Proposal of novel natural inhibitors of severe acute respiratory syndrome coronavirus 2 main protease: Molecular docking and ab initio fragment molecular orbital calculations

Shaji, Divya; Yamamoto, Shohei; Saito, Ryosuke; Suzuki, Ryo; Nakamura, Shunya; Kurita, Noriyuki

doi:10.1016/j.bpc.2021.106608

Cited by 17 publications

(25 citation statements)

References 43 publications

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“…In our previous molecular simulations [23], we considered 12 natural compounds extracted from Moringa oleifera and investigated their binding a nities against Mpro. Their chemical properties and structures are shown in Table S1 and Figure S1 of the Supplementary material (SM).…”

Section: Optimized Structures Of the Main Protease-ligand Complexesmentioning

confidence: 99%

“…Compound The total IFIEs of the Mpro residues and the compounds extracted from Moringa oleifera [23], Aloe vera, and Nyctanthes arbor-tristis were compared, as shown in Fig. 3.…”

Section: Optimized Structures Of the Main Protease-ligand Complexesmentioning

confidence: 99%

“…In previous molecular simulations [23] based on the molecular docking and ab initio fragment molecular orbital (FMO) methods, we investigated the binding properties of compounds extracted from Moringa oleifera to the Mpro of SARS-CoV-2. Moringa oleifera is a plant belonging to the Moringaceae family and has antifungal, antioxidant, antibacterial, anti-in ammatory, diuretic, and hepato-protective properties.…”

Section: Introductionmentioning

confidence: 99%

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Natural inhibitors for severe acute respiratory syndrome coronavirus 2 main protease from Moringa oleifera, Aloe vera, and Nyctanthes arbor-tristis: Molecular docking and ab initio fragment molecular orbital calculations

Shaji

Suzuki

Yamamoto

et al. 2022

Preprint

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The novel coronavirus 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread rapidly worldwide, and new drug treatments for COVID-19 are urgently required. To find the potential inhibitors against main protease (Mpro) of SARS-CoV-2, we investigated the inhibitory potential of naturally occurring compounds from the plants Moringa oleifera, Aloe vera, and Nyctanthes arbor-tristis, using molecular docking, classical molecular mechanics optimizations, and ab initio fragment molecular orbital calculations. Of the 35 compounds that we simulated, feralolide from Aloe vera exhibited the highest binding affinity against Mpro. Therefore, we proposed novel compounds based on the feralolide and investigated their binding properties to the Mpro. The results indicated that the introduction of a hydroxyl group into feralolide significantly enhances its binding affinity against Mpro. These results provide useful information for developing potent Mpro inhibitors.

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Section: Optimized Structures Of the Main Protease-ligand Complexesmentioning

confidence: 99%

“…Compound The total IFIEs of the Mpro residues and the compounds extracted from Moringa oleifera [23], Aloe vera, and Nyctanthes arbor-tristis were compared, as shown in Fig. 3.…”

Section: Optimized Structures Of the Main Protease-ligand Complexesmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Natural inhibitors for severe acute respiratory syndrome coronavirus 2 main protease from Moringa oleifera, Aloe vera, and Nyctanthes arbor-tristis: Molecular docking and ab initio fragment molecular orbital calculations

Shaji

Suzuki

Yamamoto

et al. 2022

Preprint

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“…It is also effective against various viruses (Biswas et al, 2020). Furthermore, the active compound, niaziminin, and three flavonoids (isorhamnetin, kaempferol, and apigenin) from Moringa oleifera showed the strongest interaction with the main protease of SARS-CoV2 (Shaji et al, 2021).…”

Section: Herbs and Spices With An Viral Propertymentioning

confidence: 99%

“…. 7.Moringa oleiferaCommon name: Drumstick tree Family: MoringaceaeNiaziminin and flavonoids (isorhamnetin, kaempferol and apigenin)Show the strongest interaction with the main protease of SARS-CoV-2(Sen et al, 2021;Shaji et al, 2021).N a t u r a l R e s o u r c e f o r H u m a n H e a l t h 2022, 2, 32-51 | 38Table 1 continued 11. Piper nigrum Common name: Black pepper Family: Piperaceae PN Antidiabetic activity.…”

mentioning

confidence: 99%

Herbal spices-based therapeutics for diabetic patients with COVID-19 infection: A review

Rajasekar¹,

Vel²

2021

NRFHH

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The COVID-19 pandemic is a highly challenging situation and affects people's lives severely. Nowadays, the original coronavirus gets mutated into different variants and infects all age groups. Elderly people with comorbidities like diabetes are highly susceptible to coronavirus infection due to poor glycemic control, and immunity. The mechanism of COVID-19 infection is not fully understood. However, the scenario of current infection is similar to the history of pandemics that the world faced earlier (i.e.) the persisted hyperglycemia is considered as the major root cause of severe viral infections. The uncontrolled hyperglycemia can produce low-grade inflammation and impaired immunity mediated cytokine storm that can cause multiple organs failure and sudden death in diabetic patients with COVID-19 infection. The available hypoglycemic and antiviral drugs and vaccines are not sufficiently efficient against COVID-19 and also cause several side effects. As the traditional medicines are considered life-saving drugs for various human diseases, the present review has analyzed the herbs-spices with antiviral, antidiabetic, antioxidant, anti-inflammatory, and immunomodulatory properties. The intake of this herbal-spices formulation could exert both therapeutic and prophylactic effects against the COVID-19. However, the proper scientific studies are necessary for the validation of its efficacy and mode of action against COVID-19.

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Antiviral foods in the battle against viral infections: Understanding the molecular mechanism

Azam,

Islam,

Wahiduzzaman

et al. 2023

Food Science & Nutrition

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Viruses produce a variety of illnesses, which may also cause acute respiratory syndrome. All viral infections, including COVID‐19, are associated with the strength of the immune system. Till now, traditional medicine or vaccines for most viral diseases have not been effective. Antiviral and immune‐boosting diets may provide defense against viral diseases by lowering the risk of infection and assisting rapid recovery. The purpose of this review was to gather, analyze, and present data based on scientific evidence in order to provide an overview of the mechanistic insights of antiviral bioactive metabolites. We have covered a wide range of food with antiviral properties in this review, along with their potential mechanism of action against viral infections. Additionally, the opportunities and challenges of using antiviral food have been critically reviewed. Bioactive plant compounds, not only help in maintaining the body's normal physiological mechanism and good health but are also essential for improving the body's immunity and therefore can be effective against viral diseases. These agents fight viral diseases either by incorporating the body's defense mechanism or by enhancing the cell's immune system. Regular intake of antiviral foods may prevent future pandemic and consumption of these antiviral agents with traditional medicine may reduce the severity of viral diseases. Therefore, the synergistic effect of antiviral foods and medication needs to be investigated.

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Proposal of novel natural inhibitors of severe acute respiratory syndrome coronavirus 2 main protease: Molecular docking and ab initio fragment molecular orbital calculations

Cited by 17 publications

References 43 publications

Natural inhibitors for severe acute respiratory syndrome coronavirus 2 main protease from Moringa oleifera, Aloe vera, and Nyctanthes arbor-tristis: Molecular docking and ab initio fragment molecular orbital calculations

Natural inhibitors for severe acute respiratory syndrome coronavirus 2 main protease from Moringa oleifera, Aloe vera, and Nyctanthes arbor-tristis: Molecular docking and ab initio fragment molecular orbital calculations

Herbal spices-based therapeutics for diabetic patients with COVID-19 infection: A review

Antiviral foods in the battle against viral infections: Understanding the molecular mechanism

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