scholarly journals Computational Approach for Covalent Lead Identification against Spike Glycoprotein of SARS-CoV-2

2021 ◽  
Author(s):  
Ravi BHUSHAN ◽  
Pawan K Dubey ◽  
Akhtar Ali ◽  
Harshit Dwivedi ◽  
Anuj Kumar ◽  
...  
Keyword(s):  
Binding Energy ◽  
Virtual Screening ◽  
Binding Affinity ◽  
Spike Glycoprotein ◽  
Lipinski’S Rule ◽  
Discovery Studio ◽  
Synthetic Molecules ◽  
Docking Approach

Abstract Background: A global outbreak of coronavirus disease 19 (COVID-19) led researchers to investigate various active compounds that can inhibit the replication of SARS-CoV2 (severe acute respiratory syndrome coronavirus 2). The present work targets to evaluate small covalent synthetic molecules through a virtual screening and docking approach that can efficiently inhibit Spike Glycoprotein of SARS CoV2.Methods: We retrieved around 50,000 small covalent synthetic molecules through the American chemical society (CAS) database. The initial evaluation of these synthetic molecules depends on the ADMET screening. A Lipinski's Rule of Five (RO5) was also applied to find whether the drug met the criteria of good bioavailability. Then, the further selection was made through virtual screening using BIOVIA Discovery Studio. Further, comparison among top hits was performed via a docking approach based on the binding energy (kcal/mol) calculated using the AutoDock Vina plugin and Patch Dock-like docking engines. Finally, the selected top five molecules were compared for their binding efficiency with reference drugs like Favipiravir, Chloroquine, Ribavirin, Hydroxychloroquine (approved by the FDA), and molecules with better binding affinity than reference drugs was selected.Results: In the first tier of selection, 215 molecules were screened out, satisfying all the necessary conditions of RO5 and ADMET. Among 215 molecules screened, only 203 molecules were stable in structure to undergo the second tier of target-based virtual screening. Further, based upon the LibDock score generated by virtual screening, the top five molecules with the highest LibD score were selected. Molecular docking of these five selected compounds reveals compound2 (3-ethyl-5-propyladamantan-1-amine) with the best binding energy. Furthermore, we compared the binding affinity of 3-ethyl-5-propyladamantan-1-amine with reported drugs that show 3-ethyl-5-propyladamantan-1-amine as the most promising ligand efficient hydrogen bond interactions with amino acid residues of protein which provides more excellent stability in the docked region of the protein with efficient binding energy as compared to the reference molecule. Moreover, Compound2 also has a high oral bioavailability, non-mutagenicity, non-toxicity and follows all RO5 criteria.Conclusion: Thus, it has potential as an antiviral covalent synthetic molecule that may prevent the replication of spike protein. These findings are just preliminary selection to facilitate the upcoming tests from in vivo and in vitro studies.

scholarly journals Nature Potential for COVID-19: Targeting SARS-CoV-2 Mpro Inhibitor with Bioactive Compound

2021 ◽  
Author(s):  
Kaushik Kumar Bharadwaj ◽  
Tanmay Sarkar ◽  
Arabinda Ghosh ◽  
Debabrat Baishya ◽  
Bijuli Rabha ◽  
...  
Keyword(s):  
Binding Energy ◽  
Antiviral Activity ◽  
Binding Free Energy ◽  
Bioactive Compound ◽  
Binding Pocket ◽  
Stable Conformation ◽  
Lipinski’S Rule ◽  
Macrolactin A

<p>Corona viruses were first identified in 1931 and SARS-CoV-2 is the most recent. COVID-19 is a pandemic that put most of the world on lockdown and the search for therapeutic drugs is still on-going. Therefore, this study uses <i>in silico</i> screening to identify natural bioactive compounds from fruits, herbaceous plants and marine invertebrates that are able to inhibit protease activity in SARS-CoV-2(PDB: 6LU7). We have used various screening strategies such as drug likeliness, antiviral activity value prediction, molecular docking, ADME (absorption, distribution, metabolism, and excretion), molecular dynamics (MD) simulation and MM/GBSA (molecular mechanics/generalized born and surface area continuum solvation). 17 compounds were shortlisted using Lipinski’s rule. 5 compounds revealed significantly good predicted antiviral activity values and out of them only 2 compounds, Macrolactin A and Stachyflin, showed good binding energy values of -9.22 and -8.00 kcal/mol within the binding pocket, catalytic residues (HIS 41 and CYS 145) of M<sup>pro</sup>. These two compounds were further analyzed for their ADME properties. The ADME evaluation of these 2 compounds suggested that they could be effective as therapeutic agents for developing drugs for clinical trials. MD simulations showed that protein-ligand complexes of Macrolactin A and Stachyflin were stable for 100 nano seconds. The MM/GBSA calculations of M<sup>pro</sup> – Macrolactin A complex indicated higher binding free energy (-42.58 ± 6.35 kcal/mol) with M<sup>pro </sup>protein target receptor (6LU7). DCCM and PCA analysis on the residual movement in the MD trajectories confirmed the good stability on Macrolactin A bound state of 6LU7. This signify the stable conformation of 6LU7 with high binding energy with Macrolactin A. Thus, this study showed that Macrolactin A could be an effective therapeutical agent for SARS-CoV-2protease (6LU7) inhibition. Additional <i>in vitro </i>and<i> in vivo </i>validations are needed to determine efficacy and dose of Macrolactin A in biological systems.</p>

scholarly journals Nature Potential for COVID-19: Targeting SARS-CoV-2 Mpro Inhibitor with Bioactive Compound

2021 ◽  
Author(s):  
Kaushik Kumar Bharadwaj ◽  
Tanmay Sarkar ◽  
Arabinda Ghosh ◽  
Debabrat Baishya ◽  
Bijuli Rabha ◽  
...  
Keyword(s):  
Binding Energy ◽  
Antiviral Activity ◽  
Binding Free Energy ◽  
Bioactive Compound ◽  
Binding Pocket ◽  
Stable Conformation ◽  
Lipinski’S Rule ◽  
Macrolactin A

<p>Corona viruses were first identified in 1931 and SARS-CoV-2 is the most recent. COVID-19 is a pandemic that put most of the world on lockdown and the search for therapeutic drugs is still on-going. Therefore, this study uses <i>in silico</i> screening to identify natural bioactive compounds from fruits, herbaceous plants and marine invertebrates that are able to inhibit protease activity in SARS-CoV-2(PDB: 6LU7). We have used various screening strategies such as drug likeliness, antiviral activity value prediction, molecular docking, ADME (absorption, distribution, metabolism, and excretion), molecular dynamics (MD) simulation and MM/GBSA (molecular mechanics/generalized born and surface area continuum solvation). 17 compounds were shortlisted using Lipinski’s rule. 5 compounds revealed significantly good predicted antiviral activity values and out of them only 2 compounds, Macrolactin A and Stachyflin, showed good binding energy values of -9.22 and -8.00 kcal/mol within the binding pocket, catalytic residues (HIS 41 and CYS 145) of M<sup>pro</sup>. These two compounds were further analyzed for their ADME properties. The ADME evaluation of these 2 compounds suggested that they could be effective as therapeutic agents for developing drugs for clinical trials. MD simulations showed that protein-ligand complexes of Macrolactin A and Stachyflin were stable for 100 nano seconds. The MM/GBSA calculations of M<sup>pro</sup> – Macrolactin A complex indicated higher binding free energy (-42.58 ± 6.35 kcal/mol) with M<sup>pro </sup>protein target receptor (6LU7). DCCM and PCA analysis on the residual movement in the MD trajectories confirmed the good stability on Macrolactin A bound state of 6LU7. This signify the stable conformation of 6LU7 with high binding energy with Macrolactin A. Thus, this study showed that Macrolactin A could be an effective therapeutical agent for SARS-CoV-2protease (6LU7) inhibition. Additional <i>in vitro </i>and<i> in vivo </i>validations are needed to determine efficacy and dose of Macrolactin A in biological systems.</p>

scholarly journals Nature Potential for COVID-19: Targeting SARS-CoV-2 Mpro Inhibitor with Bioactive Compound

2021 ◽  
Author(s):  
Kaushik Kumar Bharadwaj ◽  
Tanmay Sarkar ◽  
Arabinda Ghosh ◽  
Debabrat Baishya ◽  
Bijuli Rabha ◽  
...  
Keyword(s):  
Binding Energy ◽  
Antiviral Activity ◽  
Binding Free Energy ◽  
Bioactive Compound ◽  
Binding Pocket ◽  
Stable Conformation ◽  
Lipinski’S Rule ◽  
Macrolactin A

<p>Corona viruses were first identified in 1931 and SARS-CoV-2 is the most recent. COVID-19 is a pandemic that put most of the world on lockdown and the search for therapeutic drugs is still on-going. Therefore, this study uses <i>in silico</i> screening to identify natural bioactive compounds from fruits, herbaceous plants and marine invertebrates that are able to inhibit protease activity in SARS-CoV-2(PDB: 6LU7). We have used various screening strategies such as drug likeliness, antiviral activity value prediction, molecular docking, ADME (absorption, distribution, metabolism, and excretion), molecular dynamics (MD) simulation and MM/GBSA (molecular mechanics/generalized born and surface area continuum solvation). 17 compounds were shortlisted using Lipinski’s rule. 5 compounds revealed significantly good predicted antiviral activity values and out of them only 2 compounds, Macrolactin A and Stachyflin, showed good binding energy values of -9.22 and -8.00 kcal/mol within the binding pocket, catalytic residues (HIS 41 and CYS 145) of M<sup>pro</sup>. These two compounds were further analyzed for their ADME properties. The ADME evaluation of these 2 compounds suggested that they could be effective as therapeutic agents for developing drugs for clinical trials. MD simulations showed that protein-ligand complexes of Macrolactin A and Stachyflin were stable for 100 nano seconds. The MM/GBSA calculations of M<sup>pro</sup> – Macrolactin A complex indicated higher binding free energy (-42.58 ± 6.35 kcal/mol) with M<sup>pro </sup>protein target receptor (6LU7). DCCM and PCA analysis on the residual movement in the MD trajectories confirmed the good stability on Macrolactin A bound state of 6LU7. This signify the stable conformation of 6LU7 with high binding energy with Macrolactin A. Thus, this study showed that Macrolactin A could be an effective therapeutical agent for SARS-CoV-2protease (6LU7) inhibition. Additional <i>in vitro </i>and<i> in vivo </i>validations are needed to determine efficacy and dose of Macrolactin A in biological systems.</p>

scholarly journals Therapeutic Potentials of Syzygium fruticosum Fruit (Seed) Reflected into an Array of Pharmacological Assays and Prospective Receptors-Mediated Pathways

Life ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 155
Author(s):  
Jannatul Nasma Rupa Moni ◽  
Md. Adnan ◽  
Abu Montakim Tareq ◽  
Md. Imtiazul Kabir ◽  
A.S.M. Ali Reza ◽  
...  
Keyword(s):  
Bioactive Compounds ◽  
Integrated Approach ◽  
Gas Chromatography Mass Spectrometry ◽  
Clot Lysis ◽  
Lipinski’S Rule ◽  
Lysis Activity ◽  
In Silico Studies ◽  
Immobility Time

Syzygium fruticosum (SF), a valuable Bangladeshi fruit, is considered an alternative therapeutic agent. Mainly, seeds are used as nutritional phytotherapy to ease physical and mental status by preventing chronic diseases. Here, we scrutinized the S. fruticosum seed’s fundamental importance in traditional medicine by following an integrated approach combining in vivo, in vitro, and in silico studies. The SF was fractionated with different solvents, and the ethyl acetate fraction of SF (EaF-SF) was further studied. Mice treated with EaF-SF (200 and 400 mg/kg) manifested anxiolysis evidenced by higher exploration in elevated plus maze and hole board tests. Similarly, a dose-dependent drop of immobility time in a forced swimming test ensured significant anti-depressant activity. Moreover, higher dose treatment exposed reduced exploratory behaviour resembling decreased movement and prolonged sleeping latency with a quick onset of sleep during the open field and thiopental-induced sleeping tests, respectively. In parallel, EaF-SF significantly (p < 0.001) and dose-dependently suppressed acetic acid and formalin-induced pain in mice. Also, a noteworthy anti-inflammatory activity and a substantial (p < 0.01) clot lysis activity (thrombolytic) was observed. Gas chromatography-mass spectrometry (GC–MS) analysis resulted in 49 bioactive compounds. Among them, 12 bioactive compounds with Lipinski’s rule and safety confirmation showed strong binding affinity (molecular docking) against the receptors of each model used. To conclude, the S. fruticosum seed is a prospective source of health-promoting effects that can be an excellent candidate for preventing degenerative diseases.

scholarly journals Synthesis and Evaluation of [18F]FEtLos and [18F]AMBF3Los as Novel 18F-Labelled Losartan Derivatives for Molecular Imaging of Angiotensin II Type 1 Receptors

Molecules ◽  
2020 ◽  
Vol 25 (8) ◽  
pp. 1872
Author(s):  
Martha Sahylí Ortega Pijeira ◽  
Paulo Sérgio Gonçalves Nunes ◽  
Sofia Nascimento dos Santos ◽  
Zhengxing Zhang ◽  
Arian Pérez Nario ◽  
...  
Keyword(s):  
Angiotensin Ii ◽  
Binding Affinity ◽  
Renin Angiotensin System ◽  
Prosthetic Group ◽  
Positron Emission ◽  
One Step ◽  
Group 2

Losartan is widely used in clinics to treat cardiovascular related diseases by selectively blocking the angiotensin II type 1 receptors (AT1Rs), which regulate the renin-angiotensin system (RAS). Therefore, monitoring the physiological and pathological biodistribution of AT1R using positron emission tomography (PET) might be a valuable tool to assess the functionality of RAS. Herein, we describe the synthesis and characterization of two novel losartan derivatives PET tracers, [18F]fluoroethyl-losartan ([18F]FEtLos) and [18F]ammoniomethyltrifluoroborate-losartan ([18F]AMBF3Los). [18F]FEtLos was radiolabeled by 18F-fluoroalkylation of losartan potassium using the prosthetic group 2-[18F]fluoroethyl tosylate; whereas [18F]AMBF3Los was prepared following an one-step 18F-19F isotopic exchange reaction, in an overall yield of 2.7 ± 0.9% and 11 ± 4%, respectively, with high radiochemical purity (>95%). Binding competition assays in AT1R-expressing membranes showed that AMBF3Los presented an almost equivalent binding affinity (Ki 7.9 nM) as the cold reference Losartan (Ki 1.5 nM), unlike FEtLos (Ki 2000 nM). In vitro and in vivo assays showed that [18F]AMBF3Los displayed a good binding affinity for AT1R-overexpressing CHO cells and was able to specifically bind to renal AT1R. Hence, our data demonstrate [18F]AMBF3Los as a new tool for PET imaging of AT1R with possible applications for the diagnosis of cardiovascular, inflammatory and cancer diseases.

scholarly journals Steroidal glycoalkaloids fromSolanum nigrumtarget cytoskeletal proteins: anin silicoanalysis

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6012 ◽  
Author(s):  
Rumana Ahmad
Keyword(s):  
Binding Affinity ◽  
Anticancer Agents ◽  
Principal Component ◽  
Cytoskeletal Proteins ◽  
Hydroxyl Group ◽  
Docking Analysis ◽  
Drug Candidates ◽  
Division Cell

BackgroundSolanum nigrum(black nightshade;S. nigrum), a member of family Solanaceae, has been endowed with a heterogeneous array of secondary metabolites of which the steroidal glycoalkaloids (SGAs) and steroidal saponins (SS) have vast potential to serve as anticancer agents. Since there has been much controversy regarding safety of use of glycoalkaloids as anticancer agents, this area has remained more or less unexplored. Cytoskeletal proteins like actin play an important role in maintaining cell shape, synchronizing cell division, cell motility, etc. and along with their accessory proteins may also serve as important therapeutic targets for potential anticancer candidates. In the present study, glycoalkaloids and saponins fromS. nigrumwere screened for their interaction and binding affinity to cytoskeletal proteins, using molecular docking.MethodsBioactivity score and Prediction of Activity Spectra for Substances (PASS) analysis were performed using softwares Molinspiration and Osiris Data Explorer respectively, to assess the feasibility of selected phytoconstituents as potential drug candidates. The results were compared with two standard reference drugs doxorubicin hydrochloride (anticancer) and tetracycline (antibiotic). Multivariate data obtained were analyzed using principal component analysis (PCA).ResultsDocking analysis revealed that the binding affinities of the phytoconstituents towards the target cytoskeletal proteins decreased in the order coronin>villin>ezrin>vimentin>gelsolin>thymosin>cofilin. Glycoalkaloid solasonine displayed the greatest binding affinity towards the target proteins followed by alpha-solanine whereas amongst the saponins, nigrumnin-I showed maximum binding affinity. PASS Analysis of the selected phytoconstituents revealed 1 to 3 violations of Lipinski’s parameters indicating the need for modification of their structure-activity relationship (SAR) for improvement of their bioactivity and bioavailability. Glycoalkaloids and saponins all had bioactivity scores between −5.0 and 0.0 with respect to various receptor proteins and target enzymes. Solanidine, solasodine and solamargine had positive values of druglikeness which indicated that these compounds have the potential for development into future anticancer drugs. Toxicity potential evaluation revealed that glycoalkaloids and saponins had no toxicity, tumorigenicity or irritant effect(s). SAR analysis revealed that the number, type and location of sugar or the substitution of hydroxyl group on alkaloid backbone had an effect on the activity and that the presence of α-L-rhamnopyranose sugar at C-2 was critical for a compound to exhibit anticancer activity.ConclusionThe present study revealed some cytoskeletal target(s) forS. nigrumphytoconstituents by docking analysis that have not been previously reported and thus warrant further investigations bothin vitroandin vivo.

In Vitro Androgen Receptor Binding Affinity and in Vivo Inhibitory Activity of 5?-Pregnane-3, 20-Dione

1988 ◽  
Vol 529 (1 Fourth Colloq) ◽  
pp. 239-241
Author(s):  
SAUDHAMINI PARTHASARATHY ◽  
ANDREA CHIN ◽  
VIRGINIA MALLOY ◽  
JONATHAN MATIAS
Keyword(s):  
Androgen Receptor ◽  
Binding Affinity ◽  
Receptor Binding ◽  
Inhibitory Activity ◽  
Receptor Binding Affinity

scholarly journals In Silico De Novo Curcuminoid Derivatives From the Compound Library of Natural Products Research Laboratories Inhibit COVID-19 3CLpro Activity

2020 ◽  
Vol 15 (9) ◽  
pp. 1934578X2095326
Author(s):  
Jai-Sing Yang ◽  
Jo-Hua Chiang ◽  
Shih‑Chang Tsai ◽  
Yuan-Man Hsu ◽  
Da-Tian Bau ◽  
...  
Keyword(s):  
Natural Products ◽  
Virtual Screening ◽  
Binding Affinity ◽  
High Throughput ◽  
In Silico ◽  
De Novo ◽  
Compound Library ◽  
Therapeutic Success ◽  
High Throughput Virtual Screening

The coronavirus disease 2019 (COVID‐19) outbreak caused by the 2019 novel coronavirus (2019-nCOV) is becoming increasingly serious. In March 2019, the Food and Drug Administration (FDA) designated remdesivir for compassionate use to treat COVID-19. Thus, the development of novel antiviral agents, antibodies, and vaccines against COVID-19 is an urgent research subject. Many laboratories and research organizations are actively investing in the development of new compounds for COVID-19. Through in silico high-throughput virtual screening, we have recently identified compounds from the compound library of Natural Products Research Laboratories (NPRL) that can bind to COVID-19 3Lpro polyprotein and block COVID-19 3Lpro activity through in silico high-throughput virtual screening. Curcuminoid derivatives (including NPRL334, NPRL339, NPRL342, NPRL346, NPRL407, NPRL415, NPRL420, NPRL472, and NPRL473) display strong binding affinity to COVID-19 3Lpro polyprotein. The binding site of curcuminoid derivatives to COVID-19 3Lpro polyprotein is the same as that of the FDA-approved human immunodeficiency virus protease inhibitor (lopinavir) to COVID-19 3Lpro polyprotein. The binding affinity of curcuminoid derivatives to COVID-19 3Lpro is stronger than that of lopinavir and curcumin. Among curcuminoid derivatives, NPRL-334 revealed the strongest binding affinity to COVID-19 3Lpro polyprotein and is speculated to have an anti-COVID-19 effect. In vitro and in vivo ongoing experiments are currently underway to confirm the present findings. This study sheds light on the drug design for COVID-19 3Lpro polyprotein. Basing on lead compound development, we provide new insights on inhibiting COVID-19 attachment to cells, reducing COVID-19 infection rate and drug side effects, and increasing therapeutic success rate.

0155 SUVN-G3031, A Potent and Selective Histamine H3 Receptor Inverse Agonist - Differentiating Features Over Current Treatments of Narcolepsy

SLEEP ◽  
2020 ◽  
Vol 43 (Supplement_1) ◽  
pp. A61-A61
Author(s):  
A Shinde ◽  
R Subramanian ◽  
R Palacharla ◽  
S Pandey ◽  
V Benade ◽  
...  
Keyword(s):  
Binding Affinity ◽  
Abuse Liability ◽  
Species Variation ◽  
Pharmacological Agents ◽  
Histamine H3 Receptor ◽  
Inverse Agonists ◽  
H3 Receptor ◽  
Histamine H3

Abstract Introduction Majority of pharmacological agents used in the treatment of narcolepsy have several limitations. Both nonclinical and clinical evidences suggest usefulness of the histamine H3 receptor (H3R) inverse agonists for the treatment of narcolepsy and addressing several of the current limitations. Methods Extensive nonclinical studies were carried out for SUVN-G3031 and other pharmacological agents that are currently being used for the treatment of narcolepsy. Nonclinical parameters like inter-species binding affinity, selectivity profile, in vivo and in vitro ADME features, nonclinical efficacy, neurochemistry and safety were compared. Results SUVN-G3031 has no inter-species variation in binding affinity at H3R with less than 50% inhibition at 1 µM against 70 other targets. Unlike pitolisant, SUVN-G3031 has no significant binding affinity at sigma 1 and 2 receptor. SUVN-G3031 has no inhibition and induction liability towards major CYP enzymes and transporters. Pitolisant is reported to be a CYP3A4, CYP2B6, and CYP1A2 inducer and a CYP2D6 and OCT1 inhibitor. SUVN-G3031 has robust wake promoting effects. SUVN-G3031 showed negligible affinity towards hERG channel with IC50 &gt; 10 µM and had no effects on any ECG parameters in dog telemetry study. SUVN-G3031 did not show convulsion in rats up to the tested dose of 100 mg/kg, p.o. Most of the pharmacological agents used for the treatment of narcolepsy have abuse liability; SUVN-G3031 produced no change in the striatal and accumbal dopamine levels in rats suggesting no propensity to induce abuse liability. Unlike competing H3R inverse agonists, SUVN-G3031 has no effects on fertility and embryo-fetal development up to the highest tested doses. Conclusion Nonclinical studies demonstrate superiority of SUVN-G3031 over pharmacological agents currently used in the treatment of narcolepsy. SUVN-G3031 is being evaluated in a Phase 2 study as monotherapy for the treatment of narcolepsy with and without cataplexy (ClinicalTrials.gov Identifier: NCT04072380). Support None

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