scholarly journals Digging for the Discovery of SARS-CoV-2 nsp12 Inhibitors: A Pharmacophore-Based and Molecular Dynamics Simulation Study

2021 ◽  
Author(s):  
Fatemeh Sana Askari ◽  
Mohsen Ebrahimi ◽  
Jabbar Parhiz ◽  
Mina Hassanpour ◽  
Alireza Mohebbi ◽  
...  
Keyword(s):  
Conformational Changes ◽  
High Throughput Screening ◽  
Direct Interaction ◽  
Dynamics Simulation ◽  
Crystallographic Structure ◽  
Lead Compound ◽  
Autodock Vina ◽  
Chemical Library ◽  
Global Threat ◽  
Hit Identification

Abstract Background: The severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) is a grave global threat causing Coronavirus Disease 2019 (COVID-19). The therapeutics are urgently needed to cure patients severely infected with COVID-19. The aim of the study was to investigate for potential candidates of nsp12 inhibitors by searching for druggable cavity pockets within the viral protein and drug discovery.Methods: The crystallographic structure of SARS-CoV-2 nsp12 was searched for strong druggable cavity pockets and pharmacophore features by the CavityPlus server. The features were selected for high-throughput screening (HTS) of a chemical library of ZINC natural products and hit identification database by ZINCPharmer. Autodock Vina was furthered utilized for estimation of hits' affinities to nsp12. A lead compound with the highest affinity to nsp12 was simulated dynamically by GROMACS for 10 nanoseconds (ns) to measure the hit stability in complex with nsp12 and conformational changes.Results: 1 of 6 cavities with the highest score was selected for extraction of pharmacophore features and hit-identification. 9 pharmacophores were screened, and a total of unique 1274 hits were identified. One compound, ZINV03977803, with an -11.0 Kcal.mol-1 affinity was selected as the lead compound for molecular dynamic simulation (MDS). The results showed stable interaction between ZINV03977803 and nsp12 during 10 ns of simulation. The room-mean-square of deviation (RMSD) measure showed dramatically high conformational changes in the complex of ZINV03977803 and nsp12 compare two the viral proteins alone.Conclusions: The lead compound ZINV03977803 showed stable interaction with higher potential and hydrogen bonding with the catalytic subunit of SARS-CoV-2, nsp12. It could also inhibit the SARS-CoV-2 life cycle by direct interaction with nsp12 and inhibits RdRp complex formation.

scholarly journals Tackling the Moving Mutant Target: Taxifolin Derivatives as Novel Putative E571K Exportin-1 Inhibitors for KRAS-mutant Lung Adenocarcinoma Therapy

2020 ◽  
Author(s):  
Temidayo Adigun ◽  
Oluwatobi Medayedupin ◽  
Ireoluwa Joel ◽  
Idowu Fakolujo ◽  
Bankole Ofeniforo ◽  
...  
Keyword(s):  
Lung Adenocarcinoma ◽  
Bioactive Compounds ◽  
Molecular Modelling ◽  
Active Site ◽  
High Throughput Screening ◽  
Drug Resistant ◽  
Lead Compound ◽  
Autodock Vina ◽  
Juglans Mandshurica ◽  
Synthetic Accessibility

Aim: To establish, through molecular modelling, safe and clinically acceptable putative antagonists of E571K-mutated exportin-1 among the bioactive compounds in various parts of Juglans mandshurica. Methods: The bioactive compounds were subjected to compendium of druglikeness and lead-likeness filter workflows prior to docking of the resultant compounds into E571K exportin-1 active site using PyRx AutoDock vina to establish their binding affinity and interaction profile. The evolutionary algorithm of Osiris property explorer DataWarrior software as well as lead-likeness filter were employed for generation of novel non-promiscuous analogues of the lead compound with better putative selectivity and clinical acceptability as E571K Exportin-1 antagonists.Results: The findings of this study present taxifolin as the putatively effective and lead-like E571K Exportin-1 inhibitor with high potential of qualifying for clinical evaluation but is associated with high promiscuity tendency in high throughput screening. The evolutionary derivation of novel analogues of the compound, however, results in the generation of putatively non-promiscuous, non-toxic, and lead-like E571K Exportin-1 antagonists with high synthetic accessibility and clinical developability for evaluation in the strategy for treatment of drug-resistant KRAS-mutant lung adenocarcinoma condition.

scholarly journals Virtual Screening Approach to Identify High-Affinity Inhibitors of Serum and Glucocorticoid-Regulated Kinase 1 among Bioactive Natural Products: Combined Molecular Docking and Simulation Studies

Molecules ◽  
2020 ◽  
Vol 25 (4) ◽  
pp. 823 ◽  
Author(s):  
Taj Mohammad ◽  
Shiza Siddiqui ◽  
Anas Shamsi ◽  
Mohamed F. Alajmi ◽  
Afzal Hussain ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Cancer Progression ◽  
Conformational Changes ◽  
High Throughput Screening ◽  
Transcriptional Control ◽  
Interaction Analysis ◽  
Interaction Mechanism ◽  
Principal Component ◽  
Dynamics Simulation

Serum and glucocorticoid-regulated kinase 1 (SGK1) is a serine/threonine kinase that works under acute transcriptional control by several stimuli, including serum and glucocorticoids. It plays a significant role in the cancer progression and metastasis, as it regulates inflammation, apoptosis, hormone release, neuro-excitability, and cell proliferation. SGK1 has recently been considered as a potential drug target for cancer, diabetes, and neurodegenerative diseases. In the present study, we have performed structure-based virtual high-throughput screening of natural compounds from the ZINC database to find potential inhibitors of SGK1. Initially, hits were selected based on their physicochemical, absorption, distribution, metabolism, excretion, and toxicity (ADMET), and other drug-like properties. Afterwards, PAINS filter, binding affinities estimation, and interaction analysis were performed to find safe and effective hits. We found four compounds bearing appreciable binding affinity and specificity towards the binding pocket of SGK1. The docking results were complemented by all-atom molecular dynamics simulation for 100 ns, followed by MM/PBSA, and principal component analysis to investigate the conformational changes, stability, and interaction mechanism of SGK1 in-complex with the selected compound ZINC00319000. Molecular dynamics simulation results suggested that the binding of ZINC00319000 stabilizes the SGK1 structure, and it leads to fewer conformational changes. In conclusion, the identified compound ZINC00319000 might be further exploited as a scaffold to develop promising inhibitors of SGK1 for the therapeutic management of associated diseases, including cancer.

Exploiting the Tr3 Interaction with Bcl-2 as a Novel Therapeutic Strategy of Cancer and Leukemia Therapy.

Blood ◽  
2006 ◽  
Vol 108 (11) ◽  
pp. 256-256
Author(s):  
Dayong Zhai ◽  
Eduard Sergienko ◽  
Shinichi Kitada ◽  
Frederic Luciano ◽  
Arnold C. Satterswait ◽  
...  
Keyword(s):  
High Throughput ◽  
Conformational Changes ◽  
High Throughput Screening ◽  
Kinase Inhibitor ◽  
Leukemia Cell ◽  
Chemical Library ◽  
Over Expression ◽  
Amino Acid Peptide ◽  
Starting Point ◽  
Novel Therapeutic

Abstract TR3 (Nur77) is an orphan member of the retinoid/steroid family of nuclear receptors, which translocates from nucleus to mitochondria where it binds Bcl-2 and converts Bcl-2 from an anti-apoptotic to a pro-apoptotic protein (Li, et al. Science289: 1159, 2000; Lin, et al CELL116: 527, 2004). Because Bcl-2 is pathologically over-expressed in many ca cancers and leukemias, contributing to chemoresistance, we sought to exploit the TR3 interaction with Bcl-2 as a novel therapeutic approach. Mutagenesis studies identified a 9 amino-acid peptide from TR3 that mimics the effects of the full-length protein in terms of binding Bcl-2 and inducing conformational changes that covert Bcl-2 into a killer. A cell-permeable version of this TR3 peptide induced apoptosis of cultured leukemia cell lines (CEM; Jurkat), such that gene transfer-mediated over-expression of Bcl-2 enhanced sensitivity to the TR3 peptide. In contrast, Bcl-2 over-expression rendered these leukemia cells resistant to other inducers of apoptosis, such as the broad-spectrum kinase inhibitor Staurosporine. Mutant TR3 peptides that fail to bind Bcl-2 did not induce apoptosis. To identify chemical compounds that mimic the pro-apoptotic TR3 peptide, a Fluorescence Polarization Assay (FPA) was developed in which FITC-conjugated TR3 peptide binding to Bcl-2 or other appropriate anti-apoptotic Bcl-2-family proteins was measured in high-throughput mode. This high-throughput screening (HTS) assay performs well in 384 well format, with Z′ > 0.75. A chemical library of ~70,000 compounds was screened to identify compounds that displace the TR3 peptide, thus yielding hits that may serve as a potential starting point for drug discovery. Characterization of the properties of these compounds and their analogs will be described. (Supported by NIH grants R01-GM60554 and U54-HG003916).

scholarly journals Druggability of cavity pockets within SARS-CoV-2 spike glycoprotein and pharmacophore-based drug discovery

2021 ◽  
Author(s):  
Alireza Mohebbi ◽  
Fatemeh Sana Askari ◽  
Ali Salehnia Sammak ◽  
Mohsen Ebrahimi ◽  
Zahra Najafimemar
Keyword(s):  
Drug Discovery ◽  
Viral Entry ◽  
Spike Protein ◽  
Lead Compound ◽  
Autodock Vina ◽  
Spike Glycoprotein ◽  
Viral Glycoprotein ◽  
Chemical Derivatives ◽  
Good Target ◽  
Hit Identification

Aim: Virus spike glycoprotein of SARS-CoV-2 is a good target for drug discovery. Objective: To examine the potential for druggability of spike protein for pharmacophore-based drug discovery and to investigate the binding affinity of natural products with SARS-CoV-2 spike protein. Methods: Druggable cavities were searched though CavityPlus. A pharmacophore was built and used for hit identification. Autodock Vina was used to evaluate the hits' affinities. 10 chemical derivatives were also made from the chemical backbone to optimize the lead compound. Results: 10 druggable cavities were found within the glycoprotein spike. Only one cavity with the highest score at the binding site was selected for pharmacophore extraction. Hit identification resulted in the identification of 410 hits. Discussion: This study provides a druggable region within viral glycoprotein and a candidate compound to block viral entry.

scholarly journals First Nonphosphorylated Inhibitors of Phosphoglucose Isomerase Identified by Chemical Library Screening

2018 ◽  
Vol 23 (10) ◽  
pp. 1051-1059
Author(s):  
Sabrina G. R. Mota ◽  
Gustavo F. Mercaldi ◽  
José G. C. Pereira ◽  
Paulo S. L. Oliveira ◽  
Ana Rodriguez ◽  
...  
Keyword(s):  
High Throughput Screening ◽  
Phosphoglucose Isomerase ◽  
New Drugs ◽  
Inhibition Mechanism ◽  
Crystallographic Structure ◽  
Chemical Library ◽  
Promising Target ◽  
Antiparasitic Drugs ◽  
Potential Binding Site ◽  
Human Infections

Human African trypanosomiasis, Chagas disease, and leishmaniasis are human infections caused by kinetoplastid parasites of the genera Trypanosoma and Leishmania. Besides their severity and global impact, treatments are still challenging. Currently available drugs have important limitations, highlighting the urgent need to develop new drugs. Phosphoglucose isomerase (PGI) is considered a promising target for the development of antiparasitic drugs, as it acts on two essential metabolic pathways, glycolysis and gluconeogenesis. Herein, we describe the identification of new nonphosphorylated inhibitors of Leishmania mexicana PGI ( LmPGI), with the potential for the development of antiparasitic drugs. A fluorescence-based high-throughput screening (HTS) assay was developed by coupling the activities of recombinant LmPGI with glucose-6-phosphate dehydrogenase and diaphorase. This coupled assay was used to screen 42,720 compounds from ChemBridge and TimTec commercial libraries. After confirmatory assays, selected LmPGI inhibitors were tested against homologous Trypanosoma cruzi and humans. The PGI hits are effective against trypanosomatid PGIs, with IC50 values in the micromolar range, and also against the human homologous enzyme. A computational analysis of cavities present on PGI’s crystallographic structure suggests a potential binding site for the proposed mixed-type inhibition mechanism.

19F-NMR in Target-based Drug Discovery

2019 ◽  
Vol 26 (26) ◽  
pp. 4964-4983 ◽  
Author(s):  
CongBao Kang
Keyword(s):  
Drug Discovery ◽  
Conformational Changes ◽  
Protein Structures ◽  
19F Nmr ◽  
Binding Affinities ◽  
Protein Ligand Interactions ◽  
Compound Libraries ◽  
Ligand Interactions ◽  
Reference Ligand ◽  
Hit Identification

Solution NMR spectroscopy plays important roles in understanding protein structures, dynamics and protein-protein/ligand interactions. In a target-based drug discovery project, NMR can serve an important function in hit identification and lead optimization. Fluorine is a valuable probe for evaluating protein conformational changes and protein-ligand interactions. Accumulated studies demonstrate that 19F-NMR can play important roles in fragment- based drug discovery (FBDD) and probing protein-ligand interactions. This review summarizes the application of 19F-NMR in understanding protein-ligand interactions and drug discovery. Several examples are included to show the roles of 19F-NMR in confirming identified hits/leads in the drug discovery process. In addition to identifying hits from fluorinecontaining compound libraries, 19F-NMR will play an important role in drug discovery by providing a fast and robust way in novel hit identification. This technique can be used for ranking compounds with different binding affinities and is particularly useful for screening competitive compounds when a reference ligand is available.

scholarly journals Identification of a juvenile-hormone signaling inhibitor via high-throughput screening of a chemical library

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Takumi Kayukawa ◽  
Kenjiro Furuta ◽  
Keisuke Nagamine ◽  
Tetsuro Shinoda ◽  
Kiyoaki Yonesu ◽  
...  
Keyword(s):  
Juvenile Hormone ◽  
Cell Line ◽  
Signaling Pathway ◽  
High Throughput ◽  
High Throughput Screening ◽  
Large Scale ◽  
Ex Vivo ◽  
Agricultural Field ◽  
Chemical Library ◽  
Field Development

Abstract Insecticide resistance has recently become a serious problem in the agricultural field. Development of insecticides with new mechanisms of action is essential to overcome this limitation. Juvenile hormone (JH) is an insect-specific hormone that plays key roles in maintaining the larval stage of insects. Hence, JH signaling pathway is considered a suitable target in the development of novel insecticides; however, only a few JH signaling inhibitors (JHSIs) have been reported, and no practical JHSIs have been developed. Here, we established a high-throughput screening (HTS) system for exploration of novel JHSIs using a Bombyx mori cell line (BmN_JF&AR cells) and carried out a large-scale screening in this cell line using a chemical library. The four-step HTS yielded 69 compounds as candidate JHSIs. Topical application of JHSI48 to B. mori larvae caused precocious metamorphosis. In ex vivo culture of the epidermis, JHSI48 suppressed the expression of the Krüppel homolog 1 gene, which is directly activated by JH-liganded receptor. Moreover, JHSI48 caused a parallel rightward shift in the JH response curve, suggesting that JHSI48 possesses a competitive antagonist-like activity. Thus, large-scale HTS using chemical libraries may have applications in development of future insecticides targeting the JH signaling pathway.

scholarly journals New Inhibitory Effects of Cilnidipine on Microglial P2X7 Receptors and IL-1β Release: An Involvement in its Alleviating Effect on Neuropathic Pain

Cells ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 434
Author(s):  
Tomohiro Yamashita ◽  
Sawako Kamikaseda ◽  
Aya Tanaka ◽  
Hidetoshi Tozaki-Saitoh ◽  
Jose M. M. Caaveiro ◽  
...  
Keyword(s):  
Neuropathic Pain ◽  
High Throughput Screening ◽  
Inflammatory Responses ◽  
Therapeutic Potential ◽  
Inhibitory Effect ◽  
Intrathecal Administration ◽  
Chemical Library ◽  
P2x7 Receptors ◽  
Approved Drugs ◽  
Cardinal Symptom

P2X7 receptors (P2X7Rs) belong to a family of ATP-gated non-selective cation channels. Microglia represent a major cell type expressing P2X7Rs. The activation of microglial P2X7Rs causes the release of pro-inflammatory cytokines such as interleukin-1β (IL-1β). This response has been implicated in neuroinflammatory states in the central nervous system and in various diseases, including neuropathic pain. Thus, P2X7R may represent a potential therapeutic target. In the present study, we screened a chemical library of clinically approved drugs (1979 compounds) by high-throughput screening and showed that the Ca2+ channel blocker cilnidipine has an inhibitory effect on rodent and human P2X7R. In primary cultured rat microglial cells, cilnidipine inhibited P2X7R-mediated Ca2+ responses and IL-1β release. Moreover, in a rat model of neuropathic pain, the intrathecal administration of cilnidipine produced a reversal of nerve injury-induced mechanical hypersensitivity, a cardinal symptom of neuropathic pain. These results point to a new inhibitory effect of cilnidipine on microglial P2X7R-mediated inflammatory responses and neuropathic pain, proposing its therapeutic potential.

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