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Virtual screening, ADME/T, and binding free energy analysis of anti-viral, anti-protease, and anti-infectious compounds against NSP10/NSP16 methyltransferase and main protease of SARS CoV-2.
Maurya, Santosh K; Maurya, Akhilesh Kumar; Mishra, Nidhi; Siddique, Hifzur R.
  • Maurya SK; Molecular Cancer Genetics & Translational Research Lab, Section of Genetics, Department of Zoology, Aligarh Muslim University, Aligarh, India.
  • Maurya AK; Indian Institute of Information Technology Allahabad, Prayagraj, India.
  • Mishra N; Indian Institute of Information Technology Allahabad, Prayagraj, India.
  • Siddique HR; Molecular Cancer Genetics & Translational Research Lab, Section of Genetics, Department of Zoology, Aligarh Muslim University, Aligarh, India.
J Recept Signal Transduct Res ; 40(6): 605-612, 2020 Dec.
Article in English | MEDLINE | ID: covidwho-457256
Semantic information from SemMedBD (by NLM)
1. Methyltransferase PART_OF 2019 novel coronavirus
Subject
Methyltransferase
Predicate
PART_OF
Object
2019 novel coronavirus
2. Peptide Hydrolases PART_OF 2019 novel coronavirus
Subject
Peptide Hydrolases
Predicate
PART_OF
Object
2019 novel coronavirus
3. Coronavirus Infections CAUSES Pneumonia
Subject
Coronavirus Infections
Predicate
CAUSES
Object
Pneumonia
4. peptidase complex PART_OF 2019 novel coronavirus
Subject
peptidase complex
Predicate
PART_OF
Object
2019 novel coronavirus
5. Methyltransferase INTERACTS_WITH Pharmaceutical Preparations
Subject
Methyltransferase
Predicate
INTERACTS_WITH
Object
Pharmaceutical Preparations
6. Peptide Hydrolases INTERACTS_WITH Pharmaceutical Preparations
Subject
Peptide Hydrolases
Predicate
INTERACTS_WITH
Object
Pharmaceutical Preparations
7. Methyltransferase PART_OF 2019 novel coronavirus
Subject
Methyltransferase
Predicate
PART_OF
Object
2019 novel coronavirus
8. Peptide Hydrolases PART_OF 2019 novel coronavirus
Subject
Peptide Hydrolases
Predicate
PART_OF
Object
2019 novel coronavirus
9. Coronavirus Infections CAUSES Pneumonia
Subject
Coronavirus Infections
Predicate
CAUSES
Object
Pneumonia
10. peptidase complex PART_OF 2019 novel coronavirus
Subject
peptidase complex
Predicate
PART_OF
Object
2019 novel coronavirus
11. Methyltransferase INTERACTS_WITH Pharmaceutical Preparations
Subject
Methyltransferase
Predicate
INTERACTS_WITH
Object
Pharmaceutical Preparations
12. Peptide Hydrolases INTERACTS_WITH Pharmaceutical Preparations
Subject
Peptide Hydrolases
Predicate
INTERACTS_WITH
Object
Pharmaceutical Preparations
ABSTRACT
Recently, a pathogen has been identified as a novel coronavirus (SARS-CoV-2) and found to trigger novel pneumonia (COVID-19) in human beings and some other mammals. The uncontrolled release of cytokines is seen from the primary stages of symptoms to last acute respiratory distress syndrome (ARDS). Thus, it is necessary to find out safe and effective drugs against this deadly coronavirus as soon as possible. Here, we downloaded the three-dimensional model of NSP10/NSP16 methyltransferase (PDB-ID 6w6l) and main protease (PDB-ID 6lu7) of COVID-19. Using these molecular models, we performed virtual screening with our anti-viral, inti-infectious, and anti-protease compounds, which are attractive therapeutics to prevent infection of the COVID-19. We found that top screened compound binds with protein molecules with good dock score with the help of hydrophobic interactions and hydrogen bonding. We observed that protease complexed with Cyclocytidine hydrochloride (anti-viral and anti-cancer), Trifluridine (anti-viral), Adonitol, and Meropenem (anti-bacterial), and Penciclovir (anti-viral) bound with a good docking score ranging from -6.8 to -5.1 (Kcal/mol). Further, NSP10/NSP16 methyltransferase complexed with Telbivudine, Oxytetracycline dihydrate (anti-viral), Methylgallate (anti-malarial), 2-deoxyglucose and Daphnetin (anti-cancer) from the docking score of -7.0 to -5.7 (Kcal/mol). In conclusion, the selected compounds may be used as a novel therapeutic agent to combat this deadly pandemic disease, SARS-CoV-2 infection, but needs further experimental research.HighlightsNSP10/NSP16 methyltransferase and main protease complex of SARS CoV-2 bind with selected drugs.NSP10/NSP16 methyltransferase and protease interacted with drugs by hydrophobic interactions.Compounds show good DG binging free energy with protein complexes.Ligands were found to follow the Lipinski rule of five.
Subject(s)
Keywords

Full text: Available Collection: International databases Database: MEDLINE Document Type: Article Main subject: Antiviral Agents / Pneumonia, Viral / Viral Nonstructural Proteins / Coronavirus Infections / Viral Regulatory and Accessory Proteins Subject: Antiviral Agents / Pneumonia, Viral / Viral Nonstructural Proteins / Coronavirus Infections / Viral Regulatory and Accessory Proteins Type of study: Diagnostic study / Prognostic study / Screening study Language: English Journal: J Recept Signal Transduct Res Clinical aspect: Prognosis / Therapy Year: 2020

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Full text: Available Collection: International databases Database: MEDLINE Document Type: Article Main subject: Antiviral Agents / Pneumonia, Viral / Viral Nonstructural Proteins / Coronavirus Infections / Viral Regulatory and Accessory Proteins Subject: Antiviral Agents / Pneumonia, Viral / Viral Nonstructural Proteins / Coronavirus Infections / Viral Regulatory and Accessory Proteins Type of study: Diagnostic study / Prognostic study / Screening study Language: English Journal: J Recept Signal Transduct Res Clinical aspect: Prognosis / Therapy Year: 2020
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