scholarly journals On the Generation of Novel Ligands for SARS-CoV-2 Protease and ACE2 Receptor via Constrained Graph Variational Autoencoders

2020 ◽  
Author(s):  
Jasper Kyle Catapang ◽  
Junie B. Billones
Keyword(s):  
Clinical Trials ◽  
Drug Discovery ◽  
Effective Treatment ◽  
Protease Inhibitors ◽  
Drug Repurposing ◽  
The Novel ◽  
Main Protease ◽  
Receptor Blockers ◽  
Approved Drugs ◽  
Novel Drug

SARS-CoV-2 has no known vaccine nor any effective treatment that has been released for clinical trials yet. This has ultimately paved the way for novel drug discovery approaches since although there are multiple efforts focused on drug repurposing of clinically-approved drugs for SARS-CoV-2, it is also worth considering that these existing drugs can be surpassed in effectivity by novel ones. This research focuses on the generation of novel candidate inhibitors via constrained graph variational autoencoders and the calculation of their Tanimoto similarities against existing drugs---repurposing these existing drugs and considering the novel ligands as possible SARS-CoV-2 main protease inhibitors and ACE2 receptor blockers by docking them through PyRx and ranking these ligands.

scholarly journals On the Generation of Novel Ligands for SARS-CoV-2 Protease and ACE2 Receptor via Constrained Graph Variational Autoencoders

2020 ◽  
Author(s):  
Jasper Kyle Catapang ◽  
Junie B. Billones
Keyword(s):  
Clinical Trials ◽  
Drug Discovery ◽  
Effective Treatment ◽  
Protease Inhibitors ◽  
Drug Repurposing ◽  
The Novel ◽  
Main Protease ◽  
Receptor Blockers ◽  
Approved Drugs ◽  
Novel Drug

SARS-CoV-2 has no known vaccine nor any effective treatment that has been released for clinical trials yet. This has ultimately paved the way for novel drug discovery approaches since although there are multiple efforts focused on drug repurposing of clinically-approved drugs for SARS-CoV-2, it is also worth considering that these existing drugs can be surpassed in effectivity by novel ones. This research focuses on the generation of novel candidate inhibitors via constrained graph variational autoencoders and the calculation of their Tanimoto similarities against existing drugs---repurposing these existing drugs and considering the novel ligands as possible SARS-CoV-2 main protease inhibitors and ACE2 receptor blockers by docking them through PyRx and ranking these ligands. Additionally, this research has successfully generated three novel ligands for the SARS-CoV-2 main protease and four novel ligands for the ACE2 receptor.

scholarly journals On the Generation of Novel Ligands for SARS-CoV-2 Protease and ACE2 Receptor via Constrained Graph Variational Autoencoders

2020 ◽  
Author(s):  
Jasper Kyle Catapang ◽  
Junie B. Billones
Keyword(s):  
Clinical Trials ◽  
Drug Discovery ◽  
Effective Treatment ◽  
Protease Inhibitors ◽  
Drug Repurposing ◽  
The Novel ◽  
Main Protease ◽  
Receptor Blockers ◽  
Approved Drugs ◽  
Novel Drug

SARS-CoV-2 has no known vaccine nor any effective treatment that has been released for clinical trials yet. This has ultimately paved the way for novel drug discovery approaches since although there are multiple efforts focused on drug repurposing of clinically-approved drugs for SARS-CoV-2, it is also worth considering that these existing drugs can be surpassed in effectivity by novel ones. This research focuses on the generation of novel candidate inhibitors via constrained graph variational autoencoders and the calculation of their Tanimoto similarities against existing drugs---repurposing these existing drugs and considering the novel ligands as possible SARS-CoV-2 main protease inhibitors and ACE2 receptor blockers by docking them through PyRx and ranking these ligands. Additionally, this research has successfully generated three novel ligands for the SARS-CoV-2 main protease and four novel ligands for the ACE2 receptor.

scholarly journals On the Generation of Novel Ligands for SARS-CoV-2 Protease and ACE2 Receptor via Constrained Graph Variational Autoencoders

2020 ◽  
Author(s):  
Jasper Kyle Catapang ◽  
Junie B. Billones
Keyword(s):  
Clinical Trials ◽  
Drug Discovery ◽  
Effective Treatment ◽  
Protease Inhibitors ◽  
Drug Repurposing ◽  
The Novel ◽  
Main Protease ◽  
Receptor Blockers ◽  
Approved Drugs ◽  
Novel Drug

SARS-CoV-2 has no known vaccine nor any effective treatment that has been released for clinical trials yet. This has ultimately paved the way for novel drug discovery approaches since although there are multiple efforts focused on drug repurposing of clinically-approved drugs for SARS-CoV-2, it is also worth considering that these existing drugs can be surpassed in effectivity by novel ones. This research focuses on the generation of novel candidate inhibitors via constrained graph variational autoencoders and the calculation of their Tanimoto similarities against existing drugs---repurposing these existing drugs and considering the novel ligands as possible SARS-CoV-2 main protease inhibitors and ACE2 receptor blockers by docking them through PyRx and ranking these ligands.

scholarly journals Shotgun Drug Repurposing Biotechnology to Tackle Epidemics and Pandemics

2020 ◽  
Author(s):  
William Mangione ◽  
Zackary Falls ◽  
Thomas Melendy ◽  
Gaurav Chopra ◽  
Ram Samudrala
Keyword(s):  
Clinical Trials ◽  
Drug Discovery ◽  
Computational Analysis ◽  
Drug Repurposing ◽  
The Future ◽  
Respiratory Coronavirus ◽  
Novel Drug

In this manuscript we highlight consensus between the list of drugs currently in clinical trials to treat COVID-19, the worldwide pandemic caused by severe acute respiratory coronavirus 2 (SARS-CoV-2), and the list of predictions made using our shotgun drug discovery, repurposing, and design platform known as CANDO (Computational Analysis of Novel Drug Opportunities). We make the argument that increased funding and development for drug repurposing biotechnology like ours will help combat the inevitable pathogenic outbreaks of the future. <br>

scholarly journals Identification of Potential Molecules Against COVID-19 Main Protease Through Structure-Guided Virtual Screening Approach

2020 ◽  
Author(s):  
Lovika Mittal ◽  
Anita Kumari ◽  
Mitul Srivastava ◽  
Mrityunjay Singh ◽  
Shailendra Asthana
Keyword(s):  
Virtual Screening ◽  
Design Method ◽  
Hot Spot ◽  
Drug Repurposing ◽  
Inhibitory Effect ◽  
Drug Molecules ◽  
Main Protease ◽  
Approved Drugs ◽  
Novel Drug

<p>In this work, computer-aided drug design method has been implemented to quickly identify promising drug repurposing candidates against COVID-19 main protease (M<sup>pro</sup>)<sup> </sup>. The world is facing an epidemic and in absence of vaccine or any effective treatment, it has created a sense of urgency for novel drug discovery approaches. We have made an immediate effort by performing virtual screening of clinically approved drugs or molecules under clinical trials against COVID-19 M<sup>pro</sup> to identify potential drug molecules. With given knowledge of this system, N3 and 13B compounds have shown inhibitory effect against COVID-19 M<sup>pro</sup>. Both the compounds were considered as control to filter out the screened molecules. Overall, we have identified six potential compounds, Leupeptin Hemisulphate, Pepstatin A, Nelfinavir , Birinapant, Lypression and Octeotide which have shown the docking energy > -8.0 kcal/mol and MMGBSA > -68.0 kcal/mol. The binding pattern of these compounds suggests that they interacted with key <i>hot-spot</i> residues. Also, their pharmacokinetic annotations and therapeutic importance have indicated that they possess drug-like properties and could pave their way for<i> in-vitro</i> studies. The findings of this work will be significant for structure and pharmacophore-based designing. </p>

scholarly journals Identification of Potential Molecules Against COVID-19 Main Protease Through Structure-Guided Virtual Screening Approach

2020 ◽  
Author(s):  
Lovika Mittal ◽  
Anita Kumari ◽  
Mitul Srivastava ◽  
Mrityunjay Singh ◽  
Shailendra Asthana
Keyword(s):  
Virtual Screening ◽  
Design Method ◽  
Hot Spot ◽  
Drug Repurposing ◽  
Inhibitory Effect ◽  
Drug Molecules ◽  
Main Protease ◽  
Approved Drugs ◽  
Novel Drug

<p>In this work, Computer-aided drug design method has been implemented to quickly identify promising drug repurposing candidates against COVID-19. The world is facing an epidemic and in absence of vaccine or any effective treatment, it has created a sense of urgency for novel drug discovery approaches. We have made an immediate effort by performing virtual screening of clinically approved drugs or molecules under clinical trials against COVID-19 to identify potential drug molecules.</p> <p>With given knowledge of this system, N3 and 13B compounds have shown inhibitory effect against COVD-19. Both the compounds were considered as control to filter out the screened molecules. Overall, we have identified six potential compounds, Leupeptin Hemisulphate, Pepstatin A, Nelfinavir , Birinapant, Lypression and Octeotide which have shown the docking energy > -8 kcal/mol and MMGBSA > -90 kcal/mol. The binding pattern of these compounds suggests that they interact with key <i>hot-spot</i> residues. Also, the pharmacokinetic annotations and their biological activity have indicated that they possess drug-like properties and pave their way for in vitro studies</p> <p>The findings of this work will be significant for structure and pharmacophore-based designing</p>

Repositioning of drugs to counter COVID-19 pandemic - An Insight

2020 ◽  
Vol 21 ◽  
Author(s):  
Sai M. Akilesh ◽  
Rajesh J ◽  
Dhanabal Palanisamy ◽  
Ashish Wadhwani
Keyword(s):  
Clinical Trials ◽  
Drug Repurposing ◽  
Review Article ◽  
The Novel ◽  
Phylogenetic Relation ◽  
Scientific Investigations ◽  
Realistic Approach ◽  
Life Threatening ◽  
Novel Coronavirus ◽  
Approved Drugs

: COVID-19 is a coronavirus pandemic, caused by the novel coronavirus 2 (SARS-CoV-2) severe acute respiratory syndrome. The devastating impact of this novel coronavirus outbreak has necessitated the need for rapid and effective anti-viral therapies against SARS-CoV-2, to contain the spread of disease and importantly, alleviate the severe life-threatening symptoms and disorders. Drug repurposing strategy offers an attractive, immediate and realistic approach to tackle this growing pandemic of COVID-19. Due to the similarities with SARS-CoV-1 virus and phylogenetic relation to MERS-CoV virus, accelerated screening of approved drugs and development of repositioning strategies have proved to be critical in the survival of many COVID-19 patients. Numerous scientific investigations from the initial years of coronavirus outbreak along with upcoming advances of immunotherapy and vaccines may prove to be beneficial. Currently, several repurposing strategies are under different phases of clinical trials and provide with definitive framework for the development of future therapies for the effective treatment of COVID-19. This review article summarizes the latest developments and trends in drug repurposing strategy for COVID-19 treatment.

scholarly journals Shotgun Drug Repurposing Biotechnology to Tackle Epidemics and Pandemics

2020 ◽  
Author(s):  
William Mangione ◽  
Zackary Falls ◽  
Thomas Melendy ◽  
Gaurav Chopra ◽  
Ram Samudrala
Keyword(s):  
Clinical Trials ◽  
Drug Discovery ◽  
Computational Analysis ◽  
Drug Repurposing ◽  
The Future ◽  
Respiratory Coronavirus ◽  
Novel Drug

In this manuscript we highlight consensus between the list of drugs currently in clinical trials to treat COVID-19, the worldwide pandemic caused by severe acute respiratory coronavirus 2 (SARS-CoV-2), and the list of predictions made using our shotgun drug discovery, repurposing, and design platform known as CANDO (Computational Analysis of Novel Drug Opportunities). We make the argument that increased funding and development for drug repurposing biotechnology like ours will help combat the inevitable pathogenic outbreaks of the future. <br>

scholarly journals Identification of Potential Molecules Against COVID-19 Main Protease Through Structure-Guided Virtual Screening Approach

2020 ◽  
Author(s):  
Lovika Mittal ◽  
Anita Kumari ◽  
Mitul Srivastava ◽  
Mrityunjay Singh ◽  
Shailendra Asthana
Keyword(s):  
Virtual Screening ◽  
Design Method ◽  
Hot Spot ◽  
Drug Repurposing ◽  
Inhibitory Effect ◽  
Drug Molecules ◽  
Main Protease ◽  
Approved Drugs ◽  
Novel Drug

<p>In this work, computer-aided drug design method has been implemented to quickly identify promising drug repurposing candidates against COVID-19 main protease (M<sup>pro</sup>)<sup> </sup>. The world is facing an epidemic and in absence of vaccine or any effective treatment, it has created a sense of urgency for novel drug discovery approaches. We have made an immediate effort by performing virtual screening of clinically approved drugs or molecules under clinical trials against COVID-19 M<sup>pro</sup> to identify potential drug molecules. With given knowledge of this system, N3 and 13B compounds have shown inhibitory effect against COVID-19 M<sup>pro</sup>. Both the compounds were considered as control to filter out the screened molecules. Overall, we have identified six potential compounds, Leupeptin Hemisulphate, Pepstatin A, Nelfinavir , Birinapant, Lypression and Octeotide which have shown the docking energy > -8.0 kcal/mol and MMGBSA > -68.0 kcal/mol. The binding pattern of these compounds suggests that they interacted with key <i>hot-spot</i> residues. Also, their pharmacokinetic annotations and therapeutic importance have indicated that they possess drug-like properties and could pave their way for<i> in-vitro</i> studies. The findings of this work will be significant for structure and pharmacophore-based designing. </p>

scholarly journals Shotgun Drug Repurposing Biotechnology to Tackle Epidemics and Pandemics

2020 ◽  
Author(s):  
William Mangione ◽  
Zackary Falls ◽  
Thomas Melendy ◽  
Gaurav Chopra ◽  
Ram Samudrala
Keyword(s):  
Clinical Trials ◽  
Drug Discovery ◽  
Computational Analysis ◽  
Drug Repurposing ◽  
The Future ◽  
Respiratory Coronavirus ◽  
Novel Drug

In this manuscript we highlight consensus between the list of drugs currently in clinical trials to treat COVID-19, the worldwide pandemic caused by severe acute respiratory coronavirus 2 (SARS-CoV-2), and the list of predictions made using our shotgun drug discovery, repurposing, and design platform known as CANDO (Computational Analysis of Novel Drug Opportunities). We make the argument that increased funding and development for drug repurposing biotechnology like ours will help combat the inevitable pathogenic outbreaks of the future. <br>

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