scholarly journals In Silico Guided Drug Repurposing to Combat SARS-CoV-2 by Targeting Mpro, the Key Virus Specific Protease

2020 ◽  
Author(s):  
Ruchi Rani ◽  
Ankur Singh ◽  
Akshay Pareek ◽  
Shailly Tomar
Keyword(s):  
Binding Energy ◽  
Large Population ◽  
Drug Repurposing ◽  
Binding Pocket ◽  
World Health ◽  
Binding Modes ◽  
Specific Protease ◽  
Health Organization

<p>The reemergence of SARS-CoV named, as SARS-CoV-2 has been highly infectious and able to infect a large population around the globe. The World Health Organization (WHO) has declared this SARS-CoV-2 associated Coronavirus Disease 2019 (COVID-19) as pandemic. SARS-CoV-2 genome is translated into polyproteins and has been processed by its protease enzymes. 3CLprotease is named as main protease (M<sup>pro</sup>) enzyme which cleaves nsp4-nsp16. This crucial role of M<sup>pro</sup> makes this enzyme a prime and promising antiviral target. The drug repurposing is a fast alternative method than the discovery of novel antiviral molecules. We have used high-throughput virtual screening approach to examine FDA approved LOPAC1280 library against M<sup>pro</sup>. Primary screening have identified few potential drug molecule for the target among which 10 molecules were studied further. Molecular docking of selected molecules was done to detailed study about their binding energy and binding modes. Positively, Etoposide, BMS_195614, KT185, Idarubicin and WIN_62577 were found interacting with substrate binding pocket of M<sup>pro</sup> with higher binding energy. These molecules are being advanced by our group for <i>in vitro </i>and <i>in vivo</i> testing to study the efficacy of identified drugs. As per our understanding, these molecules have the potential to efficiently interrupt the viral life cycle and may reduce or eliminate the expeditious outspreading of SARS-CoV-2.</p>

scholarly journals In Silico Guided Drug Repurposing to Combat SARS-CoV-2 by Targeting Mpro, the Key Virus Specific Protease

2020 ◽  
Author(s):  
Ruchi Rani ◽  
Ankur Singh ◽  
Akshay Pareek ◽  
Shailly Tomar
Keyword(s):  
Binding Energy ◽  
Large Population ◽  
Drug Repurposing ◽  
Binding Pocket ◽  
World Health ◽  
Binding Modes ◽  
Specific Protease ◽  
Health Organization

<p>The reemergence of SARS-CoV named, as SARS-CoV-2 has been highly infectious and able to infect a large population around the globe. The World Health Organization (WHO) has declared this SARS-CoV-2 associated Coronavirus Disease 2019 (COVID-19) as pandemic. SARS-CoV-2 genome is translated into polyproteins and has been processed by its protease enzymes. 3CLprotease is named as main protease (M<sup>pro</sup>) enzyme which cleaves nsp4-nsp16. This crucial role of M<sup>pro</sup> makes this enzyme a prime and promising antiviral target. The drug repurposing is a fast alternative method than the discovery of novel antiviral molecules. We have used high-throughput virtual screening approach to examine FDA approved LOPAC1280 library against M<sup>pro</sup>. Primary screening have identified few potential drug molecule for the target among which 10 molecules were studied further. Molecular docking of selected molecules was done to detailed study about their binding energy and binding modes. Positively, Etoposide, BMS_195614, KT185, Idarubicin and WIN_62577 were found interacting with substrate binding pocket of M<sup>pro</sup> with higher binding energy. These molecules are being advanced by our group for <i>in vitro </i>and <i>in vivo</i> testing to study the efficacy of identified drugs. As per our understanding, these molecules have the potential to efficiently interrupt the viral life cycle and may reduce or eliminate the expeditious outspreading of SARS-CoV-2.</p>

scholarly journals FDA Approved Drugs and Herbal Based Inhibitors Target SARS CoV-2 RNA Dependent RNA Polymerase

2021 ◽  
Vol 11 (3) ◽  
pp. 3811-3821
Keyword(s):  
Rna Polymerase ◽  
Drug Repurposing ◽  
World Health ◽  
In Vivo Studies ◽  
Rna Dependent Rna Polymerase ◽  
Novel Coronavirus ◽  
Health Organization ◽  
Approved Drugs

The recent outburst of COVID-19 started as an epidemic in Wuhan city, China, in December 2019. It was declared a pandemic by World Health Organization on 30 January 2020. The rapid spread of the novel coronavirus leads to more deaths worldwide. Also, it has spared many lives in its second wave of disease in many countries. Although scientists had produced vaccines, it does not suit every human being, and they are getting infected again, which is due to a lack of extensive clinical trials. Also, drug repurposing is ineffective. There is a need for more research; using in silico methods may be the better option in the current situation to save the lives of virus-affected individuals. The drugs used for other diseases and herbal compounds might help target the coronavirus. In this study, a protein, RNA-dependent RNA polymerase (RdRp), was chosen as a target from the virus for molecular docking. It was docked against several drugs on the market and also several herbal compounds. This study will help further in vitro and in vivo studies with new lead compounds, new horizons for drugs in trials, and a new approach for Insilco analysis to treat COVID-19.

Antimicrobial peptides for the treatment of pulmonary tuberculosis, allies or foes?

2018 ◽  
Vol 24 (10) ◽  
pp. 1138-1147
Author(s):  
Bruno Rivas-Santiago ◽  
Flor Torres-Juarez
Keyword(s):  
Pulmonary Tuberculosis ◽  
Antimicrobial Peptides ◽  
Experimental Models ◽  
New Drugs ◽  
World Health ◽  
Public Health Issue ◽  
Health Organization ◽  
Drug Resistant Strains

Tuberculosis is an ancient disease that has become a serious public health issue in recent years, although increasing incidence has been controlled, deaths caused by Mycobacterium tuberculosis have been accentuated due to the emerging of multi-drug resistant strains and the comorbidity with diabetes mellitus and HIV. This situation is threatening the goals of World Health Organization (WHO) to eradicate tuberculosis in 2035. WHO has called for the creation of new drugs as an alternative for the treatment of pulmonary tuberculosis, among the plausible molecules that can be used are the Antimicrobial Peptides (AMPs). These peptides have demonstrated remarkable efficacy to kill mycobacteria in vitro and in vivo in experimental models, nevertheless, these peptides not only have antimicrobial activity but also have a wide variety of functions such as angiogenesis, wound healing, immunomodulation and other well-described roles into the human physiology. Therapeutic strategies for tuberculosis using AMPs must be well thought prior to their clinical use; evaluating comorbidities, family history and risk factors to other diseases, since the wide function of AMPs, they could lead to collateral undesirable effects.

Novel Phytochemical Constituents and their Potential to Manage Diabetes

2020 ◽  
Vol 26 ◽  
Author(s):  
Shaik Ibrahim Khalivulla ◽  
Arifullah Mohammed ◽  
Kokkanti Mallikarjuna
Keyword(s):  
Natural Products ◽  
Large Population ◽  
World Health ◽  
In Vivo Studies ◽  
Antidiabetic Activity ◽  
Therapeutic Drug ◽  
Pharmacological Activities ◽  
Chemical Structures

Background: Diabetes is a chronic disease affecting a large population worldwide and stands as one of the major global health challenges to be tackled. According to World Health Organization, about 400 million are having diabetes worldwide and it is the seventh leading cause of deaths in 2016. Plant based natural products had been in use from ancient time as ethnomedicine for the treatment of several diseases including diabetes. As a result of that, there are several reports on plant based natural products displaying antidiabetic activity. In the current review, such antidiabetic potential compounds reported from all plant sources along with their chemical structures are collected, presented and discussed. This kind of reports are essential to pool the available information to one source followed by statistical analysis and screening to check the efficacy of all known compounds in a comparative sense. This kind of analysis can give rise to few numbers of potential compounds from hundreds, whom can further be screened through in vitro and in vivo studies, and human trails leading to the drug development. Methods: Phytochemicals along with their potential antidiabetic property were classified according to their basic chemical skeleton. The chemical structures of all the compounds with antidiabetic activities were elucidated in the present review. In addition to this, the distribution and their other remarkable pharmacological activities of each species is also included. Results: The scrutiny of literature led to identification of 44 plants with antidiabetic compounds (70) and other pharmacological activities. For the sake of information, the distribution of each species in the world is given. Many plant derivatives may exert antidiabetic properties by improving or mimicking the insulin production or action. Different classes of compounds including sulfur compounds (1-4), alkaloids (5-11), phenolic compounds (12-17), tannins (18-23), phenylpropanoids (24-27), xanthanoids (28-31), amino acid (32), stilbenoid (33), benzofuran (34), coumarin (35), flavonoids (36-49) and terpenoids (50-70) were found to be active potential compounds for antidiabetic activity. Of the 70 listed compounds, majorly 17 compounds are from triterpenoids, 13 flavonoids and 7 are from alkaloids. Among all the 44 plant species, maximum number (7) of compounds are reported from Lagerstroemia speciosa followed by Momordica charantia (6) and S. oblonga with 5 compounds. Conclusion: This is the first paper to summarize the established chemical structures of phytochemicals that have been successfully screened for antidiabetic potential and their mechanisms of inhibition. The reported compounds could be considered as potential lead molecules for the treatment of type-2 diabetes. Further, molecular and clinical trials are required to select and establish the therapeutic drug candidates.

scholarly journals Virtual Screening and Statistical Analysis in the Design of New Caffeine Analogues Molecules with Potential Epithelial Anticancer Activity

2018 ◽  
Vol 24 (5) ◽  
pp. 576-594 ◽  
Author(s):  
Josivan da Silva Costa ◽  
Karina da Silva Lopes Costa ◽  
Josiane Viana Cruz ◽  
Ryan da Silva Ramos ◽  
Luciane Barros Silva ◽  
...  
Keyword(s):  
Anticancer Activity ◽  
Binding Free Energy ◽  
Inhibitory Effect ◽  
Parametric Models ◽  
World Health ◽  
Pharmacokinetic Properties ◽  
Clinically Significant ◽  
Health Organization

About 132 thousand cases of melanoma (more severe type of skin cancer) were registered in 2014 according to the World Health Organization. This type of cancer significantly affects the quality of life of individuals. Caffeine has shown potential inhibitory effect against epithelial cancer. In this study, it was proposed to obtain new caffeine-based molecules with potential epithelial anticancer activity. For this, a training set of 21 molecules was used for pharmacophore perception procedures. Multiple linear regression analyses were used to propose mono-, bi-, tri-, and tetra-parametric models applied in the prediction of the activity. The generated pharmacophore was used to select 350 molecules available at the ZINCpharmer server, followed by reduction to 24 molecules, after selection using the Tanimoto index, yielding 10 molecules after final selection by predicted activity values > 1.5229. These ten molecules had better pharmacokinetic properties than the other ones used as reference and within the clinically significant limits. Only two molecules show minor hits of toxicity and were submitted to molecular docking procedures, showing BFE (binding free energy) values lower than the reference values. Statistical analyses indicated strong negative correlations between BFE and pharmacophoric properties (high influence on BFE lowering) and practically null correlation between BFE and BBB. The two most promising molecules can be indicated as candidates for further in vitro and in vivo analyzes.

scholarly journals Therapeutic Effectiveness and Safety of Repurposing Drugs for the Treatment of COVID-19: Position Standing in 2021

2021 ◽  
Vol 12 ◽  
Author(s):  
Safaet Alam ◽  
Taslima Binte Kamal ◽  
Md. Moklesur Rahman Sarker ◽  
Jin-Rong Zhou ◽  
S. M. Abdur Rahman ◽  
...  
Keyword(s):  
Clinical Trials ◽  
Case Series ◽  
Basic Knowledge ◽  
World Health ◽  
Current Status ◽  
Drug Candidates ◽  
Health Organization ◽  
Meta Analyses

COVID-19, transmitted by SARS-CoV-2, is one of the most serious pandemic situations in the history of mankind, and has already infected a huge population across the globe. This horrendously contagious viral outbreak was first identified in China and within a very short time it affected the world's health, transport, economic, and academic sectors. Despite the recent approval of a few anti-COVID-19 vaccines, their unavailability and insufficiency along with the lack of other potential therapeutic options are continuing to worsen the situation, with valuable lives continuing to be lost. In this situation, researchers across the globe are focusing on repurposing prospective drugs and prophylaxis such as favipiravir, remdesivir, chloroquine, hydroxychloroquine, ivermectin, lopinavir-ritonavir, azithromycin, doxycycline, ACEIs/ARBs, rivaroxaban, and protease inhibitors, which were preliminarily based on in vitro and in vivo pharmacological and toxicological study reports followed by clinical applications. Based on available preliminary data derived from limited clinical trials, the US National Institute of Health (NIH) and USFDA also recommended a few drugs to be repurposed i.e., hydroxychloroquine, remdesivir, and favipiravir. However, World Health Organization later recommended against the use of chloroquine, hydroxychloroquine, remdesivir, and lopinavir/ritonavir in the treatment of COVID-19 infections. Combining basic knowledge of viral pathogenesis and pharmacodynamics of drug molecules as well as in silico approaches, many drug candidates have been investigated in clinical trials, some of which have been proven to be partially effective against COVID-19, and many of the other drugs are currently under extensive screening. The repurposing of prospective drug candidates from different stages of evaluation can be a handy wellspring in COVID-19 management and treatment along with approved anti-COVID-19 vaccines. This review article combined the information from completed clinical trials, case series, cohort studies, meta-analyses, and retrospective studies to focus on the current status of repurposing drugs in 2021.

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 THE ROLE OF IN VIVO MODELS IN PREDICTING TRANSDERMAL PERMEABILITY

2021 ◽  
Vol 91 (1) ◽  
pp. 86-98
Author(s):  
S. S. Malchenkova ◽  
◽  
N. S. Golyak ◽  
V. M. Tsarenkov ◽  
◽  
...  
Keyword(s):  
Structural Features ◽  
World Health ◽  
Laboratory Animals ◽  
Tape Stripping ◽  
In Vivo Models ◽  
Advantages And Disadvantages ◽  
Health Organization ◽  
Transdermal Permeability

The article presents the main types of laboratory animals that are used to study the transdermal permeability of chemical compounds. We described the structural features of epidermis, derma and skin appendages in humans and laboratory animals (small rodents, pigs, monkeys). We also emphasized advantages and disadvantages of various laboratory animals as objects for in vivo transdermal modeling. A method of extrapolation called “The parallelogram method” or «Triple Pack» has been singled out to predict the permeability of the human skin in the presence of experimental data on the permeability of the skin of animals in vivo and humans in vitro. The article describes the experimental design (including preparation of animals, premises and the substance applied) to determine transdermal permeability of substances in vivo under the guidelines of the World Health Organization and the Organization for Economic Cooperation and Development. Tissue microdialysis in volunteers has been identified as the most perfect and safest ways to promptly detect substances in the derma and tape stripping has been made in the cells of the stratum corneum.

scholarly journals Accelerated repurposing and drug development of pulmonary hypertension therapies for COVID-19 treatment using an AI-integrated biosimulation platform

2020 ◽  
Author(s):  
Kaushik Chakravarty ◽  
Victor Antontsev ◽  
Aditya Jagarapu ◽  
Yogesh Bundey ◽  
Hypatia Hou ◽  
...  
Keyword(s):  
Pulmonary Hypertension ◽  
Renin Angiotensin System ◽  
The United States ◽  
Mechanistic Modeling ◽  
World Health ◽  
Channel Blockers ◽  
Health Organization ◽  
Line Of Therapy

Abstract A World Health Organization-declared pandemic, COVID-19, has affected more than 4 million people worldwide with over 100,000 deaths and growing in the United States. Due to the fast-spreading and multi-targeted nature of the virus, it is clear that drugs and/or vaccines need to be developed at an accelerated rate, and a combinatorial approach may stand to be more successful than a single drug therapy. Among several targets and pathways that are under investigation, the renin-angiotensin system (RAS) and specifically Angiotensin converting enzyme (ACE), and Ca2+ -mediated SARS-CoV-2 cellular entry and replication are noteworthy. A combination of ACE inhibitors (e.g. benazepril) and calcium channel blockers (CCB, e.g. amlodipine), a critical line of therapy for pulmonary hypertension, has shown therapeutic relevance in COVID-19 when investigated independently. To that end, we conducted in silico modeling using BIOiSIM, an AI-integrated mechanistic modeling platform by utilizing known preclinical in vitro and in vivo datasets to accurately simulate systemic therapy disposition and site-of-action penetration of the CCB and ACEI compounds to tissues implicated in COVID-19 pathogenesis.

scholarly journals Molecular docking studies of some selected gallic acid derivatives against five non-structural proteins of novel coronavirus

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Haruna Isiyaku Umar ◽  
Bushra Siraj ◽  
Adeola Ajayi ◽  
Tajudeen O. Jimoh ◽  
Prosper Obed Chukwuemeka
Keyword(s):  
Binding Energy ◽  
Gallic Acid ◽  
High Plasma ◽  
Protein Crystal ◽  
World Health ◽  
Structural Proteins ◽  
Protein Database ◽  
Therapeutic Compounds

Abstract Background The World Health Organization has recently declared a new coronavirus disease (COVID-19) a pandemic and a global health emergency. The pressure to produce drugs and vaccines against the ongoing pandemic has resulted in the use of some drugs such as azithromycin, chloroquine (sulfate and phosphate), hydroxychloroquine, dexamethasone, favipiravir, remdesivir, ribavirin, ivermectin, and lopinavir/ritonavir. However, reports from some of the clinical trials with these drugs have proved detrimental on some COVID-19 infected patients with side effects more of which cardiomyopathy, cardiotoxicity, nephrotoxicity, macular retinopathy, and hepatotoxicity have been recently reported. Realizing the need for potent and harmless therapeutic compounds to combat COVID-19, we attempted in this study to find promising therapeutic compounds against the imminent threat of this virus. In this current study, 16 derivatives of gallic acid were docked against five selected non-structural proteins of SARS-COV-2 known to be a good target for finding small molecule inhibitors against the virus, namely, nsp3, nsp5, nsp12, nsp13, and nsp14. All the protein crystal structures and 3D structures of the small molecules (16 gallic acid derivatives and 3 control drugs) were retrieved from the Protein database (PDB) and PubChem server respectively. The compounds with lower binding energy than the control drugs were selected and subjected to pharmacokinetics screening using AdmetSAR server. Results 4-O-(6-galloylglucoside) gave binding energy values of − 8.4, − 6.8, − 8.9, − 9.1, and − 7.5 kcal/mol against Mpro, nsp3, nsp12, nsp13, and nsp15 respectively. Based on the ADMET profile, 4-O-(6-galloylglucoside) was found to be metabolized by the liver and has a very high plasma protein binding. Conclusion The result of this study revealed that 4-O-(6-galloylglucoside) could be a promising inhibitor against these SAR-Cov-2 proteins. However, there is still a need for further molecular dynamic simulation, in vivo and in vitro studies to support these findings.

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