Letters in Drug Design & Discovery - Volume 19, Issue 8, 2022

Objectives: 1,2-thiazine and pyridine heterocycles drew much attention due to their biological activities, including antioxidant activity. Based on fragment-based drug design, novel pyrido[1,2]thiazines 9a-c, thiazolidinopyrido[1,2], thiazines 10a-c and azetidinopyrido[1,2]thiazines 11a-c were designed and prepared. Methods: These novel derivatives 9a-c, 10a-c and 11a-c were subjected to screening for their antioxidant activity via various assays as DPPH radical scavenging potential, reducing power assay and metal chelating potential. Results: All the assayed derivatives exhibited excellent antioxidant potential and the tested compounds 9a, 9b, 10a, 10b, 11a and 11b exhibited higher DPPH scavenging potential (EC50 = 32.7, 53, 36.1, 60, 40.6 and 67 μM, respectively) than ascorbic acid (EC50 = 86.58 μM). While targets 9a, 10a and 11a (RP50 = 52.19, 59.16 and 52.25 μM, respectively) exhibited better reducing power than the ascorbic acid (RP50 = 84.66 μM). The computational analysis had been utilized to prophesy the bioactivity and molecular properties of the target compounds. Conclusion: To predict the binding manner of the novel derivatives as antioxidants, in-silico docking study was performed on all the newly prepared compounds inside superoxide dismutase (SOD) and catalase (CAT) active site. The most active antioxidant candidate 9a (EC50 = 32.7 μM, RP50 = 52.19 μM) displayed excellent binding with Lys134 amino acid residing at Cu-Zn loop of SOD with binding energy score = -7.54 Kcal/mol, thereby increasing SOD activity and decreasing reactive oxygen species.

Background: Alzheimer's disease affects a large part of the world’s population by prolonging the human life span and becoming an economic burden in the health system. Therefore, its treatment becomes more and more important every day. With the insufficiency of existing drug molecules, new drug targets are being searched. The most important of these is the Glycogen Synthase Kinase 3β enzyme, which is thought to be of key importance in Tau hyperphosphorylation and Amyloid β accumulation mechanisms. Objective: In this research, computational studies were conducted to develop a new GSK3β enzyme inhibitor. Methods: Leading compounds suitable for pharmacophore models obtained by the 3D QSAR method were scanned in databases. In silico ADME/Tox analyses were performed on the obtained molecules. Results: Although the three molecules (ENA99104, CNR13756, TIM405938) had strong Dock Scores (42.869, 53.344, and 41.119, respectively) in molecular docking calculations, only the CNR13756 molecule was found successful according to molecular dynamics simulations. Conclusion: All computational studies have revealed that the CNR13756 molecule can exhibit a therapeutic scaffold property, thus obtaining a selective GSK3β inhibitor with minimal side effects.

Background: Because the inflammatory pathway is triggered by the enzymes cyclooxygenase- 2 (COX-2) and inducible nitric oxide synthase (iNOS), inhibitors, such as nonsteroidal anti-inflammatory drugs (NSAIDs), are needed, although these have side effects. Therefore, the discovery and development of natural medicine as a lead compound are needed. The gorgonian corals have been reported to contain cyclic diterpenes with anti-inflammatory activities. The specific anti-inflammatory inhibitor potential has not been reported regarding these secondary metabolites, whether in COX-2 or iNOS. Thus, the in silico method is the right alternative. Objective: This study aimed to determine the potency of fifteen terpenes of the various gorgonian corals to COX-2 and iNOS enzymes as an anti-inflammatory. Methods: Molecular docking was performed using ChemDraw Ultra 12.0, Chem3D Pro 12.0, Biovia Discovery Studio 2016 Client®, Autodock Tools 4.2, prediction pharmacokinetics (Pre-ADMET), and oral administration (Lipinski rule of five). Results: Potential terpenes based on ΔG (kcal/mol) and Ki (nM) to COX-2 were gyrosanol B (-10,32; 27,15), gyrosanol A (-10,20; 33,57), echinolabdane A (-9,81; 64,76). Only nine terpenes were specific to COX-2 active sites, while for iNOS were palmonine F (-7.76; 2070), briarenol C (-7.55; 2910), and all test compounds binding to the iNOS active sites. Pre-ADMET prediction obtained that HIA was very excellent (70–100%), Caco-2 had moderate permeability (4-70 nm sec-1), and PPB had strong binding (> 90%). Eight terpenes qualified for the Lipinski rule of five. Conclusion: iNOS was a specific target for terpenes based on the free energy of binding (ΔG).

Aim: The study aims to design and synthesize novel thiazole derivatives as potent antitubercular agents with minimal side effects. Background: The emergence and rapid spread of multi-drug resistant infectious microbial flora embracing a variety of bacterial as well as mycobacterium strains are causing a threat to public health worldwide. Objective: Owing to the importance, we designed compounds with thiazole functionality coupled with Schiff base and thiosemicarbazide, predicted the molecular properties and antitubercular potency of designed compounds by the in-silico method, and synthesized fifteen novel thiazole analogs, characterized and tested in vivo antitubercular, antibacterial and antioxidant potencies. Methods: Molinspiration online tool was used to predict the molecular properties and molecular docking was used to predict the antitubercular potency. FT-IR, ¹H-NMR, ¹³C-NMR, Mass spectroscopy and bases of elemental analysis are employed to confirm the structure of compounds. 10-Fold serial dilution method, agar streak dilution test and DPPH radical scavenging methods are used to estimate antitubercular, antibacterial and antioxidant potency of title analogs, respectively. Results: Multi-step synthesis was used to synthesize a variety of novel thiazole derivatives coupled with Schiff base and thiosemicarbazide. Synthesized title compounds displayed a varying degree of antitubercular, antibacterial and antioxidant activities (mild to good). The title compounds possessing deactivating group exhibited superior activities than activating group, while unsubstituted analogs displayed intermediate activities. In addition, para-substituted analogs showed slightly higher activity than the corresponding meta substituted analogs. Conclusion: Among fifteen tested title compounds, the potent compound of this series was found to be 1- (4-nitrobenzylidene)-4-(4-(4-methoxyphenyl)thiazol-2-yl)thiosemicarbazide (BTS14), which might be extended as a novel class of antitubercular and antibacterial agents.

Background: Coronavirus disease-2019 (COVID-19) has recently emerged as a pandemic respiratory disease with mild to severe pneumonia symptoms. No clinical antiviral agent is available so far. However, several repurposing drugs and vaccines are being given to individuals or in clinical trials against SARS-CoV-2. Objective: The aim of this study is to uncover the potential effects of Luteolin (Lut) as an inhibitor of SARS-CoV2 encoded proteins via utilizing computational tools. Methods: Molecular modelling to unfold the anti-SARS-CoV2 potential of Lut along with reference drugs namely remdesivir and nafamostat was performed by the use of molecular docking, molecular dynamic (MD) simulation, absorption, distribution, metabolism, excretion, toxicity (ADMET) and density functional theory (DFT) methods against the five different SARS-CoV-2 encoded key proteins and one human receptor protein. The chemical reactivity of Luteolin is done through prediction of HOMO-LUMO gap energy and other chemical descriptors analysis. Results: In the present study, Lut binds effectively in the binding pockets of spike glycoprotein (6VSB), ADP phosphatase of NSP3 (6W02), and RNA dependent RNA polymerase (7AAP) protein receptors with significant values of docking scores -7.00, -7.25, and -6.46 respectively as compared to reference drugs remdesivir and nafamostat. Conclusion: Thus, Lut can act as a therapeutic agent and is orally safe for human consumption as predicted by molecular modelling against SARS-CoV-2 in the treatment of COVID-19.

Background: The need to develop novel antimicrobial agents is apparent as infectious diseases are increasing and resistance is rapidly developing against the drugs used in the treatment. Objective: This study aimed at the synthesis, antimicrobial susceptibility testing, and computational elucidation of the mechanism of action of benzoxazole derivatives. It also aimed to compare the results obtained in this study with the previous studies by our group. This would pave the way for designing novel molecules with better antimicrobial activity. The other goal was pharmacophore analysis and in silico ADMET analysis of them. Methods: In this study, synthesis, antimicrobial susceptibility testing, molecular docking, pharmacophore analysis, and ADMET prediction were carried out. Results: The antimicrobial activity studies demonstrated that the synthesized compounds were active against standard strains and clinical isolates at high concentrations. Then, the antimicrobial testing results were compared to similar benzoxazoles tested by our group previously. Benzoxazole derivatives without a methylene bridge between oxazole and phenyl ring were found to be more active than those with the methylene bridge. This was also confirmed by molecular modeling undertaken in this study. The computational results indicated that the antibacterial activity could be achieved by DNA gyrase inhibition. Pharmacophore analysis showed that hydrogen bond acceptor (HBA), hydrogen bond donor (HBD), and hydrophobicity features would contribute to the inhibition. In addition, in silico ADMET property investigation of the compounds exhibited that they had the desired pharmacokinetics. Conclusion: Although antibacterial activity by inhibiting DNA gyrase is selective, the synthesized compounds were active at much higher concentrations than the standards. Therefore, in prospective antimicrobial studies, it is better to focus on benzoxazole derivatives without the methylene bridge. Since the compounds had suitable in silico ADMET properties, screening them against the other pharmacologic activities should be carried out. It is recommended to support the molecular modeling results with in vitro or in vivo studies.

Background: Isoindoline derivatives exhibit a wide range of biological activities and have attracted considerable attention. However, few studies have been conducted on their antidepressant activity. Objective: Here, we designed and synthesized a series of isoindoline derivatives and studied their antidepressant activities. Methods: Forced swimming test (FST) and tail suspension test (TST) were used to evaluate the antidepressant activity of the target compounds. The most active compound was used to evaluate the exploratory activity of the animals by the open-field test. 5-HT concentration was estimated to evaluate if the compound has an effect on the mice brain by using ELISA. The biological activities of the compounds were verified by molecular docking studies. The pharmacokinetic properties of the target compounds were predicted by Discovery Studio (DS) 2020. Results: The results of the pharmacological experiments showed that most isoindoline derivatives exhibited significant antidepressant activity. Among these compounds, compound 4j showed the highest antidepressant activity. The results of the measurement of 5-HT levels in the brains of mice indicate that the antidepressant activity of isoindoline derivatives may be mediated by elevated 5-HT levels. Compound 4j was used in molecular docking experiments to simulate the possible interaction of these compounds with the 5-HT1A receptor. The results demonstrated that compound 4j had a significant interaction with amino acids around the active site of the 5-HT1A receptor in the homology model. Conclusion: Isoindoline derivatives synthesized in this study have a significant antidepressant activity. These findings can be useful in the design and synthesis of novel antidepressants.