In Silico Study of Pubchem Compounds for Solanum torvum as Antiviral Agent against SARS-CoV-2

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Abstract

Background:

The recent epidemic outbreak of a novel coronavirus called SARS-CoV-2 has caused suffering among many people in the form of respiratory tract infection. Currently, there are no targeted drugs, and effective treatment options remain limited.

Objective:

In order to rapidly discover new compounds for clinical purposes, in silico drug design and virtual drug screening have been initiated to identify new drug leads that target the main protease of the COVID-19 virus. Mpro is a key CoV enzyme, which plays a pivotal role in mediating viral replication and transcription, making it an attractive drug target for this virus.

Methods:

The present study was done to investigate the PubChem compounds of an ayurvedic herb Solanum torvum as an effective antiviral agent against COVID-19. The PubChem compounds like Torvoside H, Torvoside A, Torvoside E, Torvoside F, Torvonin A, 2,3,4-trimethyltriacontane, Torvanol A Q27134802, 5-hexatriacontanone, Jurubine, Tritriacontan-3-one, Torvanol A, Chlorogenone Spirostane-3,6-dione of Solanum torvum were downloaded from NCBI PubChem database acting as ligands for protein ligand docking. The 3D structure of the viral MPro (PDB ID: 6yb7) was retrieved from the RCSB PDB database. The active sites and binding sites were analyzed, and Docking molecular simulations were realized among a total of 12 ligands against COVID-19.

Results:

The PubChem compounds from the fruits of Solanum torvum showed good docking score and protein-ligand interaction, indicating that the PubChem compounds can cure the COVID-19 disease and act as an effective antiviral agent.

Conclusion:

Most of the PubChem compounds in the fruits of Solanum torvum showed better paramagnetic parameters.

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Most cited references 28

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Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China

Chaolin Huang, Yeming Wang, Xingwang Li … (2020)

Summary Background A recent cluster of pneumonia cases in Wuhan, China, was caused by a novel betacoronavirus, the 2019 novel coronavirus (2019-nCoV). We report the epidemiological, clinical, laboratory, and radiological characteristics and treatment and clinical outcomes of these patients. Methods All patients with suspected 2019-nCoV were admitted to a designated hospital in Wuhan. We prospectively collected and analysed data on patients with laboratory-confirmed 2019-nCoV infection by real-time RT-PCR and next-generation sequencing. Data were obtained with standardised data collection forms shared by WHO and the International Severe Acute Respiratory and Emerging Infection Consortium from electronic medical records. Researchers also directly communicated with patients or their families to ascertain epidemiological and symptom data. Outcomes were also compared between patients who had been admitted to the intensive care unit (ICU) and those who had not. Findings By Jan 2, 2020, 41 admitted hospital patients had been identified as having laboratory-confirmed 2019-nCoV infection. Most of the infected patients were men (30 [73%] of 41); less than half had underlying diseases (13 [32%]), including diabetes (eight [20%]), hypertension (six [15%]), and cardiovascular disease (six [15%]). Median age was 49·0 years (IQR 41·0–58·0). 27 (66%) of 41 patients had been exposed to Huanan seafood market. One family cluster was found. Common symptoms at onset of illness were fever (40 [98%] of 41 patients), cough (31 [76%]), and myalgia or fatigue (18 [44%]); less common symptoms were sputum production (11 [28%] of 39), headache (three [8%] of 38), haemoptysis (two [5%] of 39), and diarrhoea (one [3%] of 38). Dyspnoea developed in 22 (55%) of 40 patients (median time from illness onset to dyspnoea 8·0 days [IQR 5·0–13·0]). 26 (63%) of 41 patients had lymphopenia. All 41 patients had pneumonia with abnormal findings on chest CT. Complications included acute respiratory distress syndrome (12 [29%]), RNAaemia (six [15%]), acute cardiac injury (five [12%]) and secondary infection (four [10%]). 13 (32%) patients were admitted to an ICU and six (15%) died. Compared with non-ICU patients, ICU patients had higher plasma levels of IL2, IL7, IL10, GSCF, IP10, MCP1, MIP1A, and TNFα. Interpretation The 2019-nCoV infection caused clusters of severe respiratory illness similar to severe acute respiratory syndrome coronavirus and was associated with ICU admission and high mortality. Major gaps in our knowledge of the origin, epidemiology, duration of human transmission, and clinical spectrum of disease need fulfilment by future studies. Funding Ministry of Science and Technology, Chinese Academy of Medical Sciences, National Natural Science Foundation of China, and Beijing Municipal Science and Technology Commission.

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A Novel Coronavirus from Patients with Pneumonia in China, 2019

Na Zhu, Dingyu Zhang, Wenling Wang … (2020)

Summary In December 2019, a cluster of patients with pneumonia of unknown cause was linked to a seafood wholesale market in Wuhan, China. A previously unknown betacoronavirus was discovered through the use of unbiased sequencing in samples from patients with pneumonia. Human airway epithelial cells were used to isolate a novel coronavirus, named 2019-nCoV, which formed a clade within the subgenus sarbecovirus, Orthocoronavirinae subfamily. Different from both MERS-CoV and SARS-CoV, 2019-nCoV is the seventh member of the family of coronaviruses that infect humans. Enhanced surveillance and further investigation are ongoing. (Funded by the National Key Research and Development Program of China and the National Major Project for Control and Prevention of Infectious Disease in China.)

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Early Transmission Dynamics in Wuhan, China, of Novel Coronavirus–Infected Pneumonia

Qun Li, Xuhua Guan, Peng Wu … (2020)

Abstract Background The initial cases of novel coronavirus (2019-nCoV)–infected pneumonia (NCIP) occurred in Wuhan, Hubei Province, China, in December 2019 and January 2020. We analyzed data on the first 425 confirmed cases in Wuhan to determine the epidemiologic characteristics of NCIP. Methods We collected information on demographic characteristics, exposure history, and illness timelines of laboratory-confirmed cases of NCIP that had been reported by January 22, 2020. We described characteristics of the cases and estimated the key epidemiologic time-delay distributions. In the early period of exponential growth, we estimated the epidemic doubling time and the basic reproductive number. Results Among the first 425 patients with confirmed NCIP, the median age was 59 years and 56% were male. The majority of cases (55%) with onset before January 1, 2020, were linked to the Huanan Seafood Wholesale Market, as compared with 8.6% of the subsequent cases. The mean incubation period was 5.2 days (95% confidence interval [CI], 4.1 to 7.0), with the 95th percentile of the distribution at 12.5 days. In its early stages, the epidemic doubled in size every 7.4 days. With a mean serial interval of 7.5 days (95% CI, 5.3 to 19), the basic reproductive number was estimated to be 2.2 (95% CI, 1.4 to 3.9). Conclusions On the basis of this information, there is evidence that human-to-human transmission has occurred among close contacts since the middle of December 2019. Considerable efforts to reduce transmission will be required to control outbreaks if similar dynamics apply elsewhere. Measures to prevent or reduce transmission should be implemented in populations at risk. (Funded by the Ministry of Science and Technology of China and others.)

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Author and article information

Journal

Title: The Open COVID Journal

Abbreviated Title: TOCOVIDJ

Publisher: Bentham Science Publishers Ltd.

ISSN (Print): 2666-9587

Publication date Created: December 31 2021

Publication date (Print): December 31 2021

Volume: 1

Issue: 1

Pages: 235-242

Article

DOI: 10.2174/2666958702101010235

SO-VID: b6ac28d0-e824-421e-9d32-2410f479b9ac

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Free to read

https://creativecommons.org/licenses/by/4.0/legalcode

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ScienceOpen disciplines: Medicine,Chemistry,Life sciences

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ScienceOpen disciplines: Medicine, Chemistry, Life sciences

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In Silico Study of Pubchem Compounds for Solanum torvum as Antiviral Agent against SARS-CoV-2

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Abstract

Background:

Objective:

Methods:

Results:

Conclusion:

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Bentham Science - Open Access

Most cited references 28

Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China

A Novel Coronavirus from Patients with Pneumonia in China, 2019

Early Transmission Dynamics in Wuhan, China, of Novel Coronavirus–Infected Pneumonia

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