scholarly journals Discovery of potential drug-like compounds against Viral protein (VP40) of Marburg Virus using pharmacophoric based virtual screening from ZINC database.

2021 ◽  
Author(s):  
Sameer Quazi ◽  
Javid Ahmad Malik ◽  
Komal Singh Suman ◽  
Arnaud Martino Capuzzo ◽  
Zeshan Haider
Keyword(s):  
Binding Energy ◽  
Hemorrhagic Fever ◽  
Inhibitory Effect ◽  
Marburg Virus ◽  
Working Environment ◽  
Computer Aided Drug Design ◽  
Lipinski’S Rule ◽  
Zinc Database ◽  
Novel Drug ◽  
Selection Of

Marburg virus (MARV) has been confirmed to cause extreme hemorrhagic fever (HFM) in human and animals. The effective and suitable vaccine to treat the MARV virus is not commercialized in public and demands rigorously tested on several scales. This research used a CADD (Computer-Aided Drug Design) computational based technology to find novel drug-like compounds that could inhibit the replicating of the VP40. The pharmacophoric features bases screening was done using an online computational based software, "ZINC Pharmer". We retrieved about 32456 compounds mainly focused on the properties of pharmacophores from the ZINC database. Lipinski's rule was also used to predict these drug-like compounds. as well as molecular coupling-dependent screening and selection of VP40 screening ligand complexes based on S-rank (lower than reference) and value of root, mean square (RMSD) (bottom) to examine for reference) using the Molecular Working Environment (MOE) machine. As a result, 100 compounds were found to have a close interaction with MARV VP40, followed by the Binding energy (BE) analysis of these 100 compounds. Only 50 were the strongest binding energy than favipiravir [reference inhibitor] after using the MOE-LigX algorithm to compare their binding energy. After that, ADMET analysis predicted only five compounds (ZINC95457352, ZINC38752258, ZINC38752253, ZINC39272175, and ZINC38752377) passed the ADMET parameters and have the strongest inhibitory effect against the MARV's VP40. It has been suggested that these "drug-like" candidates have an increased ability to inhibit MARV replication, leading to treatment of MARVD.

scholarly journals In-silico Structural and Molecular Docking-Based Drug Discovery Against Viral Protein (VP40) of Marburg Virus: A Causative Agent of MAVD

2021 ◽  
Author(s):  
Sameer Quazi ◽  
Tanya Golani ◽  
Nashat Akhta ◽  
Christina Elsa Thomas ◽  
Zeshan Haider
Keyword(s):  
Molecular Docking ◽  
Binding Energy ◽  
Viral Protein ◽  
Multiple Scales ◽  
Hemorrhagic Fever ◽  
Marburg Virus ◽  
Ligand Complex ◽  
Lipinski’S Rule ◽  
High Degree ◽  
Autodock 4.2

AbstractThe Marburg virus (MARV) is reported to induce extreme hemorrhagic fever (MHF) with a high degree of infectivity and lethality in both human and non-human primates. An appropriate vaccination for this virus’s treatment is not yet usable, and thus needs intensive attempts on multiple scales. In this study, we employed the Computer-Aided Drug Design (CADD) based approach to identify the drug-like compounds inhibiting the replication of the Viral protein (VP40) of MARV. Our database search using an online database “PubChem” retrieved ∼3000 compounds structure-based similarity. Lipinski’s rule was applied to evaluate further the drug-like compounds, followed by molecular docking-based screening, and the selection of screening ligand complex with VP40 based on S-score (lower than reference Favipiravir inhibitor) and root-mean-square-deviation (RMSD) value (probably less than 2) using AutoDock 4.2. Resultantly, ∼100 compounds were identified having strong interaction with VP40 of MARV. After evaluating their binding energy using the AutoDock 4.2 software, four compounds (CID-67534452, CID-72201087, CID-123273976, CID-153708661) were identified that showed strongest binding energy with VP40 of MARV and strong inhibition effect than the Favipiravir. Robust binding energy, useful ADMET parameters and drug-likeness suggest that these candidates “CID-67534452, CID-72201087, CID-123273976, CID-153708661” have tremendous potential to stop the replication of MARV, hence might lead to the cure of MAVD.

scholarly journals In-silico Structural and Molecular Docking-Based Drug Discovery Against Viral Protein (VP35) of Marburg Virus: A potent Agent of MAVD

2021 ◽  
Author(s):  
Sameer Quazi ◽  
Javed Malik ◽  
Arnaud Martino Capuzzo ◽  
Kamal Singh Suman ◽  
Zeshan Haider
Keyword(s):  
Molecular Docking ◽  
Binding Energy ◽  
Viral Protein ◽  
In Silico ◽  
Core Protein ◽  
Hemorrhagic Fever ◽  
Inhibitory Effect ◽  
Marburg Virus ◽  
Pubchem Database ◽  
Strong Inhibitory Effect

ABSTRACTThe Marburg virus (MARV) is a highly etiological agent of hemorrhagic fever in humans. MARV has spread across the world, including America, Australia, Europe, and different Asia countries. However, there is no approved vaccine to combat MARV, combined with a high mortality rate, which makes antiviral drugs against MARV urgent. The viral protein (VP35) is a core protein of MARV that involves multiple functions of the infection cycle. This research used an in-silico drug design technique to discover the new drug-like small molecules that inhibit VP35 replication. First, several combinations of ∼ 4260 showed that structure-based similarity above 90% was retrieved from an online “PubChem” database. Molecular docking was performed using AutoDock 4.2, and ligands were selected based on docking / S score lower than reference CID_5477931 and RMSD value between 1-2. Finally, about 50 compounds showed greater bonding producing hydrogen, Van der Waals, and polar interactions with VP35. After evaluating their binding energy strength and ADMET analysis, only CID_ 3007938 and CID_11427396 were finalized, which showed the most vital binding energy and a strong inhibitory effect with MARV’s VP35. The higher binding energy, suitable ADMET, and drug similarity parameters suggest that these “CID_ 3007938 and CID_11427396” candidates have incredible latency to inhibit MARV replication; hence, these strengths led to the treatment of MAVD.

In Silico Discovery of Novel Inhibitors Against Main Protease (Mpro) of SARS-CoV-2 Using Pharmacophore and Molecular Docking Based Virtual Screening from ZINC Database

2020 ◽  
Author(s):  
Zeshan Haider ◽  
Muhammad Muneeb Subhani ◽  
Muhammad Ansar Farooq ◽  
Maryum Ishaq ◽  
Maryam Khalid ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Binding Energy ◽  
Effective Vaccine ◽  
Ligand Complex ◽  
Online Tool ◽  
Public Health Emergencies ◽  
Main Protease ◽  
Zinc Database ◽  
Recent Outbreak ◽  
Selection Of

Recent outbreak of Coronavirus Disease 2019 (COVID-19) caused by a novel ‘SARS-CoV-2’ virus resulted public health emergencies across the world. An effective vaccine to cure this virus is not yet available, thus requires concerted efforts at various scales. In this study, we employed Computer Aided Drug Design (CADD) based approach to identify the drug-like compounds - inhibiting the replication of main protease (Mpro) of SARS-CoV-2. Our database search using online tool “ZINC pharmer” retrieved ~1500 compounds based on pharmacophore features. Lipinski’s rule was applied to further evaluate the drug-like compounds, followed by molecular docking-based screening, and the selection of screening ligand complex with Mpro based on S-score (higher than reference inhibitor) and root-mean-square deviation (RMSD) value (less than reference inhibitor) using Molecular Operating Environment (MOE) system. Resultantly, ~200 compounds were identified having strong interaction with Mpro of SARS-CoV-2. After evaluating their binding energy using the MOE LigX algorithm, three compounds (ZINC20291569, ZINC90403206, ZINC95480156) were identified that showed highest binding energy with Mpro of SARS-CoV-2 and strong inhibition effect than the reference inhibitor. It is suggested that these candidate “drug-like compounds” have greater potential to stop the replication of SARS-CoV-2, hence might lead to the cure of COVID-19.

scholarly journals In-silico pharmacophore and Molecular Docking based drug discovery against Marburg Virus Viral Protein VP35; A potent of MAVD.

2021 ◽  
Author(s):  
Sameer Quazi ◽  
Shreelaxmi Gavas ◽  
Javed Ahmad Malik ◽  
Komal Singh Suman ◽  
Zeshan Haider
Keyword(s):  
Molecular Docking ◽  
Viral Protein ◽  
Virus Disease ◽  
Antiviral Drug ◽  
Computational Approach ◽  
Marburg Virus ◽  
Online Tool ◽  
Lipinski’S Rule ◽  
Zinc Database ◽  
Lipinski’S Rule Of Five

Marburg virus is a member of filoviridae and spreads severe Marburg hemorrhagic illness in humans and animals. Nowadays, there is no vaccine available that can completely stop the replication of Marburg replication. Therefore, this study is designed to repurpose the effective therapeutic antiviral drug by using a computational approach against exploring the mechanism of Marburg virus Viral protein 35. We have retrieved about 40570 drug-like small compounds from the ZINC database using the "ZINC Pharmer" online tool. Molecular docking of the ligands from the ready-to-dock database has been carried out using MOE. The five drugs have been identified to bind with VP35 possibly. A study was also performed to evaluate the drug-like characteristics of the substances for absorption, distribution, metabolism, and excretion (ADME). The findings clearly showed that ligands are interacting with the MARV VP35 protein. Interestingly, Lipinski's rule of five was observed by all ligands. These findings provide the foundation for reconstituting and utilizing molecules as a possible therapy for Marburg Virus Disease (MVD).

In Silico Discovery of Novel Inhibitors Against Main Protease (Mpro) of SARS-CoV-2 Using Pharmacophore and Molecular Docking Based Virtual Screening from ZINC Database

2020 ◽  
Author(s):  
Zeshan Haider ◽  
Muhammad Muneeb Subhani ◽  
Muhammad Ansar Farooq ◽  
Maryum Ishaq ◽  
Maryam Khalid ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Binding Energy ◽  
Effective Vaccine ◽  
Ligand Complex ◽  
Online Tool ◽  
Public Health Emergencies ◽  
Main Protease ◽  
Zinc Database ◽  
Recent Outbreak ◽  
Selection Of

Recent outbreak of Coronavirus Disease 2019 (COVID-19) caused by a novel ‘SARS-CoV-2’ virus resulted public health emergencies across the world. An effective vaccine to cure this virus is not yet available, thus requires concerted efforts at various scales. In this study, we employed Computer Aided Drug Design (CADD) based approach to identify the drug-like compounds - inhibiting the replication of main protease (Mpro) of SARS-CoV-2. Our database search using online tool “ZINC pharmer” retrieved ~1500 compounds based on pharmacophore features. Lipinski’s rule was applied to further evaluate the drug-like compounds, followed by molecular docking-based screening, and the selection of screening ligand complex with Mpro based on S-score (higher than reference inhibitor) and root-mean-square deviation (RMSD) value (less than reference inhibitor) using Molecular Operating Environment (MOE) system. Resultantly, ~200 compounds were identified having strong interaction with Mpro of SARS-CoV-2. After evaluating their binding energy using the MOE LigX algorithm, three compounds (ZINC20291569, ZINC90403206, ZINC95480156) were identified that showed highest binding energy with Mpro of SARS-CoV-2 and strong inhibition effect than the reference inhibitor. It is suggested that these candidate “drug-like compounds” have greater potential to stop the replication of SARS-CoV-2, hence might lead to the cure of COVID-19.

scholarly journals EXAMINATION OF THE WEED FLORA OF RUDER HABITATS AND THE POSSIBILITY OF SUPPRESSION WITH HERBICIDES

2018 ◽  
Vol 6 (4) ◽  
pp. 329-332
Author(s):  
Milić Vojinović ◽  
Jelica Živić ◽  
Sanja Perić ◽  
Miroljub Aksić
Keyword(s):  
Chenopodium Album ◽  
Working Environment ◽  
Xanthium Strumarium ◽  
Weed Species ◽  
Construction Sites ◽  
Convolvulus Arvensis ◽  
Human Settlements ◽  
Time Of Application ◽  
Vegetation Complex ◽  
Selection Of

Ruderal flora, as well as the vegetation that flora forms, represent an extremely dynamic floristic-vegetation complex and arean integral part of the most immediate living and working environment of human. It is formed and developed mainly in human settlements, as well as in the other anthropogenic environments that are occasionally or permanently under direct or indirect influence of various forms of human activity. Ruderal vegetation is found not only directly around the settlements, but also around all urban and accompanying facilities: along roads, paths and fences around houses, yards, walls and roofs, in avenues, on ruins, construction sites, landfills, along railway tracks, road and defense embankments, on wet and nitrified banks of rivers, near human settlements, in abandoned lawns, on the street walks with sandy areas, cemeteries, in degraded pastures, forests, etc. This essay presents the distribution and representation of economically harmful, invasive and quarantine weed species (Abutilon theophrasti, Agropyrumrepens, Amaranthusretroflexus, Calystegiasepium, Cirsiumarvense, Chenopodium album, Chenopodiumhybridum, Convolvulus arvensis, Cynodondactylon, Daturastramonium, Sonchusarvensis, Sorghum halepense, Xanthium strumarium…) at ten sites in the Nisava district. The assessment of species representation was done in two shootings (May and August) according to scale 1-4. The proper selection of herbicides depends, in a large extent, on the presence of dominant weed species and on the time of application.

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 Sorting of Marburg Virus Surface Protein and Virus Release Take Place at Opposite Surfaces of Infected Polarized Epithelial Cells

2001 ◽  
Vol 75 (3) ◽  
pp. 1274-1283 ◽  
Author(s):  
Christian Sänger ◽  
Elke Mühlberger ◽  
Elena Ryabchikova ◽  
Larissa Kolesnikova ◽  
Hans-Dieter Klenk ◽  
...  
Keyword(s):  
Epithelial Cells ◽  
Apical Membrane ◽  
Basolateral Membrane ◽  
Surface Protein ◽  
Hemorrhagic Fever ◽  
Marburg Virus ◽  
Virus Surface ◽  
Mdckii Cells ◽  
Vesicular Stomatitis ◽  
Polarized Epithelial Cells

ABSTRACT Marburg virus, a filovirus, causes severe hemorrhagic fever with hitherto poorly understood molecular pathogenesis. We have investigated here the vectorial transport of the surface protein GP of Marburg virus in polarized epithelial cells. To this end, we established an MDCKII cell line that was able to express GP permanently (MDCK-GP). The functional integrity of GP expressed in these cells was analyzed using vesicular stomatitis virus pseudotypes. Further experiments revealed that GP is transported in MDCK-GP cells mainly to the apical membrane and is released exclusively into the culture medium facing the apical membrane. When MDCKII cells were infected with Marburg virus, the majority of GP was also transported to the apical membrane, suggesting that the protein contains an autonomous apical transport signal. Release of infectious progeny virions, however, took place exclusively at the basolateral membrane of the cells. Thus, vectorial budding of Marburg virus is presumably determined by factors other than the surface protein.

scholarly journals Phylogeny-Guided Selection of Priority Groups for Venom Bioprospecting: Harvesting Toxin Sequences in Tarantulas as a Case Study

Toxins ◽  
2019 ◽  
Vol 11 (9) ◽  
pp. 488 ◽  
Author(s):  
Tim Lüddecke ◽  
Andreas Vilcinskas ◽  
Sarah Lemke
Keyword(s):  
Success Rate ◽  
Mechanisms Of Action ◽  
Rational Selection ◽  
Almost All ◽  
Novel Drug ◽  
Drug Leads ◽  
Novel Structures ◽  
Animal Venoms ◽  
Selection Of

Animal venoms are promising sources of novel drug leads, but their translational potential is hampered by the low success rate of earlier biodiscovery programs, in part reflecting the narrow selection of targets for investigation. To increase the number of lead candidates, here we discuss a phylogeny-guided approach for the rational selection of venomous taxa, using tarantulas (family Theraphosidae) as a case study. We found that previous biodiscovery programs have prioritized the three subfamilies Ornithoctoninae, Selenocosmiinae, and Theraphosinae, which provide almost all of the toxin sequences currently available in public databases. The remaining subfamilies are poorly represented, if at all. These overlooked subfamilies include several that form entire clades of the theraphosid life tree, such as the subfamilies Eumenophorinae, Harpactirinae, and Stromatopelminae, indicating that biodiversity space has not been covered effectively for venom biodiscovery in Theraphosidae. Focusing on these underrepresented taxa will increase the likelihood that promising candidates with novel structures and mechanisms of action can be identified in future bioprospecting programs.

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