scholarly journals Towards Novel 3-Aminopyrazinamide-Based Prolyl-tRNA Synthetase Inhibitors: In Silico Modelling, Thermal Shift Assay and Structural Studies

2021 ◽  
Vol 22 (15) ◽  
pp. 7793
Author(s):  
Luping Pang ◽  
Stephen D. Weeks ◽  
Martin Juhás ◽  
Sergei V. Strelkov ◽  
Jan Zitko ◽  
...  
Keyword(s):  
High Throughput Screening ◽  
Docking Studies ◽  
Enzyme Concentration ◽  
Trna Synthetase ◽  
Atp Binding Site ◽  
Drug Candidates ◽  
Thermal Shift Assay ◽  
Screening Protocol ◽  
New Applications ◽  
Thermal Shift

Human cytosolic prolyl-tRNA synthetase (HcProRS) catalyses the formation of the prolyl-tRNAPro, playing an important role in protein synthesis. Inhibition of HcProRS activity has been shown to have potential benefits in the treatment of fibrosis, autoimmune diseases and cancer. Recently, potent pyrazinamide-based inhibitors were identified by a high-throughput screening (HTS) method, but no further elaboration was reported. The pyrazinamide core is a bioactive fragment found in numerous clinically validated drugs and has been subjected to various modifications. Therefore, we applied a virtual screening protocol to our in-house library of pyrazinamide-containing small molecules, searching for potential novel HcProRS inhibitors. We identified a series of 3-benzylaminopyrazine-2-carboxamide derivatives as positive hits. Five of them were confirmed by a thermal shift assay (TSA) with the best compounds 3b and 3c showing EC50 values of 3.77 and 7.34 µM, respectively, in the presence of 1 mM of proline (Pro) and 3.45 µM enzyme concentration. Co-crystal structures of HcProRS in complex with these compounds and Pro confirmed the initial docking studies and show how the Pro facilitates binding of the ligands that compete with ATP substrate. Modelling 3b into other human class II aminoacyl-tRNA synthetases (aaRSs) indicated that the subtle differences in the ATP binding site of these enzymes likely contribute to its potential selective binding of HcProRS. Taken together, this study successfully identified novel HcProRS binders from our anti-tuberculosis in-house compound library, displaying opportunities for repurposing old drug candidates for new applications such as therapeutics in HcProRS-related diseases.

Discovery of the SMYD3 Inhibitor BAY-6035 Using Thermal Shift Assay (TSA)-Based High-Throughput Screening

2021 ◽  
pp. 247255522110194
Author(s):  
Stefan Gradl ◽  
Holger Steuber ◽  
Joerg Weiske ◽  
Magda M. Szewczyk ◽  
Norbert Schmees ◽  
...  
Keyword(s):  
Growth Factor ◽  
High Throughput ◽  
High Throughput Screening ◽  
Growth Factor Receptor ◽  
Mitogen Activated Protein Kinase ◽  
Cancer Drug ◽  
Titration Calorimetry ◽  
Nonhistone Proteins ◽  
Thermal Shift Assay ◽  
Thermal Shift

SMYD3 (SET and MYND domain-containing protein 3) is a protein lysine methyltransferase that was initially described as an H3K4 methyltransferase involved in transcriptional regulation. SMYD3 has been reported to methylate and regulate several nonhistone proteins relevant to cancer, including mitogen-activated protein kinase kinase kinase 2 (MAP3K2), vascular endothelial growth factor receptor 1 (VEGFR1), and the human epidermal growth factor receptor 2 (HER2). In addition, overexpression of SMYD3 has been linked to poor prognosis in certain cancers, suggesting SMYD3 as a potential oncogene and attractive cancer drug target. Here we report the discovery of a novel SMYD3 inhibitor. We performed a thermal shift assay (TSA)-based high-throughput screening (HTS) with 410,000 compounds and identified a novel benzodiazepine-based SMYD3 inhibitor series. Crystal structures revealed that this series binds to the substrate binding site and occupies the hydrophobic lysine binding pocket via an unprecedented hydrogen bonding pattern. Biochemical assays showed substrate competitive behavior. Following optimization and extensive biophysical validation with surface plasmon resonance (SPR) analysis and isothermal titration calorimetry (ITC), we identified BAY-6035, which shows nanomolar potency and selectivity against kinases and other PKMTs. Furthermore, BAY-6035 specifically inhibits methylation of MAP3K2 by SMYD3 in a cellular mechanistic assay with an IC50 <100 nM. Moreover, we describe a congeneric negative control to BAY-6035. In summary, BAY-6035 is a novel selective and potent SMYD3 inhibitor probe that will foster the exploration of the biological role of SMYD3 in diseased and nondiseased tissues.

Insights Studies for Certain Natural FDA Approved Polyphenolics and Repurposing for COVID-19

2020 ◽  
Vol 11 (SPL1) ◽  
pp. 1390-1395
Author(s):  
Arafa Musa ◽  
Ehab M. Mostafa ◽  
Mohammad M. Al-Sanea ◽  
Shaimaa R. Ahmed ◽  
Gomaa Mostafa-Hedeab ◽  
...  
Keyword(s):  
Docking Studies ◽  
Human Populations ◽  
Energy Score ◽  
Protease Enzyme ◽  
Human Disorders ◽  
Variable Chemical ◽  
Pancreatic Disorders ◽  
New Treatment ◽  
New Applications ◽  
Death Cases

Natural polyphenolic drugs were approved for treatment of various diseases. Diosmin, rutin, quercetin, aesculin, genistein, hesperidin and silybin are known for their safety and have been applied for several human disorders including cancer, cardiovascular disorders, atherosclerosis, oxidative stress, capillary fragility, liver and pancreatic disorders and others. As the structures of the selected polyphenolic compounds possess variable chemical moieties with diverse chemical and electronic characters, these properties have been employed for further insights studies to predict new applications concerning the newly occurred pandemic. COVID-19 is a terrible disease that attacked millions of human populations at the end of year 2019. As the number of death cases has increased to exceed one million of humans, the early discovery of new treatment from previously approved and safe drugs is the main target of this study. Employing the putative docking studies for the selected polyphenolic drugs were done and the results were promising, all tested drugs exhibited high affinity with the selected five proteins of protease enzyme, the docking score ranged from -8.4461 to -26.1691 kcal/mol with 3-7 variable interaction bonds. Among the tested drugs, diosmin appeared as the most promising drug as it exhibited the highest energy score and interaction bonds with the most of proteins.

Recent Advances and Computational Approaches in Peptide Drug Discovery

2019 ◽  
Vol 25 (31) ◽  
pp. 3358-3366 ◽  
Author(s):  
Neha S. Maurya ◽  
Sandeep Kushwaha ◽  
Ashutosh Mani
Keyword(s):  
Docking Studies ◽  
Computational Approaches ◽  
Simulation Tools ◽  
Drug Candidates ◽  
Recent Advances ◽  
Long Duration ◽  
Stability Of Complexes ◽  
Therapeutic Peptides ◽  
Target Binding ◽  
Druggable Targets

Background: Drug design and development is a vast field that requires huge investment along with a long duration for providing approval to suitable drug candidates. With the advancement in the field of genomics, the information about druggable targets is being updated at a fast rate which is helpful in finding a cure for various diseases. Methods: There are certain biochemicals as well as physiological advantages of using peptide-based therapeutics. Additionally, the limitations of peptide-based drugs can be overcome by modulating the properties of peptide molecules through various biomolecular engineering techniques. Recent advances in computational approaches have been helpful in studying the effect of peptide drugs on the biomolecular targets. Receptor – ligand-based molecular docking studies have made it easy to screen compatible inhibitors against a target.Furthermore, there are simulation tools available to evaluate stability of complexes at the molecular level. Machine learning methods have added a new edge by enabling accurate prediction of therapeutic peptides. Results: Peptide-based drugs are expected to take over many popular drugs in the near future due to their biosafety, lower off-target binding chances and multifunctional properties. Conclusion: This article summarises the latest developments in the field of peptide-based therapeutics related to their usage, tools, and databases.

Design, Synthesis and Pharmacological Evaluation of Novel Antiinflammatory and Analgesic O-Benzyloxime Compounds Derived From Natural Eugenol

2019 ◽  
Vol 16 (10) ◽  
pp. 1157-1166
Author(s):  
Rodrigo César da Silva ◽  
Fabiano Veiga ◽  
Fabiana Cardoso Vilela ◽  
André Victor Pereira ◽  
Thayssa Tavares da Silva Cunha ◽  
...  
Keyword(s):  
Formalin Test ◽  
Docking Studies ◽  
Paw Edema ◽  
Inhibitory Effects ◽  
Structural Pattern ◽  
Design Synthesis ◽  
Drug Candidates ◽  
Anti Inflammatory ◽  
Analgesic Activities ◽  
Cox 1

Background: : A new series of O-benzyloximes derived from eugenol was synthesized and was evaluated for its antinociceptive and anti-inflammatory properties. Methods: : The target compounds were obtained in good global 25-28% yields over 6 steps, which led us to identify compounds (Z)-5,6-dimethoxy-2,2-dimethyl-2,3-dihydro-1H-inden-1-one-O-(4- (methylthio)benzyloxime (8b), (Z)-5,6-dimethoxy-2,2-dimethyl-2,3-dihydro-1H-inden-1-one-O-4- bromobenzyloxime (8d) and (Z)-5,6-dimethoxy-2,2-dimethyl-2,3-dihydro-1H-inden-1-one-O-4- (methylsulfonyl)benzyloxime (8f) as promising bioactive prototypes. Results:: These compounds have significant analgesic and anti-inflammatory effects, as evidenced by formalin-induced mice paw edema and carrageenan-induced mice paw edema tests. In the formalin test, compounds 8b and 8f evidenced both anti-inflammatory and direct analgesic activities and in the carrageenan-induced paw edema, with compounds 8c, 8d, and 8f showing the best inhibitory effects, exceeding the standard drugs indomethacin and celecoxib. Conclusion: : Molecular docking studies have provided additional evidence that the pharmacological profile of these compounds may be related to inhibition of COX enzymes, with slight preference for COX-1. These results led us to identify the new O-benzyloxime ethers 8b, 8d and 8f as orally bioactive prototypes, with a novel structural pattern capable of being explored in further studies aiming at their optimization and development as drug candidates.

Inhibition Profiling of Urease and Carbonic Anhydrase II by High- Throughput Screening and Molecular Docking Studies of Structurally Diverse Organic Compounds

2020 ◽  
Vol 17 ◽  
Author(s):  
Majid Ali ◽  
Syed Majid Bukhari ◽  
Asma Zaidi ◽  
Farhan A. Khan ◽  
Umer Rashid ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Carbonic Anhydrase ◽  
Metal Complexes ◽  
Organic Compounds ◽  
High Throughput ◽  
High Throughput Screening ◽  
Docking Studies ◽  
Carbonic Anhydrase Ii ◽  
Molecular Docking Studies ◽  
Ic50 Values

Background:: Structurally diverse organic compounds and available drugs were screened against urease and carbonic anhydrase II in a formulation acceptable for high-throughput screening. Objective: The study was conducted to find out potential inhibitors of urease and carbonic anhydrase II. Methods:: Quantification of the possible HITs was carried out by determining their IC50 values. Results and Discussion:: of several screened compounds including derivatives of oxadiazole, coumarins, chromane-2, 4- diones and metal complexes of cysteine-omeprazole showed promising inhibitory activities with IC50 ranging from 47 μM to 412 μM against the urease. The interactions of active compounds with active sites of enzymes were investigated through molecular docking studies which revealed that (R)-1-(4-amino-4-(5-(thiophen-2-yl)-1,3,4-oxadiazol-2-yl) butyl) guanidine possessing IC50 of 47 μM, interacts with one of the nickel metal atom of urease besides further interactions as predictable hydrogen bonds with KCX490, Asp633, His492, His407 and His409 along with Ala440 and 636. Bi-ligand metal complexes of 4-aminoantipyrine based Schiff bases showed activation of urease with AC50 ranging from 68 μM to 112 μM. Almost 21 compounds with varying functional groups including pyrimidines, oxadiazoles, imidazoles, hydrazides and tin based compounds were active carbonic anhydrase II inhibitors presenting 98 μM to 390 μM IC50 values. Several N-substituted sulfonamide derivatives were inactive against carbonic anhydrase II. Conclusion:: Among all the screened compounds, highly active inhibitor of carbonic anhydrase II was (4-(3- hydroxyphenyl)-6-phenyl-2-thioxo-1,2,3,4-tetrahydropyrimidin-5-yl)phenyl) methanone with IC50 of 98.0 μM. This particular compound showed metallic interaction with Zn ion of carbonic anhydrase II through hydroxyl group of phenyl ring.

scholarly journals High-throughput computational-experimental screening protocol for the discovery of bimetallic catalysts

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Byung Chul Yeo ◽  
Hyunji Nam ◽  
Hyobin Nam ◽  
Min-Cheol Kim ◽  
Hong Woo Lee ◽  
...  
Keyword(s):  
High Throughput ◽  
Bimetallic Catalysts ◽  
High Throughput Screening ◽  
Direct Synthesis ◽  
Catalytic Performance ◽  
Platinum Group Metals ◽  
Pt Catalyst ◽  
Electronic Density ◽  
Bimetallic Alloy ◽  
Screening Protocol

AbstractTo accelerate the discovery of materials through computations and experiments, a well-established protocol closely bridging these methods is required. We introduce a high-throughput screening protocol for the discovery of bimetallic catalysts that replace palladium (Pd), where the similarities in the electronic density of states patterns were employed as a screening descriptor. Using first-principles calculations, we screened 4350 bimetallic alloy structures and proposed eight candidates expected to have catalytic performance comparable to that of Pd. Our experiments demonstrate that four bimetallic catalysts indeed exhibit catalytic properties comparable to those of Pd. Moreover, we discover a bimetallic (Ni-Pt) catalyst that has not yet been reported for H2O2 direct synthesis. In particular, Ni61Pt39 outperforms the prototypical Pd catalyst for the chemical reaction and exhibits a 9.5-fold enhancement in cost-normalized productivity. This protocol provides an opportunity for the catalyst discovery for the replacement or reduction in the use of the platinum-group metals.

Rapid Evaluation of Small Molecule Cellular Target Engagement with a Luminescent Thermal Shift Assay

2021 ◽  
Author(s):  
Jonathan D. Mortison ◽  
Ivan Cornella-Taracido ◽  
Gireedhar Venkatchalam ◽  
Anthony W. Partridge ◽  
Nirodhini Siriwardana ◽  
...  
Keyword(s):  
Small Molecule ◽  
Rapid Evaluation ◽  
Target Engagement ◽  
Thermal Shift Assay ◽  
Cellular Target ◽  
Thermal Shift

Selection of oxypeucedanin as a potential antagonist from molecular docking analysis of HSP90

2020 ◽  
Vol 0 (0) ◽  
Author(s):  
Joshua Oluwasegun Bamidele ◽  
George Oche Ambrose ◽  
Oluwaseun Suleiman Alakanse
Keyword(s):  
Molecular Docking ◽  
Liver Toxicity ◽  
Docking Study ◽  
Docking Studies ◽  
Molecular Docking Study ◽  
Docking Analysis ◽  
Computational Docking ◽  
Drug Candidates ◽  
Expression Rate ◽  
Client Proteins

AbstractHSP90 is observed as one of the copious molecular chaperones that play a key role in mediating appropriate folding, maturation, and firmness of many client proteins in cells. The expression rate of HSP90 in cancer cells is at a level of 2- to 10-fold higher than the 1- to 2-fold of its unstressed and healthy ones. To combat this, several inhibitors to HSP90 protein have been studied (such as geldanamycin and its derivative 17-AAG and 17-DMAG) and have shown some primary side effects including plague, nausea, vomiting, and liver toxicity, hence the search for the best-in-class inhibitor for this protein through in silico. This study is aimed at analyzing the inhibitory potency of oxypeucedanin-a furocoumarin derivations, which have been reported to have antipoliferative activity in human prostrate carcinoma DN145 cells, and three other drug candidates retrieved from the literature via computational docking studies. The results showed oxypeucedanin as the compound with the highest binding energy of −9.2 kcal/mol. The molecular docking study was carried out using PyRx, Auto Dock Vina option, and the target was validated to confirm the proper target and the docking procedure employed for this study.

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