compounds on the active site and a second region (determined by blind molecular docking) of the AChE of S. frugiperda was performed. Molecular dynamics and Molecular Mechanics Poisson–Boltzmann Surface Area analyses were also applied to improve the docking results. Finally, three new eugenol analogs were evaluated in vitro against S. frugiperda larvae. The virtual screening identified 1609 compounds from the chemical libraries. Control compounds were selected from the interaction fingerprint by molecular docking. Only three new eugenol analogs (1, 3, and 4) were stable at 50 ns by molecular dynamics. Compounds 1 and 4 had the best biological activity by diet (LC50 = 0.042 mg/mL) and by topical route (LC50 = 0.027 mg/mL), respectively. At least three new eugenol derivatives possessed good-to-excellent insecticidal activity against S. frugiperda.

Aim: Currently, researchers have developed a lot of new active substances as anti-inflammatory agents. One of the target proteins for anti-inflammatory agents is the selective COX-2 active site. Selective COX-2 inhibition is the regulator of the inflammatory reaction cascade. In this research, 3, 4- Dihydropyrimidone derivatives were used to design the anti-inflammatory agent through a selective COX-2 inhibition. The potential activity of 3, 4- Dihydropyrimidone derivatives maybe increase due to the preparation of the Schiff base with aromatic aldehydes. Selective COX-2 inhibition was required to predict their anti-inflammatory activity so, the aim in the present study, molecular docking study of 3,4- dihydropyrimidone derivatives have performed using COX-2 enzyme active site. Methodology: The molecular docking of 3, 4-dihydropyrimidone derivatives were carried out using AutoDock vina Ver.1.1.2. Twenty 3,4-dihydropyrimidone derivatives were docked into the COX-2 active site with Protein data bank code 3LN1. The interactions were evaluated based on the docking score. Celecoxib was used as the reference standard for this study. Results: Twenty 3, 4- dihydropyrimidone derivatives showed the approximate docking score -8.4 to -10.1 kcal/mol. Fourteen 3,4-dihydropyrimidone derivatives have a greater docking score compared to celecoxib used as a standard compound. Derivative D-1 had higher binding energy than other 3,4-dihydropyrimidone derivatives because it has the smallest docking score. Conclusion: All new 3,4-dihydropyrimidone derivatives are feasible to synthesize and performed their in-vitro evaluation.

Microtubules and the mitotic spindle have become an important target for cancer treatment due to their critical role in cell division. In this work, a novel series of benzofuran and indole derivatives were designed and synthesized, to be evaluated as tubulin polymerization inhibitors. 2-Acetylbenzofuran derivatives 1a,b and 3-acetylindole 1c were condensed with Wittig reagents 2a-d and Wittig-Horner reagents 3a-e to afford the respective 2-ethylidene derivatives 5a-j and 7a-e. Also, iminomethylene triphenylphosphine (2e) reacted with 1a,b to afford benzofuran-2-ylethylidene aniline derivatives 6a,b. In addition, compounds 1a,b reacted with trialkylphosphites 4a-c to give 1:1 adduct for which the Oxaphospholo[4,3-b]benzofuran-7-yl)diazene derivatives 8a-f, were assigned. The possible reactions mechanisms were discussed and structural reasoning for the new compounds were based upon spectroscopic data. Their antiproliferative activities against two cell lines namely, HepG2 and MCF7 cells were then evaluated. It was found that the benzofuran compounds 5b, 6a, and 8c exhibited the strongest antiproliferative activities against both cell lines compared to doxorubicin. By studying the mechanism of action, compound 6a showed good inhibition of tubulin polymerization which leads to mitotic spindle formation disruption, cell cycle arrest in the G2/M phase, and apoptosis of HepG2 cells. A conducted docking study confirmed the in vitro results indicating that compound 6a fitted properly at the colchicine binding site of tubulin. Based on these findings, compound 6a can be considered as a promising anticancer candidate that can be subjected for further development as a tubulin polymerization inhibitor for treating liver and breast cell carcinoma.

In an attempt to develop quality antimicrobial agents, a series of oxazolone-1,2,3-triazole-amide hybrids were obtained from oxazolone tethered with a terminal alkyne and in situ generated 2-azido-N-phenylacetamides. All the synthesized compounds were characterized by using various spectroscopic techniques. The developed hybrids were evaluated for their in vitro antimicrobial activity toward three Gram-positive bacteria S. aureus, B. subtilis and S. gorodonii and three Gram-negative bacteria—E. coli, S. enterica and P. aeruginosa—and two fungi, viz. C. albicans and A. niger. Oxazolone-amide-1,2,3-triazoles (8a–e, 9a–e, 10a–e) exhibited almost 15 times better efficacy than alkyne precursors, i.e., oxazolone-linked terminal alkynes (6a–c). Compound 10d exhibited very good antimicrobial activity toward all the tested microorganisms. Docking studies of compounds 10d and 6c were also carried out in the binding site of enzyme sterol-14-α-demethylase of C. albicans, which supported the in vitro experimental results.

Objectives: To study the larvicidal effect of Vitex negundo Linn against mosquito larvae by larvicidal bioassay and in silico molecular docking studies. Materials and Methods: The larvicidal bioassay of Vitex negundo Linn was assessed by using WHO standard protocol and an in silico molecular docking study was performed by using Molegro Virtual Docker against Culex quinquifasciatus. The early third instar larvae of Aedes aegypti, Aedes albopictus and Culex quinquefasciatus were exposed to the extract concentrations in three replicates and different temephos concentration were taken as positive control and solvent control was also used. Results: The study results shows that of Vitex negundo Linn possess the potential larvicidal activity against third instar larvae of Culex quinquifasciatus when compared to Aedes aegypti L and Aedes albopictus. Percentage mortality and half-maximal effective concentration (EC50) value were calculated against the above mentioned three species like wise Culex quinquifasciatus (83.77 ppm), Aedes aegypti (341.7 ppm), and Aedes albopictus (487.9 ppm). The highest larval mortality was found against Culex quinquifasciatus of 100 % at 500 parts per million. In silico molecular docking studies using Molegro Virtual Docker against Odorant binding protein (PDB: 2L2C) of Culex quinquifasciatus was performed as it showed better results in in vitro study. The results reveal that phytoconstituent like Vitexicarpin showed good docking scores against the Odorant Binding Protein 2L2C and the moldock score of Vitexicarpin was found to be -87.3733, whereas moldock score of standard Azadirachtin was found to be -110.77. Conclusion: The present study reveal that the Vitex negundo Linn possess the potential larvicidal activity against the Culex quinquifasciatus species. Key words: Vitex negundo Linn, Aedes aegypti L, Culex quinquefasciatus, Aedes albopictus, Molegro Virtual Docker 6.0, Odorant binding Protein, Larvicidal.

A series of Oxazetidine (NL1-NL12) from reacting tryptophan and aromatic aldehydes were synthesized in good yields by involving 2-{[(4-chlorophenyl) methylidene] amino}-3-(1H-indol-3-yl) propanoic acid and chloro acetyl chloride as reactive intermediates. All the synthesized derivatives were screened via spectral techniques. Synthesized molecules were virtually screened against Human A2A Adenosine receptor interactions analysis using molecular docking to elucidate CNS potential. Synthesized derivatives showed excellent binding towards the Human A2A Adenosine receptor.

Background: SARS-CoV-2 has been shown to bind the host cell ACE2 receptor through its spike protein receptor binding domain (RBD), required for its entry into the host cells. Objective: We have screened phytocompounds from a medicinal herb, Tinospora cordifolia, for their capacities to interrupt the viral RBD and host ACE2 interactions. Methods: We employed molecular docking to screen phytocompounds in T. cordifolia against the ACE2-RBD complex, performed molecular dynamics (MD) simulation, and estimated the electrostatic component of binding free energy. Results: ‘Tinocordiside’ docked very well at the center of the interface of ACE2-RBD complex, and was found to be well stabilized during MD simulation. Tinocordiside incorporation significantly decreased the electrostatic component of binding free energies of the ACE2-RBD complex (23.5 and 17.10 kcal/mol in the trajectories without or with the ligand, respectively). As the basal rate constant of protein association is in the order of 5 (105 to 106 M-1S-1), there might be no big conformational change or loop reorganization, but involves only local conformational change typically observed in the diffusion-controlled association. Taken together, the increase in global flexibility of the complex clearly indicates the start of unbinding process of the complex. Conclusion: It indicates that such an interruption of electrostatic interactions between the RBD and ACE2, and the increase in global flexibility of the complex would weaken or block SARSCoV- 2 entry and its subsequent infectivity. We postulate that natural phytochemicals like Tinocordiside could be viable options for controlling SARS-CoV-2 contagion and its entry into host cells.

A novel series of phenoxymethybenzoimidazole derivatives (9a-n) were rationally designed, synthesized, and evaluated for their α-glycosidase inhibitory activity. All tested compounds displayed promising α-glycosidase inhibitory potential with IC50 values in the range of 6.31 to 49.89 μM compared to standard drug acarbose (IC50 = 750.0 ± 10.0 μM). Enzyme kinetic studies on 9c, 9g, and 9m as the most potent compounds revealed that these compounds were uncompetitive inhibitors into α-glycosidase. Docking studies confirmed the important role of benzoimidazole and triazole rings of the synthesized compounds to fit properly into the α-glycosidase active site. This study showed that this scaffold can be considered as a highly potent α-glycosidase inhibitor. Supplementary Information The online version contains supplementary material available at 10.1007/s11030-021-10310-7.

G724S is a rare mutation induced by different generations of tyrosine kinase inhibitors (TKIs). No clinical effective drugs toward G724S mutation have been reported till now. We analyzed the interaction of three drugs (afatinib, gefitinib, osimertinib) with epidermal growth factor receptor (EGFR) from three aspects: the spatial structure of the binding region, the scoring function value, and the interaction force between drug molecules and active center of EGFR. Our results indicate that afatinib remains effective to patients with EGFR Exon19Deletion(Ex19Del) and G724S mutations whereas osimertinib and gefitinib are not, which is consistent with other reports. Afatinib is reported to be effective against G724S mutation, but no long‐term clinical survival has been reported till now. A patient with stage IV adenocarcinoma was found to have Ex19Del/G724S mutation. Treated with afatinib, he received a progression‐free survival of more than 1 year. With the guidance of this case report, we provide the clinical evidence of using afatinib for patients with G724S mutations and obtaining long‐term clinical survival. Key Points Guided by protein‐drug docking, afatinib is more effective to EGFR G724S mutation compared with osimertinib and gefitinib.A patient with Ex19Del/G724S mutation obtained long‐term survival with afatinib treatment., This brief communication presents the case of a patient with acquired Ex19Del/G724S mutation who was treated with afatinib and obtained long‐term clinical benefit.

Background: Coumarins are naturally occurring biologically active heterocyclic molecules endowed with a wide range of biological properties, including antibacterial, antifungal, and antitumor activities. Objective: The present work aimed to synthesize new coumarin-containing compounds and to investigate their cytotoxic activity. Methods: Coumarin peptide and coumarin amino alcohols were prepared by treating epoxidecontaining coumarin derivatives with suitable aromatic amines and peptides in trifluoroethanol as a solvent at 50°C. These derivatives were evaluated for their cytotoxic activity on three different cell lines: HeLa, MDA-MB-231 and L-132. Cell viability was determined by MTT (3-(4,5- dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) assay. Results: A new protocol was developed for the synthesis of thirteen novel coumarin peptide and coumarin amino alcohol derivatives. Among the tested compounds, three derivatives showed significant activity against all the tested cell lines. Docking studies indicated favorable interactions of the disubstituted peptide coumarin derivatives with the Asp 351 and Thr 347 amino acids at the active site of the human estrogen receptor. Conclusions: The results suggest that the newly synthesized compounds may be promising candidates in the research of new antitumor compounds.

Background: Cancer is a very dangerous disease whose treatment can be improved by removing the factors that cause side effects if the drugs prescribed for cancer are chiral in nature. Objectives: A computational evaluation for the most biologically active enantiomeric form of chiral drugs attacking the DNA of the cell, was made for the first time, and compared with the experimental work done by others previously. Methods: All the enantiomeric structures of the drugs taken in the present study were obtained using Marvin sketch, and the structure of DNA to be docked with enantiomers, was obtained from the protein data bank. After that, all the enantiomers of the chiral drugs were docked with DNA one by one for the evaluation of the most biologically active enantiomeric form. Results: The docking study showed that the different enantiomers interacted with DNA differently because of having different arrangements of atoms/groups. The binding affinity of one of the two enantiomeric forms was higher than that of another. Conclusion: R-methotrexate for breast cancer; R-mitotane for adrenocortical cancer; R-duvelisib for blood cancer, and S-irinotecan for colon cancer would be a suitable drug with less toxicity as well as other side effects.

Objective: Coronaviruses are a group of similar viruses which cause fatal infection and responsible for affecting the upper respiratory tract in many organisms. Throughout the time these viruses have been found to affect human life by causing major pandemics like SARS, MERS and COVID-19 due to their high rate of mutation and zoonotic transmission. Repurposing of a drug could be a solution for this challenge, as many previously available drugs hold great potential to act as a drug molecule. Interfering this interaction could be a potent mechanism to stop the viral infection and propagation. Methods: In the current study we have predicted the evolutionary relationship of nCoV using three viral proteins Nucleocapsid phosphoprotein, membrane glycoprotein and Envelop protein with accession number YP_009724397, YP_009724393 and YP_009724392 respectively. Phylogenetic tree was constructed and evaluated using the bootstrap method. Homology modeling and docking studies has been done to identify the interaction and binding affinity of SARS drugs. Results: Phylogenetic tree shows that Nucleocapsid phosphoprotein is originated from Hypsugo Bat Coronavirus, Membrane glycoprotein is originated from MERS Corona Virus and Envelop proteins have originated from Ferret coronavirus. From the docking result we concluded that Precose (glide score-8.372) shows that it has stable and strong interaction with Spike glycoprotein. Conclusion: Precose which is commonly known as Acarbose can act as a potential inhibitor for the spike glycoprotein. This paper described and highlighted the importance of repurposing of the previously available drug to act as a potent inhibitor in the newly discovered or novel diseases. © 2021 The Authors. Published by Innovare Academic Sciences Pvt Ltd.

Introduction and Aim: Phyllanthus acidus L.Skeels (Family: Phyllanthaceae) or Star Gooseberry which bears small, edible, juicy, sour, yellow berries fruit is known as a “liver tonic” in ayurvedic medicine. However, the behavior of the plant fruit or its constituents in cell apoptosis/cell survival is unknown. Hence, the purpose of thepresent study was to perform an in silico docking of selective bioactive compounds of aqueous extract of fruit of P.acidus (PAFAE) against MAPK1. Mitogen activated protein kinase is a family of serine threonine specific protein kinases- MAPK1/ERK1/2, JNK1-3, p38MAPK and ERK5.Activation ofMAPK1 promotes cell survival in certain tissues by inhibiting proapoptotic proteins and by stimulating anti apoptotic factors. Methodology: In silico docking studies was carried out using bioinformatics tools.The active compounds (Trihomovitamin D3; 2Z,6Z,8Z,12E Hexadecatetraenoic acid, Methyl prednisolone, Hydroxysalmeterol and Tridesacetoxykhivorin) ofP.acidus aqueous fruit extract were docked against MAPK1 resulting in receptor-ligand complex. Results: The binding energy is correlated with the probability of affinity and stable bound between ligand and its receptor. Conclusion: The molecular docking study of selective bioactive compounds of PAFAE with MAPK1 protein revealed that Tridesacetoxykhivorinand Methyl Prednisolone, is having good interaction in favorable pose with MAPK1 as shownfrom theireffective binding energy(-7.79kcal/mol and -7.19 kcal/mol), strong bond length and interactions with active site of MAPK1.

The previously introduced ratio of frequencies (RF ) framework provides statistically sound information on the relative interaction preferences of atoms in crystal structures. By applying the methodology to protein-ligand complexes, we can investigate the significance of interactions that are employed in structure-based drug design. Here, we revisit three aspects of molecular recognition in the light of the RF framework, namely stacking interactions of heteroaromatic rings with protein amide groups, interactions of acidified C-H groups, and interaction differences between syn and anti lone pairs of carboxylate groups. In addition, we introduce a highly interactive visualization tool that facilitates design idea generation in structure-enabled drug discovery projects. Finally, we show that applying the RF analysis as a simple rescoring tool after docking improves enrichment factors for the DUD-E diverse targets subset supporting the relevance of our approach.

Hepatitis C Virus (HCV) is a viral infection posing a severe global threat that left untreated progresses to end-stage liver disease, including cirrhosis and hepatocellular carcinoma (HCC). Moreover, no prophylactic approach exists so far enabling its prevention. The NS5B polymerase holds special significance as the target of intervention against HCV infection. The current study kindles benzothiazine derivatives against HCV NS5B polymerase through in silico and experimental approaches. Following docking, the compound 2-(3,4-dimethyl-5,5-dioxidobenzo[e]pyrazolo[4,3-c][1,2]thiazin-2(4H)-yl)-N-(2-fluorobenzyl)acetamide was revealed to form effective binding interaction in the proposed site of HCV NS5B with a score of -10 kcal/mol and subsequently was deciphered through molecular dynamics (MD) simulation study which indicated interaction of residues TYR_382, VAL_381 and HIS_467 through hydrophobic interaction and two residues such as GLU_202 and LYS_209 contributed in the formation of water bridges. The subsequent in silico pharmacological analysis revealed its safe drug profile. The cytotoxicity activity of compound 6c indicated to be non-toxic in HepG2 cells at concentration ranges from 0.001-1.0 µmol/L with >80% cell viability and diminished expression of the HCV NS5B to 98% at the dose of 1.0 µmol/L and 90% at 0.5µmol/L. Thus the hit compound 6c might be a potent NS5B polymerase inhibitor required to be validated further through in vivo and preclinical studies.

In this work a series of thiophene linked isoxazole derivatives (LK1-LK8) was synthesized by cyclization of different substituted thienyl chalcones (PL1-PL8). The structures of the synthesized compounds were characterized by IR, 1H NMR and mass spectral data. These derivatives were evaluated for antibacterial activities. Compounds LK7 showed excellent antibacterial activities amongst the synthesized compounds with MIC value 6.75 µg/ml. Molecular docking of these linked isoxazole derivatives (LK1-LK8) was also performed with crystal structure of staph gyrase B 24kDa (PDB code: 5 4URM). All the isoxazole derivatives (LK1-LK8) were docked into same groove of the binding site of native co-crystallized (1R,4aS,5S,6S,8aR)-5-{[(5S)-1-(3-O-acetyl-4-O-carbamoyl-6-deoxy-2-O-methyl-alpha-L-talopyra nosy l)-4 hydroxy 2-oxo-5-(propan-2-yl)-2,5-dihydro-1H-pyrrol-3-yl]carbonyl}-6-methyl-4 1, 2, 3, 4 methylid-ene,4a,5,6,8a-octahydronaphthalen-1-yl2,6-dideoxy-3-C-[(1S)-1-{[(3,4-dichloro-5-methyl-1 H-pyrrol-2-yl) carbonyl]amino}ethyl]-beta-D-ribo-hexopyranoside) ligand for activity explanation and exhibited good ligand interaction and binding affinity were of range -2.04 to -4.34 kcal/mol.

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a colossal loss to human health and lives and has deeply impacted socio-economic growth. Remarkable efforts have been made by the scientific community in containing the virus by successful development of vaccines and diagnostic kits. Initiatives towards drug repurposing and discovery have also been undertaken. In this study, we compiled the known natural anti-viral compounds using text mining of the literature and examined them against four major structural proteins of SARS-CoV-2, namely, spike (S) protein, nucleocapsid (N) protein, membrane (M) protein and envelope (E) protein. Following computational approaches, we identified fangchinoline and versicolactone C as the compounds to exhibit strong binding to the target proteins and causing structural deformation of three structural proteins (N, S and M). We recommend the inhibitory effects of these compounds from our study should be experimentally validated against SARS-CoV-2. Communicated by Ramaswamy H. Sarma

Abstract In this study, a set of dietary polyphenols was comprehensively studied for the selective identification of the potential inhibitors/modulators for galectin-1. Galectin-1 is a potent prognostic indicator of tumor progression and a highly regarded therapeutic target for various pathological conditions. This indicator is composed of a highly conserved carbohydrate recognition domain (CRD) that accounts for the binding affinity of β-galactosides. Although some small molecules have been identified as galectin-1 inhibitors/modulators, there are limited studies on the identification of novel compounds against this attractive therapeutic target. The extensive computational techniques include potential drug binding site recognition on galectin-1, binding affinity predictions of ~ 500 polyphenols, molecular docking, and dynamic simulations of galectin-1 with selective dietary polyphenol modulators, followed by the estimation of binding free energy for the identification of dietary polyphenol-based galectin-1 modulators. Initially, a deep neural network-based algorithm was utilized for the prediction of the druggable binding site and binding affinity. Thereafter, the intermolecular interactions of the polyphenol compounds with galectin-1 were critically explored through the extra-precision docking technique. Further, the stability of the interaction was evaluated through the conventional atomistic 100 ns dynamic simulation study. The docking analyses indicated the high interaction affinity of different amino acids at the CRD region of galectin-1 with the proposed five polyphenols. Strong and consistent interaction stability was suggested from the simulation trajectories of the selected dietary polyphenol under the dynamic conditions. Also, the conserved residue (His44, Asn46, Arg48, Val59, Asn61, Trp68, Glu71, and Arg73) associations suggest high affinity and selectivity of polyphenols toward galectin-1 protein. Graphic Abstract

A flexible docking of a series of heteroaryl compounds to the binding site of a model of human 5-HT1A/2A receptor was exercised using GLIDE docking methods. The resultant docking scores were used to correlate the in vivo affinity data. The GLIDE docking algorithm when used with a homology model of 5HT1A/2A was based on β2- adrenergic receptor template. The influence of structure and hydrophobic properties of aryl moiety on binding affinities was discussed and a model for ligand binding in the hydrophobic part of the binding site was proposed.

Graphene is a two-dimensional semiconducting material whose application for diagnostics has been a real game-changer in terms of sensitivity and response time, variables of paramount importance to stop the COVID-19 spreading. Nevertheless, strategies for the modification of docking recognition and antifouling elements to obtain covalent-like stability without the disruption of the graphene band structure are still needed. In this work, we conducted surface engineering of graphene through heterofunctional supramolecular-covalent scaffolds based on vinylsulfonated-polyamines (PA-VS). In these scaffolds, one side binds graphene through multivalent π-π interactions with pyrene groups, and the other side presents vinylsulfonated pending groups that can be used for covalent binding. The construction of PA-VS scaffolds was demonstrated by spectroscopic ellipsometry, Raman spectroscopy, and contact angle measurements. The covalent binding of -SH, -NH2, or -OH groups was confirmed, and it evidenced great chemical versatility. After field-effect studies, we found that the PA-VS-based scaffolds do not disrupt the semiconducting properties of graphene. Moreover, the scaffolds were covalently modified with poly(ethylene glycol) (PEG), which improved the resistance to nonspecific proteins by almost 7-fold compared to the widely used PEG-monopyrene approach. The attachment of recognition elements to PA-VS was optimized for concanavalin A (ConA), a model lectin with a high affinity to glycans. Lastly, the platform was implemented for the rapid, sensitive, and regenerable recognition of SARS-CoV-2 spike protein and human ferritin in lab-made samples. Those two are the target molecules of major importance for the rapid detection and monitoring of COVID-19-positive patients. For that purpose, monoclonal antibodies (mAbs) were bound to the scaffolds, resulting in a surface coverage of 436 ± 30 ng/cm2. KD affinity constants of 48.4 and 2.54 nM were obtained by surface plasmon resonance (SPR) spectroscopy for SARS-CoV-2 spike protein and human ferritin binding on these supramolecular scaffolds, respectively.

Significance 3-benzylidene chroman-4-ones share close homology with naturally occurring bioactive compounds. Objectives This study evaluated the antifungal, antioxidant and anticancer activities of novel 3-benzylidene chromanone analogues with respect to their structure-activity relationships. Methods Compounds 45e-64e were synthesized inhouse. Aspergillus niger (MTCC 1344) Aspergillus flavus and Botrytis cinareae were the fungal strains tested. Computational docking analysis were carried out for Vanin-1, estrogen receptor and Akt proteins using Auto-dock vina. Free radical scavenging, total antioxidant capacity was analyzed using spectrophotometric methods. MCF-7(breast cancer) cell line was used for anticancer assays. Flow cytometry was used to detect cell cycle and apoptosis. Results Out of the twenty compounds screened, compounds 47e,50e,52e,57e and 61e that possessed either methoxy and ethoxy/methyl/isopropyl group exhibited very good activity against all fungi. Compounds possessing methoxy group alone showed moderate activity and compounds devoid of methoxy, and ethoxy groups did not show any activity. When computationally analyzed against target proteins for antioxidant properties, the compounds exhibited excellent binging efficacy to Vanin-1 and estrogen receptors. These predictions were translated in the in vitro free-radical scavenging and antioxidant assays. The compounds exhibited anti-proliferative efficacy in breast cancer cell line, increased the sub-G0/G1 cell cycle populations and total apoptosis in MCF-7 cells. Additionally, the compounds also depicted excelling binging energy when computationally analyzed for Akt enzyme binding. Conclusion In summary, our study identified potential analogues of 3-benzylidene chroman-4-one molecules with excellent anti-fungal, anti-oxidant and anticancer activities which demands further research for drug developments.

Nucleic acid-ligand interactions play an important role in numerous cellular processes such as gene function expression and regulation. Therefore, nucleic acids such as RNAs have become more and more important drug targets, where the structural determination of nucleic acid-ligand complexes is pivotal for understanding their functions and thus developing therapeutic interventions. Molecular docking has been a useful computational tool in predicting the complex structure between molecules. However, although a number of docking algorithms have been developed for protein-ligand interactions, only a few docking programs were presented for nucleic acid-ligand interactions. Here, we have developed a fast nucleic acid-ligand docking algorithm, named NLDock, by implementing our intrinsic scoring function ITScoreNL for nucleic acid-ligand interactions into a modified version of the MDock program. NLDock was extensively evaluated on four test sets and compared with five other state-of-the-art docking algorithms including AutoDock, DOCK 6, rDock, GOLD, and Glide. It was shown that our NLDock algorithm obtained a significantly better performance than the other docking programs in binding mode predictions and achieved the success rates of 73%, 36%, and 32% on the largest test set of 77 complexes for local rigid-, local flexible-, and global flexible-ligand docking, respectively. In addition, our NLDock approach is also computationally efficient and consumed an average of as short as 0.97 and 2.08 min for a local flexible-ligand docking job and a global flexible-ligand docking job, respectively. These results suggest the good performance of our NLDock in both docking accuracy and computational efficiency.

A new series of 1,4-disubstituted 1,2,3-triazole derivatives tethered to a 2H-chromene scaffold have been synthesized via a click reaction. The synthesized chromene–triazole conjugates were screened for their antibacterial activity against E. coli, S. aureus, P. aeruginosa and B. subtilis, as well as for antifungal activity against A. niger and C. albicans. Among the 17 synthesized compounds, 6 derivatives showed the best antimicrobial activity. Molecular docking studies of the title compounds with carotenoid dehydrosqualene synthase (PDB: 2ZCS) revealed docking scores within the range 98.241–91.488 against 106.573 for the reference ligand Ciprofloxacin and with lanosterol 14α-demethylase (CYP51; PDB ID: 5V5Z), 103.672–96.917 against 110.839 for the reference ligand Voriconazole.

Demand has arisen for developing new azole antifungal agents with the growth of the resistant rate of infective fungal species to current azole antifungals in recent years. Accordingly, the present study reports the synthesis of novel fluconazole (FLC) analogues bearing urea functionality that led to discovering new azole agents with promising antifungal activities. In particular, compounds 8b and 8c displayed broad-spectrum activity and superior in vitro antifungal capabilities compared to the standard drug FLC against sensitive and resistant Candida albicans (C. albicans). The highly active compounds 8b and 8c had potent antibiofilm properties against FLC-resistant C. albicans species. Additionally, these compounds exhibited very low toxicity for three mammalian cell lines and human red blood cells. Time-kill studies revealed that our synthesized compounds displayed a fungicidal mechanism toward fungal growth. Furthermore, a density functional theory (DFT) calculation, additional docking, and independent gradient model (IGM) studies were performed to analyze their structure-activity relationship (SAR) and to assess the molecular interactions in the related target protein. Finally, in vivo results represented a significant reduction in the tissue fungal burden and improvements in the survival rate in a mice model of systemic candidiasis along with in vitro and in silico studies, demonstrating the therapeutic efficiency of compounds 8b and 8c as novel leads for candidiasis drug discovery.

The plant acyl-acyl carrier protein (ACP) desaturases are a family of soluble enzymes that convert saturated fatty acyl-ACPs into their cis-monounsaturated equivalents in an oxygen-dependent reaction. These enzymes play a key role in biosynthesis of monounsaturated fatty acids in plants. ACPs are central proteins in fatty acid biosynthesis that deliver acyl chains to desaturases. They have been reported to show a varying degree of local dynamics and structural variability depending on the acyl chain size. It has been suggested that substrate-specific changes in ACP structure and dynamics have a crucial impact on the desaturase enzymatic activity. Using molecular dynamics simulations, we investigated the intrinsic solution structure and dynamics of ACP from spinach with four different acyl chains: capric (C10), myristic (C14), palmitic (C16), and stearic (C18) acids. We found that the fatty acids can adopt two distinct structural binding motifs, which feature different binding free energies and influence the ACP dynamics in a different manner. Docking simulations of ACP to castor Δ 9 -desaturase and ivy Δ 4 -desaturase suggest that ACP desaturase interactions could lead to a preferential selection between the motifs.

Cancer is the second leading cause of death worldwide. This work is an effort to find new effective and safe anticancer agents. In accordance with thalidomide features as immunomodulator anticancer drug, we designed and synthesized ten new thalidomide analogs. The synthesized compounds were biologically evaluated for their anti-tumor activity against three human cancer cell lines namely; hepatocellular carcinoma (HepG2), prostate cancer (PC3) and breast cancer (MCF-7). Thalidomide was used as a reference drug. The obtained data showed that compound 10a is far better than thalidomide against the three cancer cell lines. It exhibited IC50 = 3.89, 4.01 and 2.91 µg/mL against the cell lines, respectively. While thalidomide exhibited IC50 values of 11.26, 14.58, and 16.87 µg/mL against the three cell lines, respectively. Moreover, compounds 7a, 6a and 8 were found to be better than thalidomide against MCF-7 cell line. As they showed IC50 values of 10.32, 12.15 and 15.32 µg/mL, respectively. Furthermore, compounds 6a, 7a, and 8 showed strong activity against the three cell lines. Results of docking studies showed that our compounds can accommodate the pocket of CRBN with binding energies too close to that of thalidomide.

Pistacia integerrima grows in some areas of Pakistan and some other south Asian countries such as Afghanistan, India, Nepal, and Myanmar. It is an important medicinal plant which has been traditionally used for the treatment of asthma, cough, and dysentery. In the present study, we intend to re-isolate bioactive compounds (I–III) from P. integerrima galls extracts. The chloroform extract was subjected to column chromatography that afforded three reported chemical constituents, 7-methoxynaringenin (I), 7-methoxy-3,5,7,4′-tetrahydroxyflavanone (II), and β-sitosterol (III). Compounds (I–III) were evaluated for multi-drug resistance (MDR) reversing effect by assessing their activity on various genes including transfected mouse gene, human mdrl gene, and transfected mouse T-lymphoma cell lines (L5178 and L5178Y). Compounds (I–III) exhibit significant dose-dependent MDR reversing effect against the T-lymphoma (mouse cell line). in-silico molecular docking investigations performed on compounds (I–III) showed a common binding site for these compounds and Rhodamine 123. Our findings indicated that the relative docking scores correlate satisfactorily with in vitro activities. It could be concluded that the inhibitory activity of compounds (I–III) is largely due to their interactions with the P-glycoprotein (P-gp). The present work could also contribute to the isolation of novel natural compounds that act as potent inhibitors for cancer treatment.

eIF4A1 is an ATP-dependent RNA helicase whose overexpression and activity have been tightly linked to oncogenesis in a number of malignancies. An understanding of the complex kinetics and conformational changes of this translational enzyme is necessary to map out all targetable binding sites and develop novel, chemically tractable inhibitors. We herein present a comprehensive quantitative analysis of eIF4A1 conformational changes using protein-ligand docking, homology modeling, and extended molecular dynamics simulations. Through this, we report the discovery of a novel, biochemically active phenyl-piperazine pharmacophore, which is predicted to target the ATP-binding site and may serve as the starting point for medicinal chemistry optimization efforts. This is the first such report of an ATP-competitive inhibitor for eiF4A1, which is predicted to bind in the nucleotide cleft. Our novel interdisciplinary pipeline serves as a framework for future drug discovery efforts for targeting eiF4A1 and other proteins with complex kinetics.

Interaction fingerprints are vector representations that summarize the three-dimensional nature of interactions in molecular complexes, typically formed between a protein and a ligand. This kind of encoding has found many applications in drug-discovery projects, from structure-based virtual-screening to machine-learning. Here, we present ProLIF, a Python library designed to generate interaction fingerprints for molecular complexes extracted from molecular dynamics trajectories, experimental structures, and docking simulations. It can handle complexes formed of any combination of ligand, protein, DNA, or RNA molecules. The available interaction types can be fully reparametrized or extended by user-defined ones. Several tutorials that cover typical use-case scenarios are available, and the documentation is accompanied with code snippets showcasing the integration with other data-analysis libraries for a more seamless user-experience. The library can be freely installed from our GitHub repository (https://github.com/chemosim-lab/ProLIF).

Palladium/BuAd2P efficiently catalyzed the direct α-arylation of ketone in the anti-Alzheimer's disease drug donepezil, leading to 15 aryldonepezil analogues exhibiting high selective inhibition of acetylcholinesterase (AChE). The cell-based assays revealed that the 3-methylpridinyl analogue (12) shows significantly lower toxicity compared to donepezil and remarkable neuroprotective activity against H2O2-induced damage in SH-SY5Y cells. Docking results of compound 12 also interpreted the possible mechanism of the selective inhibition between AChE and butyrylcholinesterase (BuChE).

The treatment of coronavirus diseases (COVID-19) is a principal aim worldwide that is required restore public health in the population. To this end, we have been studied several kinds of de novo and repurposed drugs to investigate their ability to inhibit the replication of the virus which causes the current pandemic—the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, finding a vehicle that promotes the controlled dosage is vital for avoiding secondary effects. For this reason, the present work exposes a nanostructured carrier based on ZnO, which is coupled to three repurposed drugs (Chloroquine, Dipyridamole, and Lopinavir) to understand the chemical interaction of the formed composite. The designed composites are modeled and optimized using the DFT formalism. In obtaining exergonic adsorption energies, we found values between 0.582 to 2.084 eV, depending on the used drug. At the same time, the HOMO orbitals demonstrate the electronic overlap between the ZnO-Np and the Lopinavir, which is the molecule with the higher adsorption energy. Finally, we carried out a docking assay to investigate the interaction of free drugs and composites with the main protease of the SARS-CoV-2, finding that the coupling energy of the composites (at around to 0.03 eV) was higher, compared with the free drugs. As such, our results suggest a controlled dosage of the drug on the SARS-CoV-2 target.

Caesalpinia digyna (Rottl.) (Family: Fabaceae) is well known for its numerous medicinal values against several human disorders including fever, senile pruritis, diarrhea, tuberculosis, tonic disorder, diabetes, etc. The current study is intended to investigate the in vivo antipyretic activity of the methanol extract of C. digyna leaves (MECD) and its carbon-tetrachloride (CTCD) and butanol fraction (BTCD). Besides, in silico molecular docking and ADME/T profiling of the selective identified bioactive compounds of C. digyna has been also studied to validate the experimental outcomes and establish a better insight into the possible receptor-ligand interaction affinity. In vivo antipyretic activity of MECD, CTCD and BTCD were evaluated by employing yeast induced pyrexia technique in mice model and in silico analysis of the identified compounds of C. digyna has been implemented using PyRx autodock vina, Discovery Studio 2020, UCSF Chimera software and ADME/T online tools. MECD and BTCD unveiled significant antipyretic activity in dose dependent manner whereas, CTCD failed to exhibit significant antipyretic activity. Comparing to other test sample, MECD (400 mg/kg; b.w) (p

Influenza A viruses are among the most studied viruses, however no effective prevention against influenza infection has been developed. So, designing an effective vaccine against Influenza A virus is a critical issue in the field of medical biotechnology. For this reason, to combat this disease, we have designed a novel multi-epitope vaccine candidate based on the several conserved and potential linear B-cell and T-cell binding epitopes by using the in silico approach. This vaccine consists of an ER signal conserved sequence, the PADRE conserved epitope and two conserved epitopes of Influenza matrix protein 2. T-cell binding epitopes from Matrix protein 2 were predicted by in silico tools of epitope prediction. The selected epitopes were joined by flexible linkers and physicochemical properties, toxicity, and allergenecity were investigated. The designed vaccine was antigenic, immunogenic, and non-allergenic with suitable physicochemical properties and has higher solubility. The final multi-epitope construct was modeled, confirmed by different programs and the molecular interactions with immune receptors were considered. The molecular docking assay indicated the interactions with immune-stimulatory toll-like receptor 3 (TLR3) and major histocompatibility complex class I (MHCI). The HADDOCK and H DOCK servers were used to make docking analysis, respectively. The docking analysis indicated a strong and stable binding interaction between the vaccine construct with major histocompatibility complex (MHC) class I and toll-like receptor 3. Overall, the findings suggest that the current vaccine may be a promising vaccine to prevent Influenza infection.

Since there is no general agreement on drug treatment of SARS-CoV-2, the search for a new drug capable of treating COVID-19 is of utmost priority. This study aims to dereplicate the chemical compounds of the methanol extract of Salvia officinalis and Artemisia dracunculus, and assay the inhibitory effect of these compounds as well as the previously dereplicated components of Zingiber officinale against SARS-CoV-2 in an in-silico study. A molecular networking (MN) technique was applied to find the chemical constituents of the extracts. Docking analysis was also used to find the binding affinity of dereplicated components from S. officinalis, A. dracunculus, and Z. officinale to COV-2-SP and Mpro. 57 compounds were dereplicated from the MeOH extracts of S. officinalis and A. dracunculus which include the class of polyphenols, flavonoids, coumarins, phenylpropanoids, anthocyanins, and dihydrochalcones. Molecular docking analysis indicated a high affinity of about 27 compounds from three mentioned plants against studied targets. kaempferol 3-O-rutinoside, neodiosmin, and querciturone with docking score values of -10.575, -10.208, and − 9.904 Kcal/mol and ki values of 0.016606, 0.030921, and 0.051749, respectively were found to have the highest affinities against COV-2-SP. 2-phenylethyl beta-primeveroside, curcumin PE, and kaempferol 3-O-rutinoside also indicated the highest affinity against Mpro with docking scores of -10.34, -10.126 and − 9.705 and ki values of 0.024726, 0.035529, and 0.072494, respectively. MN can be successfully used for the dereplication of metabolites from plant extracts. In addition, the in-silico binding energies introduced several inhibitors from Z. officinale, S. officinalis, and A. dracunculus for the treatment of SARS-CoV-2 disease. Supplementary Information The online version contains supplementary material available at 10.1007/s11756-021-00881-z.

COVID-19 was declared a pandemic by the World Health Organization (WHO) in March 2020. The disease is caused by severe acute respiratory syndrome coronavirus 2 (SARSCoV-2). The aim of this study is to target the SARS-CoV-2 virus main protease (Mpro) via structure-based virtual screening. Consequently, > 580,000 ligands were processed via several filtration and docking steps, then the top 21 compounds were analysed extensively via MM-GBSA scoring and molecular dynamic simulations. Interestingly, the top compounds showed favorable binding energies and binding patterns to the protease enzyme, forming interactions with several key residues. Trihydroxychroman and pyrazolone derivatives, SN02 and SN18 ligands, exhibited very promising binding modes along with the best MM-GBSA scoring of –40.9 and –41.2 kcal mol−1, resp. MD simulations of 300 ns for the ligand-protein complexes of SN02 and SN18 affirmed the previously attained results of the potential inhibition activity of these two ligands. These potential inhibitors can be the starting point for further studies to pave way for the discovery of new antiviral drugs for SARS-CoV-2.

Aim. To synthesize, study the antimicrobial activity and suggest antimicrobial activity mechanism for the novel derivatives of 6-(1H-benzimidazol-2-yl)-5-methylthieno[2,3-d]pyrimidin-4(3H)-one. Results and discussion. As the result of the targeted modification of 6-(1H-benzimidazol-2-yl)-5-methylthieno[2,3-d]-pyrimidin-4(3H)-one in position 3 with acetamide and 1,2,4-oxadiazol-5-ylmethyl substituents, the compounds, which demonstrated better antimicrobial activity in the agar well diffusion assay than the reference drug Streptomycin, were obtained. To elucidate the mechanism of action of the novel compounds, the docking studies were con-ducted to the active site of the 16S subunit of ribosomal RNA, the proven target for aminoglycoside antibiotics, as well as tRNA (Guanine37-N1)-methyltransferase (TrmD), which inhibitors were considered as a new potential class of antibiotics. Experimental part. By the interaction of 6-(1H-benzimidazol-2-yl)-5-methylthieno[2,3-d]pyrimidin-4(3H)-one with a series of N-arylchloroacetamides and 3-aryl-5-(chloromethyl)-1,2,4-oxadiazoles in DMF in the presence of K2CO3 the target compounds were obtained. The antimicrobial activity was assessed by the agar well diffusion method. The concentration of microbial cells was determined by the McFarland standard; the value was 107 cells in 1 mL of the media. The 18 – 24 hour culture of microorganisms was used for tests. For the bacteria cultivation, Müller-Hinton agar was used, Sabouraud agar was applied for C. albicans cultivation. The compounds were tested as the DMSO solution with the concentration of 100 µg/mL; the volume of the solution was 0.3 mL, the same volume was used for Streptomycin (the concentration 30 µg/mL). The docking studies were performed using Autodock Vina. Crystallographic data for the complexes of Streptomycin with the 16S subunit of ribosomal RNA (1NTB) and its active site, as well as for tRNA (Guanine37-N1)-methyltransferase (EC 2.1.1.228; TrmD) (5ZHN) and its active site were obtained from the Protein Data Bank.Conclusions. It has been determined that 2-[6-(1H-benzimidazol-2-yl)-5-methyl-4-oxothieno[2,3-d]pyrimidin-3(4H)-yl]-N-[4-(ethoxy)phenyl]acetamide, which is the most active as an antimicrobial agent among the compounds tested, also shows the best binding activity towards the active site of tRNA (guanine37-N1)-methyltransferase.

Background Crizotinib and Temozolomide are the two major chemotherapy drugs used for the treatment of cancers. Crizotinib is used as a target chemotherapy drug in many cancers. It mainly binds on the ATP binding regions of receptor tyrosine kinases (RTKs) targets and inhibits protein phosphorylation, which has already been reported. Temozolomide drug is known as the alkylating agent. Its mechanism of action is the methylation of DNA and thereby inhibiting DNA replication. However, the Temozolomide drug with protein level interaction of Glioblastoma Multiforme (GBM) and Non-small-cell lung carcinoma (NSCLC) of RTKs targets has not been reported so far. In the proposed work, we investigated the molecular level interaction of the Temozolomide drug in C-MET, C-ROS1, and ALK RTKs targets of GBM and NSCLC using an in silico study. We performed comparative analysis studies in both drugs' docked complexes based on their drug properties and complex energy (CE) to identify the better efficacy of the drug. Results From the docking studies, we could identify that the Temozolomide drug bounded protein complexes showed the least complex energy. The most stable complexes were identified from these docking studies by Molecular Dynamic simulation. In the proposed study, we found that the docked complex attained a stable conformation and least energy via solid hydrogen bond interactions between the amino acid residues and the drug at the binding sites of the proteins. The least energy and the hydrogen bond interaction of Temozolomide drug with the amino acid residues of the protein complexes of C-MET, C-ROS1 and ALK protein with their id name are: 2WGJ is − 11305.0830 (PRO1158, MET1160), 3ZBF is − 11,659.6814 (MET2029, GLU2027), and 2XP2 is − 11,734.7565 (ARG1275, ASP 1160, GLU1167). Conclusion Our studies revealed that the Temozolomide drug bounded protein complex showed the least energy when compared to Crizotinib. So it will give better interaction on the binding sites of proteins and thereby provide better inhibition in the treatment of target therapy of GBM and NSCLC.

Background: Dihydroorotate dehydrogenase (DHODH) has long been recognized as an important drug target for proliferative and parasitic diseases, including compounds that exhibit trypanocidal action and broad-spectrum antiviral activity. Despite numerous and successful efforts in structural and functional characterization of DHODHs, as well as in the development of inhibitors, DHODH hot spots remain largely unmapped and underexplored. Objective: This review describes the tools that are currently available for the identification and characterization of hot spots in protein structures and how freely available webservers can be exploited to predict DHODH hot spots. Moreover, it provides for the first time a review of the antiviral properties of DHODH inhibitors. Method: X-ray structures from human (HsDHODH) and Trypanosoma cruzi DHODH (TcDHODH) had their hot spots predicted by both FTMap and Fragment Hotspot Maps web servers. Result: FTMap showed that hot spot occupancy in HsDHODH is correlated with the ligand efficiency (LE) of its known inhibitors, and Fragment Hotspot Maps pointed out the contribution of selected moieties to the overall LE. The conformational flexibility of the active site loop in TcDHODH was found to have a major impact on the druggability of the orotate binding site. In addition, both FTMap and Fragment Hotspot Maps servers predict a novel pocket in TcDHODH dimer interface (S6 site). Conclusion: This review reports how hot spots can be exploited during hit-to-lead steps, docking studies or even to improve inhibitor binding profile and by doing so using DHODH as a model, points to new drug development opportunities.

International audience; We explored the Protein DataBank (PDB) to collect protein-ssDNA structures and create a multiconformational docking benchmark including both bound and unbound protein structures. Due to ssDNA high flexibility when not bound, no ssDNA unbound structure is included in the benchmark. For the 91 sequence-identity groups identified as bound-unbound structures of the same protein, we studied the conformational changes in the protein induced by the ssDNA binding. Moreover, based on several bound or unbound protein structures in some groups, we also assessed the intrinsic conformational variability in either bound or unbound conditions, and compared it to the supposedly binding-induced modifications. To illustrate a use case of this benchmark, we performed docking experiments using ATTRACT docking software. This benchmark is, to our knowledge, the first one made to peruse available structures of ssDNA-protein interactions to such an extent, aiming to improve computational docking tools dedicated to this kind of molecular interactions.

Activation and expansion of drug reactive T cells are key features in drug hypersensitivity reactions. Drugs may interact directly with immune receptors such as the human leukocyte antigens (HLA) or the T-cell receptors (TCR) itself, the pharmacological interaction [p-i] concept. To analyze whether the drug sulfamethoxazole (SMX) interacts directly with the TCR and thereby contributing to signaling and T cell activation, we analyze two SMX specific T cell clones (TCC “1.3”and “H13”). Proliferation to SMX and 11 related sulfanilamides, Ca++ influx in drug stimulated T-cells and the inhibitory effect of non-reactive sulfanilamides on SMX stimulation were analyzed. In silico docking of SMX and related sulfanilamide to the TCR were used to identify possible drug binding sites, and correlated to in vitro data to find the correct docking. In Ca++ influx assays, reactions occurred as early as 14 sec after adding SMX to TCC and APC. The broadly reactive clone (“H13”) was stimulated by 5 additional sulfanilamide, while one TCC (“1.3”) was reactive exclusively with SMX but not other sulfanilamides. Competition experiments with sulfanilamide inhibited SMX induced Ca++ influx and proliferation of the TCC1.3 ina dose dependent way. Docking experiments with SMX and related sulfanilamides confirmed and explained the in vitro data as docking localized binding sites for SMX and the 5 stimulating sulfanilamides on the CDR2β domain of the clone H13, while the 6 non-stimulatory SA failed to bind. In TCC 1.3, SMX could be docked on the CDR3α of the TCR. The other, non-stimulatory but inhibitory SA could also be docked to the same site. The combined analysis of in vitro and in silico data show that sulfanilamide can bind directly to TCRs. It shows that TCR, like other receptors, appear to be reamenable to manipulations by small molecules.

The voltage-gated potassium channel, KV11.1, encoded by the humanEther-à-go-go- Related Gene (hERG) is expressed in cardiac myocytes, where it is crucial for the membrane repolarization of the action potential. Gating of hERG channel is characterized by rapid, voltage-dependent, C-type inactivation, which blocks ion conduction and is suggested to involve constriction of the selectivity filter. Mutations S620T and S641A/T within the selectivity filter region of hERG have been shown to alter the voltage- dependence of channel inactivation. Because hERG channel blockade is implicated in drug-induced arrhythmias associated with both the open and inactivated states, we used Rosetta to simulate effects of hERG S620T and S641A/T mutations to elucidate conformational changes associated with hERG channel inactivation and differences in drug binding between the two states. Rosetta modeling of the S641A fast-inactivating mutation revealed a lateral shift of F627 side chain in the selectivity filter into the central channel axis along the ion conduction pathway and formation of four lateral fenestrations in the pore. Rosetta modeling of the non-inactivating mutations S620T and S641T suggested a potential molecular mechanism preventing F627 side chain from shifting into the ion conduction pathway during the proposed inactivation process. Furthermore, we used Rosetta docking to explore the binding mechanism of highly selective and potent hERG blockers - dofetilide, terfenadine, and E4031. Our structural modeling correlate well with existing experimental evidence involving interactions of these drugs with key hERG residues Y652 and F656 inside the pore and reveal potential ligand binding interactions within fenestration region in an inactivated state.Significance StatementComputational models of hERG potassium channel provide structural insights into an inactivated state and associated drug interactions. Our computational approach will be useful to study ion channel modulation by small molecules.

A large analysis of the signal transducer and activator of transcription (STAT3) in cancer is currently being carried out. It regulates gene expression, which is required for normal cellular functi...