scholarly journals A molecular modelling approach for identifying antiviral selenium-containing heterocyclic compounds that inhibit the main protease of SARS-CoV-2: an in silico investigation

2021 ◽  
Author(s):  
Ahmed Rakib ◽  
Zulkar Nain ◽  
Saad Ahmed Sami ◽  
Shafi Mahmud ◽  
Ashiqul Islam ◽  
...  
Keyword(s):  
Immune Responses ◽  
Heterocyclic Compounds ◽  
Case Fatality ◽  
Biologically Active ◽  
Dynamics Simulation ◽  
World Health ◽  
Drug Candidate ◽  
Drug Candidates ◽  
Host Immune Responses ◽  
Main Protease

Abstract Coronavirus disease 2019 (COVID-19), an infectious disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has been declared a global pandemic by the World Health Organization, and the situation worsens daily, associated with acute increases in case fatality rates. The main protease (Mpro) enzyme produced by SARS-CoV-2 was recently demonstrated to be responsible for not only viral reproduction but also impeding host immune responses. The element selenium (Se) plays a vital role in immune functions, both directly and indirectly. Thus, we hypothesised that Se-containing heterocyclic compounds might curb the activity of SARS-CoV-2 Mpro. We performed a molecular docking analysis and found that several of the selected selenocompounds showed potential binding affinities for SARS-CoV-2 Mpro, especially ethaselen (49), which exhibited a docking score of −6.7 kcal/mol compared with the −6.5 kcal/mol score for GC376 (positive control). Drug-likeness calculations suggested that these compounds are biologically active and possess the characteristics of ideal drug candidates. Based on the binding affinity and drug-likeness results, we selected the 16 most effective selenocompounds as potential anti-COVID-19 drug candidates. We also validated the structural integrity and stability of the drug candidate through molecular dynamics simulation. Using further in vitro and in vivo experiments, we believe that the targeted compound identified in this study (ethaselen) could pave the way for the development of prospective drugs to combat SARS-CoV-2 infections and trigger specific host immune responses.

scholarly journals A computational biology approach for the identification of potential SARS-CoV-2 main protease inhibitors from natural essential oil compounds.

F1000Research ◽  
2021 ◽  
Vol 10 ◽  
pp. 1313
Author(s):  
Rizone Al Hasib ◽  
Md. Chayan Ali ◽  
Md. Shahedur Rahman ◽  
Md. Mafizur Rahman ◽  
Fee Faysal Ahmed ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Essential Oil ◽  
New Drugs ◽  
Dynamics Simulation ◽  
World Health ◽  
Drug Candidates ◽  
Main Protease ◽  
Essential Oil Compounds

Background: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has fomented a climate of fear worldwide due to its rapidly spreading nature, and high mortality rate. The World Health Organization (WHO) declared it as a global pandemic on 11th March, 2020. Many endeavors have been made to find appropriate medications to restrain the SARS CoV-2 infection from spreading but there is no specific antiviral therapy to date. However, a computer-aided drug design approach can be an alternative to identify probable drug candidates within a short time. SARS-CoV-2 main protease is a proven drug target, and it plays a pivotal role in viral replication and transcription. Methods: In this study, we identified a total of 114 essential oil compounds as a feasible anti-SARS-CoV-2 agent from several online reservoirs. These compounds were screened by incorporating ADMET profiling, molecular docking, and 50 ns of molecular dynamics simulation to identify potential drug candidates against the SARS-CoV-2 main protease. The crystallized SARS-CoV-2 main protease structure was collected from the RCSB PDB database (PDB ID 6LU7). Results: According to the results of the ADMET study, none of the compounds have any side effects that could reduce their druglikeness or pharmacokinetic properties. Out of 114 compounds, we selected bisabololoxide B, eremanthin, and leptospermone as our top drug candidates based on their higher binding affinity scores, and strong interaction with the Cys 145-His 41 catalytic dyad. Finally, the molecular dynamics simulation was implemented to evaluate the structural stability of the ligand-receptor complex. MD simulations disclosed that all the hits showed conformational stability compared to the positive control α-ketoamide. Conclusions: Our study showed that the top three hits might work as potential anti-SARS-CoV-2 agents, which can pave the way for discovering new drugs, but for experimental validation, they will require more in vivo trials.

Synthesis of Pyrazolofuropyrazine via One-Pot SNAr Reaction and Intramolecular Direct C–H Arylation

Synthesis ◽  
2018 ◽  
Vol 50 (07) ◽  
pp. 1493-1498 ◽  
Author(s):  
Shinichiro Fuse ◽  
Hiroyuki Nakamura ◽  
Megumi Inaba ◽  
Shinichi Sato ◽  
Manjusha Joshi
Keyword(s):  
Drug Discovery ◽  
Rapid Development ◽  
Ring System ◽  
Biologically Active ◽  
Drug Candidate ◽  
One Pot ◽  
Ring Systems ◽  
Drug Candidates ◽  
Fused Ring ◽  
Snar Reaction

Fused-ring systems containing heterocycles are attractive templates for drug discovery. Biologically active 6-5-5+6 fused-ring systems that possess heterocycles are available, but these require a relatively large number of synthetic steps for preparation. Therefore, pyrazolofuropyrazine was designed as a 6-5-5+6 ring system template that incorporates ready accessibility for drug discovery. Pyrazolofuropyrazines were successfully constructed in only a few steps via one-pot SNAr reaction/intramolecular C–H direct arylation. As a drug candidate, pyrazolofuropyrazine has earned a favorable LogP, although significant biological activity has yet to be established; the ready accessibility of pyrazolofuropyrazine template, however, offers an opportunity for the rapid development of promising new drug candidates.

scholarly journals Screening of FDA Approved Drugs Against COVID-19 Main Protease: Coronavirus Disease

2020 ◽  
Author(s):  
Vijayakumar Balakrishnan ◽  
Karthik Lakshminarayanan
Keyword(s):  
Vaccine Development ◽  
New Drugs ◽  
World Health ◽  
Wuhan City ◽  
Drug Candidates ◽  
Human Contact ◽  
Main Protease ◽  
Potent Drug ◽  
Approved Drugs ◽  
Fda Approved Drugs

In the end of December 2019, a new strain of coronavirus was identified in the Wuhan city of Hubei province in China. Within a shorter period of time, an unprecedented outbreak of this strain was witnessed over the entire Wuhan city. This novel coronavirus strain was later officially renamed as COVID-19 (Coronavirus disease 2019) by the World Health Organization. The mode of transmission had been found to be human-to-human contact and hence resulted in a rapid surge across the globe where more than 1,100,000 people have been infected with COVID-19. In the current scenario, finding potent drug candidates for the treatment of COVID-19 has emerged as the most challenging task for clinicians and researchers worldwide. Identification of new drugs and vaccine development may take from a few months to years based on the clinical trial processes. To overcome the several limitations involved in identifying and bringing out potent drug candidates for treating COVID-19, in the present study attempts were made to screen the FDA approved drugs using High Throughput Virtual Screening (HTVS). The COVID-19 main protease (COVID-19 Mpro) was chosen as the drug target for which the FDA approved drugs were initially screened with HTVS. The drug candidates that exhibited favorable docking score, energy and emodel calculations were further taken for performing Induced Fit Docking (IFD) using Schrodinger’s GLIDE. From the flexible docking results, the following four FDA approved drugs Sincalide, Pentagastrin, Ritonavir and Phytonadione were identified. In particular, Sincalide and Pentagastrin can be considered potential key players for the treatment of COVID-19 disease.

Dual Acting Isatin-heterocyclic Hybrids: Recent Highlights as Promising Pharmacological Agents

2018 ◽  
Vol 16 (2) ◽  
pp. 220-236 ◽  
Author(s):  
Srinubabu Maddela ◽  
Githa Elizabeth Mathew ◽  
Della Grace Thomas Parambi ◽  
Fakhria Aljoufi ◽  
Bijo Mathew
Keyword(s):  
Single Molecule ◽  
Heterocyclic Compounds ◽  
Structural Modification ◽  
Drug Efficacy ◽  
Biologically Active ◽  
Synergistic Activity ◽  
Pharmacological Activities ◽  
Pharmacological Agents ◽  
Drug Candidates ◽  
Derivatives Of

Background: For the development of suitable lead molecules to different diseases is a highly challenging task for medicinal chemists. Nowadays, hybrid pharmacophore concept has developed as a useful structural modification tool in the drug design of new drug candidates for different diseases. Hybrid pharmacophore approach consists of combination of two or more pharmacophoric moieties from different biologically active compounds with complementary functions or different mechanisms of action into a single molecule. This often results in synergistic activity or enhanced drug efficacy. Objective: To develop the suitable leads for different diseases there will be a lot of scope to study the substitution of heterocyclic moieties on the different positions of isatin ring. The broad and potent activities of the isatin and their derivatives have been established them as pharmacologically significant scaffolds. In this review, an attempt has been made with specifically emphasizing the hybridization of Isatin with different derivatives of heterocyclic compounds on the different positions of the isatin ring (aryl ring, isatin nitrogen and C2/C3 carbonyl moieties). Conclusion: This review highlighted the recent advances of dual acting isatin-heterocyclic hybrids presenting various pharmacological activities viz., anticancer, antitubercular, anti-inflammatory and antimicrobial.

scholarly journals In Silico Prediction of Inhibitory Potential of a Punicalagin β-anomer Against SARS-COV-2 Main Protease (Mpro)

2021 ◽  
Author(s):  
Norberto Monteiro ◽  
Vitória Monteiro ◽  
Lorena Lima ◽  
Anna Karolline ◽  
Richele Machado
Keyword(s):  
Molecular Dynamics ◽  
In Silico ◽  
Treatment Strategies ◽  
Punica Granatum ◽  
Drug Candidate ◽  
Fruit Peel ◽  
Drug Candidates ◽  
Potential Inhibitor ◽  
Main Protease ◽  
Inhibitory Potential

Abstract The pandemic caused by the new coronavirus has resulted in a global health emergency and has prompted an urgent need for new treatment strategies. No target-specific drugs are currently available for SARS-CoV-2, but new drug candidates targeting the viral replication cycle are being explored. A prime target of drug-discovery efforts is the SARS-CoV-2 main protease (Mpro). In this work, we identified a potential inhibitor for SARS-CoV-2 main protease using in silico methodologies. Molecular docking and molecular dynamics studies were carried out to ascertain the inhibitory action of α and β anomers of Punicalagin from fruit peel of Punica granatum against the Mpro protease. The molecular dynamics results revealed that the β-anomeric configuration of punicalagin allowed access to more hydrogen bonds and hydrophobic interaction leading to higher selectivity and specificity of β-anomer than α-anomer. Therefore, the β-anomer of Punicalagin could act as potential inhibitor against the main protease of SARS-CoV-2 and may act as a potential drug candidate.

scholarly journals The impact of curcumin derived polyphenols on the structure and flexibility COVID-19 main protease binding pocket: a molecular dynamics simulation study

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11590
Author(s):  
Aweke Mulu ◽  
Mulugeta Gajaa ◽  
Haregewoin Bezu Woldekidan ◽  
Jerusalem Fekadu W/mariam
Keyword(s):  
Molecular Dynamics ◽  
Binding Affinity ◽  
Binding Pocket ◽  
Dynamics Simulation ◽  
World Health ◽  
Main Protease ◽  
Health Organization ◽  
Dynamics Simulations ◽  
Simulation Parameters ◽  
The Impact

The newly occurred SARS-CoV-2 caused a leading pandemic of coronavirus disease (COVID-19). Up to now it has infected more than one hundred sixty million and killed more than three million people according to 14 May 2021 World Health Organization report. So far, different types of studies have been conducted to develop an anti-viral drug for COVID-19 with no success yet. As part of this, silico were studied to discover and introduce COVID-19 antiviral drugs and results showed that protease inhibitors could be very effective in controlling. This study aims to investigate the binding affinity of three curcumin derived polyphenols against COVID-19 the main protease (Mpro), binding pocket, and identification of important residues for interaction. In this study, molecular modeling, auto-dock coupled with molecular dynamics simulations were performed to analyze the conformational, and stability of COVID-19 binding pocket with diferuloylmethane, demethoxycurcumin, and bisdemethoxycurcumin. All three compounds have shown binding affinity −39, −89 and −169.7, respectively. Demethoxycurcumin and bisdemethoxycurcumin showed an optimum binding affinity with target molecule and these could be one of potential ligands for COVID-19 therapy. And also, COVID-19 main protease binding pocket binds with the interface region by one hydrogen bond. Moreover, the MD simulation parameters indicated that demethoxycurcumin and bisdemethoxycurcumin were stable during the simulation run. These findings can be used as a baseline to develop therapeutics with curcumin derived polyphenols against COVID-19.

scholarly journals Natural xanthone compounds as promising drug candidates against COVID-19 - An integrated molecular docking and dynamics simulation study

2020 ◽  
Author(s):  
Shravan Kumar Gunda ◽  
Hima Kumari P ◽  
Gourav Choudhir ◽  
Anuj Kumar ◽  
P B. Kavi Kishor ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Antiviral Agents ◽  
Binding Energies ◽  
Dynamics Simulation ◽  
Lipinski’S Rule ◽  
Drug Candidates ◽  
Main Protease ◽  
Lipinski’S Rule Of Five ◽  
Dynamics Simulations ◽  
Potential Inhibitors

Abstract Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes coronavirus disease2019 (COVID-19). SARS-CoV-2 is known for its high pathogenicity and transmission due to thepresence of polybasic cleavage sites. No specific drug is available for the treatment. To identifythe potential inhibitors, we have performed molecular docking against the SARS-CoV-2 mainprotease (6Y84) with fifteen important natural xanthone compounds. The docking results showedall the compounds exhibited good binding energies and interactions with the main protease. Thevalidation of representative docking complexes through molecular dynamics simulations showedthat xanthones binds with a higher binding affinity and lower free energy than the standardligand with Brasixanthone C and Brasixanthone B on 50 ns. Natural xanthone compounds havealso passed the Absorption, Distribution, Metabolism, and Excretion (ADME) property criteriaas well as Lipinski’s rule of five. The present integrated molecular docking and dynamicssimulations study unveil the use of xanthones as potential antiviral agents against SARS-CoV-2.

scholarly journals Prospective Role of Peptide-Based Antiviral Therapy Against the Main Protease of SARS-CoV-2

2021 ◽  
Vol 8 ◽  
Author(s):  
Shafi Mahmud ◽  
Gobindo Kumar Paul ◽  
Suvro Biswas ◽  
Shamima Afrose ◽  
Mohasana Akter Mita ◽  
...  
Keyword(s):  
Stability Index ◽  
Dynamics Simulation ◽  
World Health ◽  
Economic Sectors ◽  
Negative Results ◽  
Main Protease ◽  
And Control ◽  
Control Complex ◽  
Nonbonded Interaction

The recently emerged coronavirus (SARS-CoV-2) has created a crisis in world health, and economic sectors as an effective treatment or vaccine candidates are still developing. Besides, negative results in clinical trials and effective cheap solution against this deadly virus have brought new challenges. The viral protein, the main protease from SARS-CoV-2, can be effectively targeted due to its viral replication and pathogenesis role. In this study, we have enlisted 88 peptides from the AVPdb database. The peptide molecules were modeled to carry out the docking interactions. The four peptides molecules, P14, P39, P41, and P74, had more binding energy than the rest of the peptides in multiple docking programs. Interestingly, the active points of the main protease from SARS-CoV-2, Cys145, Leu141, Ser139, Phe140, Leu167, and Gln189, showed nonbonded interaction with the peptide molecules. The molecular dynamics simulation study was carried out for 200 ns to find out the docked complex’s stability where their stability index was proved to be positive compared to the apo and control complex. Our computational works based on peptide molecules may aid the future development of therapeutic options against SARS-CoV-2.

scholarly journals Biochemical and Computational Approach of Selected Phytocompounds from Tinospora crispa in the Management of COVID-19

Molecules ◽  
2020 ◽  
Vol 25 (17) ◽  
pp. 3936 ◽  
Author(s):  
Ahmed Rakib ◽  
Arkajyoti Paul ◽  
Md. Nazim Uddin Chy ◽  
Saad Ahmed Sami ◽  
Sumit Kumar Baral ◽  
...  
Keyword(s):  
Immune Responses ◽  
Docking Study ◽  
Computational Approach ◽  
The Novel ◽  
Molecular Docking Study ◽  
Host Immune Responses ◽  
Main Protease ◽  
Gas Chromatography Mass Spectroscopy ◽  
Novel Coronavirus ◽  
Viral Reproduction

A pandemic caused by the novel coronavirus (SARS-CoV-2 or COVID-19) began in December 2019 in Wuhan, China, and the number of newly reported cases continues to increase. More than 19.7 million cases have been reported globally and about 728,000 have died as of this writing (10 August 2020). Recently, it has been confirmed that the SARS-CoV-2 main protease (Mpro) enzyme is responsible not only for viral reproduction but also impedes host immune responses. The Mpro provides a highly favorable pharmacological target for the discovery and design of inhibitors. Currently, no specific therapies are available, and investigations into the treatment of COVID-19 are lacking. Therefore, herein, we analyzed the bioactive phytocompounds isolated by gas chromatography–mass spectroscopy (GC-MS) from Tinospora crispa as potential COVID-19 Mpro inhibitors, using molecular docking study. Our analyses unveiled that the top nine hits might serve as potential anti-SARS-CoV-2 lead molecules, with three of them exerting biological activity and warranting further optimization and drug development to combat COVID-19.

Sign in / Sign up

Export Citation Format

Share Document