Design,synthesis and evaluation of novel 2-hydroxypyrrolobenzodiazepine-5,11-dione analogues as potent angiotensin converting enzyme (ACE) inhibitors

A series of novel 10-substituted 2-hydroxypyrrolobenzodiazepine-5,11-diones designed through structure based rational hybridization approach, synthesized by the cyclodehydration of isotonic anhydride with (2S,4R)-4-hydroxypyrrolidine-2-carboxylic acid followed by N-substitution, were evaluated as angiotensin converting enzyme (ACE) inhibitors. Among all the new compounds screened (2R,11aS)-10-((4-bromothiophen-2-yl)methyl)-2-hydroxy-2,3-dihydro-1H-benzo[e]pyrrolo[1,2-a][1,4]diazepine-5,11(10H,11aH)dione, 5v (IC₅₀: 0.272 μM) emerged as most active non-carboxylic acid ACE inhibitor with minimal toxicity comparable to clinical drugs Lisinopril, Benazepril and Ramipril. Favorable binding characteristics in docking studies also supported the experimental results.     

Probing molecular interaction between concanavalin A and mannose ligands by means of SFM

Recently, the scanning force microscope (SFM) has been widely used for direct monitoring of specific interactions between biologically active molecules. Such studies have employed the SFM liquid-cell setup, which allows measurements to be made in the native environment with force resolution down to a tenth of a picoNewton. In this study, the ligand–receptor strength of monoclonal anti-human prostatic acid phosphatase and prostatic acid phosphatase, representing an antigen–antibody system with a single type of interaction, was determined. Then, the interaction force occurring between concanavalin A and the carbohydrate component of the glycoproteins arylsulfatase A and carboxypeptidase Y was measured. High mannose-type glycans were sought on the human prostate carcinoma cell surface. Application of an analysis based on the Poisson distribution of the number of bonds formed in all these measured systems allowed the strength of the molecular interaction to be calculated. The values of the force acting between two single molecules were 530±25, 790±32, and 940±39 pN between prostatic acid phosphatase and monoclonal anti-human prostatic acid phosphatase, between concanavalin A and arylsulfatase A, and between concanavalin A and carboxypeptidase Y, respectively. The value calculated from data collected for the force between concanavalin A and mannose-containing ligands present on the surface of human prostate carcinoma cells was smaller, 116±17 pN. The different values of the binding force between concanavalin A and mannose-containing ligands were attributed to the structural changes of the carbohydrate components.     

Synthesis and biological evaluation of salicylate-based compounds as a novel class of methionine aminopeptidase inhibitors

A series of salicylate-based compounds were designed and synthesized based on the simple function group replacement from our previously reported catechol-containing inhibitors of methionine aminopeptidase (MetAP). Some of these salicylate derivatives showed similar potency and metalloform selectivity, and some showed considerable antibacterial activity. These findings are consistent with our previous conclusion that Fe(II) is the likely metal used by MetAP in bacterial cells and provide new lead structures that can be further developed as novel antibacterial agents.     

Design,synthesis, biological evaluation and molecular modelling studies of indole glyoxylamides as a new class of potential pancreatic lipase inhibitors

A series of eighteen indole glyoxylamide analogues were synthesized, characterized and evaluated for their pancreatic lipase inhibitory activity. Porcine pancreatic lipase (Type II) was used with 4-nitrophenyl butyrate (as substrate) for the in vitro assay. Compound 8f exhibited competitive inhibition against pancreatic lipase with IC₅₀ value of 4.92 µM, comparable to that of the standard drug, orlistat (IC₅₀ = 0.99 µM). Compounds 7a-i and 8a-i were subjected to molecular docking into the active site of human PL (PDB ID: 1LPB) wherein compound 8f possessed a potential MolDock score of −153.037 kcal/mol. Molecular dynamics simulation of 8f complexed with pancreatic lipase, confirmed the role of aromatic substitution in stabilizing the ligand through hydrophobic interactions (maximum observed RMSD = 3.5 Å).     

In vitro and in silico evaluation of new thiazole compounds as monoamine oxidase inhibitors

New twenty compounds bearing thiazole ring (3a-3t) were designed and synthesized as monoamine oxidase (MAO) inhibitors. The fluorometric enzyme inhibition assay was used to determine the biological effects of synthesized compounds. Most of them showed remarkable inhibitory activity against both MAO-A and MAO-B. By comparing their IC₅₀ values, it can be seen that active derivatives displayed generally selectivity on MAO-B enzyme. Compounds 3j and 3t, which bear dihydroxy moiety at the 3rd and 4th position of phenyl ring, were the most active derivatives in the series against both isoenzymes. Compounds 3j and 3t showed significant inhibition profile on MAO-A with the IC₅₀ values of 0.134 ± 0.004 µM and 0.123 ± 0.005 µM, respectively, while they performed selectivity against MAO-B with the IC₅₀ values of 0.027 ± 0.001 µM and 0.025 ± 0.001 µM, respectively. Also, docking studies about these compounds were carried out to evaluate their binding modes on the active regions of MAO-A and MAO-B.     

根据分子连接性指数和基团校正因子预测有机化合物在鱼体中的生物富集因子

研究了２３９种有机化合物的ＢＣＦ预测模型,结果显示根据分子连接性指数（ＭＣＩ）的线性模型不能准确计算及极性化合物的ＢＣＦ,也不适用于超疏水性化合物,在模型中引入基团校正因子后,极性经合物的计算误差明显降低。对数据进行曲线拟合,所得模型的估算精度进一步提高,最终确定以（＾０ｘ＾ｖ）＾２、（＾２ｘ＾ｖ）＾１／２、＾２ｘ、＾３ｘｃ、＾０ｘ＾ｖ及ＯＨ、ＮＨ２、ＮＯ２、ＮＣＯＯ等１０个基团校正团子为参数建立     

Synthesis and identification of novel pyridazinylpyrazolone based diazo compounds as inhibitors of human islet amyloid polypeptide aggregation

We have carried out a docking inspired synthesis and screening of a library of diazenyl-derivatives of pyridazinylpyrazolone molecules for their ability to modulate the amyloidogenic self-assembly of human islet amyloid polypeptide (hIAPP). hIAPP is a 37-residue peptide which is involved in glycemic control along with insulin. Its extracellular fibrillar assemblies in pancreatic β-cells are responsible for type 2 diabetes. A three-step synthetic scheme was used to prepare these novel compounds using 2-(6-chloropyridazin-3-yl)-5-methyl-2,4-dihydro-3H-pyrazol-3-one as a key intermediate that was reacted with various diazo electrophiles to generate a library of compounds with yields ranging from 64 to 85%. The effect of the compounds on hIAPP amyloid fibril formation was evaluated with a thioflavin T (ThT) fluorescence-based kinetic assay. Furthermore, TEM imaging was carried out to corroborate the interactions of the compounds with hIAPP and subsequent hIAPP inhibition at the different level of fibrillization. The CD spectroscopy showed that upon incubation with SSE15314 for 12 h, the percentage of α-helices was maintained to a level of hIAPP at 0 h. The current study presents identification and characterization of SSE15314 as the hit, which completely inhibited the fibril formation and can be further optimized into a lead compound.     

Analysis of maslinic acid and gallic acid compounds as xanthine oxidase inhibitors in isoprenaline administered myocardial necrotic rats

ObjectiveThis research designed to analyze the in vivo and in silico ameliorative action of maslinic acid (MA) and gallic acid (GA) on reactive oxygen species generating enzyme xanthine oxidase (XO) in isoprenaline or isoproterenol (ISO) induced myocardial infarcted rats.MethodsAlbino Wistar rats were categorized into four groups with eight rats in each group. A dose of 15 mg/kg of MA and GA were pretreated to each MA and GA groups for seven days. A dose of 85 mg/kg of ISO administered to the ISO group along with MA and GA groups except normal group on two consecutive days of pretreatment. All animals sacrificed and the heart tissues were collected for the analysis of XO. The in silico molecular docking analysis of the compounds MA and GA with XO was analyzed by using Gold 3.0.1 software.ResultsXO enzyme levels were significantly increased in the heart homogenate of ISO administered rats when compared to normal rats. Pretreatment of MA and GA to ISO treated rats significantly brought XO enzyme to the near normal levels which indicate the protective action of MA and GA against myocardial necrosis. The in vivo results were further supported by the in silico molecular docking study which revealed the inhibition of XO enzyme by the formation of enzyme and ligand complex with the compounds MA and GA.ConclusionMA and GA compounds manifested the ameliorative effect against ISO administrated myocardial necrosis by inhibiting the free radical generating enzyme XO which is evidenced by both in vivo and in silico studies.     

An in silico approach unveils the potential of antiviral compounds in preclinical and clinical trials as SARS-CoV-2 omicron inhibitors

The increased transmissibility and highly infectious nature of the new variant of concern (VOC) that is severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron and lack of effective therapy need the rapid discovery of therapeutic antivirals against it. The present investigation aimed to identify antiviral compounds that would be effective against SARS-CoV-2 Omicron. In this study, molecular docking experiments were carried out using the recently reported experimental structure of omicron spike protein in complex with human angiotensin-converting enzyme 2 (ACE2) and various antivirals in preclinical and clinical trial studies. Out of 36 tested compounds, Abemaciclib, Dasatinib and Spiperone are the three top-ranked molecules which scored binding energies of ?10.08 kcal/mol, ?10.06 kcal/mol and ?9.54 kcal/mol respectively. Phe338, Asp339, and Asp364 are crucial omicron receptor residues involved in hydrogen bond interactions, while other residues were mostly involved in hydrophobic interactions with the lead molecules. The identified lead compounds also scored well in terms of drug-likeness. Molecular dynamics (MD) simulation, essential dynamics (ED) and entropic analysis indicate the ability of these molecules to modulate the activity of omicron spike protein. Therefore, Abemaciclib, Dasatinib and Spiperone are likely to be viable drug-candidate molecules that can block the interaction between the omicron spike protein and the host cellular receptor ACE2. Though our findings are compelling, more research into these molecules is needed before they can be employed as drugs to treat SARS-CoV-2 omicron infections.     

N-(thiazol-2-yl)-2-thiophene carboxamide derivatives as Abl inhibitors identified by a pharmacophore-based database screening of commercially available compounds

Suggestions derived from a previous ligand-based ligand design approach and docking calculations aimed at finding compound with affinity toward Abl and molecular scaffolds previously untested as Abl inhibitors, led to the identification of commercially available N-(thiazol-2-yl)-2-thiophene carboxamide derivatives with affinity in a cell-free assay up to low nanomolar concentrations, significantly enhanced with respect to that of their parent compounds previously reported. In particular, among compounds of the Asinex database, molecular docking simulations guided the choice of high-affinity ligands, predicting their binding mode and their interaction pattern with the Abl catalytic binding site. Moreover, affinity of the new compounds was also rationalized in terms of their interactions with the enzyme.     

Identification of natural compounds as potent inhibitors of SARS-CoV-2 main protease using combined docking and molecular dynamics simulations

Coronavirus disease 2019 (COVID-19) has emerged from China and globally affected the entire population through the human-to-human transmission of a newly emerged virus called severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The genome of SARS-CoV-2 encodes several proteins that are essential for multiplication and pathogenesis. The main protease (M^pro or 3CL^pro) of SARS-CoV-2 plays a central role in its pathogenesis and thus is considered as an attractive drug target for the drug design and development of small-molecule inhibitors. We have employed an extensive structure-based high-throughput virtual screening to discover potential natural compounds from the ZINC database which could inhibit the M^pro of SARS-CoV-2. Initially, the hits were selected on the basis of their physicochemical and drug-like properties. Subsequently, the PAINS filter, estimation of binding affinities using molecular docking, and interaction analyses were performed to find safe and potential inhibitors of SARS-CoV-2 M^pro. We have identified ZINC02123811 (1-(3-(2,5,9-trimethyl-7-oxo-3-phenyl-7H-furo[3,2-g]chromen-6-yl)propanoyl)piperidine-4-carboxamide), a natural compound bearing appreciable affinity, efficiency, and specificity towards the binding pocket of SARS-CoV-2 M^pro. The identified compound showed a set of drug-like properties and preferentially binds to the active site of SARS-CoV-2 M^pro. All-atom molecular dynamics (MD) simulations were performed to evaluate the conformational dynamics, stability and interaction mechanism of M^pro with ZINC02123811. MD simulation results indicated that M^pro with ZINC02123811 forms a stable complex throughout the trajectory of 100 ns. These findings suggest that ZINC02123811 may be further exploited as a promising scaffold for the development of potential inhibitors of SARS-CoV-2 M^pro to address COVID-19.     

Molecular Modeling and docking of Wheat Hydroquinone Glucosyl transferase by using Hydroquinone,Phenyl phosphorodiamate and n-(n butyl) Phosphorothiocic Triamide as Inhibitors

In agriculture high urease activity during urea fertilization causes substantial environmental and economical problems by releasingabnormally large amount of ammonia into the atmosphere which leads to plant damage as well as ammonia toxicity. All over theworld, urea is the most widely applied nitrogen fertilizer. Due to the action of enzyme urease; urea nitrogen is lost as volatileammonia. For efficient use of nitrogen fertilizer, urease inhibitor along with the urea fertilizer is one of the best promisingstrategies. Urease inhibitors also provide an insight in understanding the mechanism of enzyme catalyzed reaction, the role ofvarious amino acids in catalytic activity present at the active site of enzyme and the importance of nickel to this metallo enzyme. Bykeeping it in view, the present study was designed to dock three urease inhibitors namely Hydroquinone (HQ), PhenylPhosphorodiamate (PPD) and N-(n-butyl) Phosphorothiocic triamide (NBPT) against Hydroquinone glucosyltransferase usingmolecular docking approach. The 3D structure of Hydroquinone glucosyltransferase was predicted using homology modelingapproach and quality of the structure was assured using Ramachandran plot. This study revealed important interactions amongthe urease inhibitors and Hydroquinone glucosyltransferase. Thus, it can be inferred that these inhibitors may serve as future antitoxic constituent against plant toxins.