Curcumin inhibits spike protein of new SARS-CoV-2 variant of concern (VOC) Omicron, an in silico study

A top-down approach for studying the in-silico effect of the novel phytocompound tribulusamide B on the inhibition of Nipah virus transmission through targeting fusion glycoprotein and matrix protein

The proteins of Nipah virus ascribe to its lifecycle and are crucial to infections caused by the virus. In the absence of approved therapeutics, these proteins can be considered as drug targets. This study examined the potential of fifty-three (53) natural compounds to inhibit Nipah virus fusion glycoprotein (NiV F) and matrix protein (NiV M) in silico. The molecular docking experiment, supported by the principal component analysis (PCA), showed that out of all the phytochemicals considered, Tribulusamide B had the highest inhibitory potential against the target proteins NiV F and NiV M (-9.21 and -8.66 kcal mol-1, respectively), when compared to the control drug, Ribavirin (-7.01 and -6.52 kcal mol-1, respectively). Furthermore, it was found that Tribulusamide B pharmacophores, namely, hydrogen donors, acceptors, aromatic and hydrophobic groups, contributed towards the effective residual interactions with the target proteins. The molecular dynamic simulation further validated the results of the docking studies and concluded that Tribulusamide B formed a stable complex with the target proteins. The data obtained from MM-PBSA study further explained that the phytochemical could strongly bind with NiV F (-31.26 kJ mol-1) and NiV M (-40.26 kJ mol-1) proteins in comparison with the control drug Ribavirin (-13.12 and -13.94 kJ mol-1, respectively). Finally, the results indicated that Tribulusamide B, a common inhibitor effective against multiple proteins, can be considered a potential therapeutic entity in treating the Nipah virus infection.

Curcumin as a natural potential drug candidate against important zoonotic viruses and prions: A narrative review

Zoonotic diseases are major public health concerns and undeniable threats to human health. Among Zoonotic diseases, zoonotic viruses and prions are much more difficult to eradicate, as they result in higher infections and mortality rates. Several investigations have shown curcumin, the active ingredient of turmeric, to have wide spectrum properties such as anti-microbial, anti-vascular, anti-inflammatory, anti-tumor, anti-neoplastic, anti-oxidant, and immune system modulator properties. In the present study, we performed a comprehensive review of existing in silico, in vitro, and in vivo evidence on the antiviral (54 important zoonotic viruses) and anti-prion properties of curcumin and curcuminoids in PubMed, Google Scholar, Science Direct, Scopus, and Web of Science databases. Database searches yielded 13,380 results, out of which 216 studies were eligible according to inclusion criteria. Of 216 studies, 135 (62.5%), 24 (11.1%), and 19 (8.8%) were conducted on the effect of curcumin and curcuminoids against SARS-CoV-2, Influenza A virus, and dengue virus, respectively. This review suggests curcumin and curcuminoids as promising therapeutic agents against a wide range of viral zoonoses by targeting different proteins and signaling pathways.

Natural products as a source of Coronavirus entry inhibitors

The COVID-19 pandemic has had a significant and lasting impact on the world. Four years on, despite the existence of effective vaccines, the continuous emergence of new SARS-CoV-2 variants remains a challenge for long-term immunity. Additionally, there remain few purpose-built antivirals to protect individuals at risk of severe disease in the event of future coronavirus outbreaks. A promising mechanism of action for novel coronavirus antivirals is the inhibition of viral entry. To facilitate entry, the coronavirus spike glycoprotein interacts with angiotensin converting enzyme 2 (ACE2) on respiratory epithelial cells. Blocking this interaction and consequently viral replication may be an effective strategy for treating infection, however further research is needed to better characterize candidate molecules with antiviral activity before progressing to animal studies and clinical trials. In general, antiviral drugs are developed from purely synthetic compounds or synthetic derivatives of natural products such as plant secondary metabolites. While the former is often favored due to the higher specificity afforded by rational drug design, natural products offer several unique advantages that make them worthy of further study including diverse bioactivity and the ability to work synergistically with other drugs. Accordingly, there has recently been a renewed interest in natural product-derived antivirals in the wake of the COVID-19 pandemic. This review provides a summary of recent research into coronavirus entry inhibitors, with a focus on natural compounds derived from plants, honey, and marine sponges.

Exploring the potential of Andrographis paniculata for developing novel HDAC inhibitors: an in silico approach

Cancer is one of the dreaded diseases of the twentieth century, emerging the major global causes of human morbidity. Cancer research in the last 15 years has provided unprecedented information on the role of epigenetics in cancer initiation and progression. Histone deacetylases (HDACs) are recognized as important epigenetic markers in cancer, whose overexpression leads to increased metastasis and angiogenesis. In the current study, thirty-four (34) compounds from Andrographis paniculata were screened for the identification of potential candidate drugs, targeting three Class I HDACs (Histone deacetylases), namely HDAC1 (PDB id 5ICN), HDAC3 (PDB id 4A69) and HDAC8 (PDB id 5FCW) through computer-assisted drug discovery study. Results showed that some of the phytochemicals chosen for this study exhibited significant drug-like properties. In silico molecular docking study further revealed that out of 34 compounds, the flavonoid Andrographidine E had the highest binding affinities towards HDAC1 (-9.261 Kcal mol-1) and 3 (-9.554 Kcal mol-1) when compared with the control drug Givinostat (-8.789 and -9.448 Kcal mol-1). The diterpenoid Andrographiside displayed the highest binding affinity (-9.588 Kcal mol-1) to HDAC8 compared to Givinostat (-8.947 Kcal mol-1). Statistical analysis using Principal Component Analysis tool revealed that all 34 phytocompounds could be clustered in four statistical groups. Most of them showed high or comparable inhibitory potentials towards HDAC target protein. Finally, the stability of top-ranked complexes (Andrographidine E-HDAC1 and HDAC3; Andrographiside-HDAC8) at the physiological condition was validated by Molecular Dynamic Simulation and MM-PBSA study.Communicated by Ramaswamy H. Sarma.

Curcumin as an antiviral agent and immune-inflammatory modulator in COVID-19: A scientometric analysis

Background

Reports regarding the antiviral activity of curcumin have surfaced. However, to date there has been no scientometric analysis of the relationship between curcumin and Coronavirus Disease 2019 (COVID-19). To comprehensively understand the studies involving curcumin in the context of COVID-19, we conducted a scientometric analysis to provide an exhaustive review of these studies.

Methods

We systematically searched the Web of Science core collection database for bibliographic data indexed from January 1, 2020, to December 31, 2022, using keywords such as 'curcumin', 'COVID-19', and their synonyms. To clarify the research content and trends related to curcumin in COVID-19, we utilized VOSviewer, Origin 2023, and Charticulator for analysis, supplemented by external data.

Results

The final count of publications included in this study was 252. These publications originated from 63 countries or territories, with India contributing the highest number of publications. They were published across 170 journals. Notably, the Egyptian Knowledge Bank (EKB) emerged as the most important institution that carried out this study. The most cited publication had been referenced 166 times. The main elements involved in the keyword analysis were reflected in the antiviral activity of curcumin and the immuno-inflammatory modulation of the inflammatory cytokine storm. Furthermore, the pharmacological mechanisms of curcumin for treating COVID-19 emerged as a prominent area of research. Simultaneously, there exists direct evidence of clinical usage of curcumin to enhance COVID-19 outcomes.

Conclusions

The scientometric analysis underscores the burgeoning professional domain of curcumin-based treatment for COVID-19. Ongoing studies have focused on the antiviral activity of curcumin and its immunomodulatory effects on inflammatory cytokine storms. On the other hand, the pharmacological mechanism of curcumin in the treatment of COVID-19 is a hot spot in the research field at present, which may become the main research trend in this field in the future. While maintaining a focus on foundational research, the clinical application of curcumin in COVID-19 infection is developing in parallel, highlighting its obvious guiding value in clinical practice. These insights offer researchers a snapshot of the present state of curcumin treatment for COVID-19 and guide further mechanistic validation efforts in the future.

Clinical Approach to Post-acute Sequelae After COVID-19 Infection and Vaccination

The spike protein of SARS-CoV-2 has been found to exhibit pathogenic characteristics and be a possible cause of post-acute sequelae after SARS-CoV-2 infection or COVID-19 vaccination. COVID-19 vaccines utilize a modified, stabilized prefusion spike protein that may share similar toxic effects with its viral counterpart. The aim of this study is to investigate possible mechanisms of harm to biological systems from SARS-CoV-2 spike protein and vaccine-encoded spike protein and to propose possible mitigation strategies. We searched PubMed, Google Scholar, and 'grey literature' to find studies that (1) investigated the effects of the spike protein on biological systems, (2) helped differentiate between viral and vaccine-generated spike proteins, and (3) identified possible spike protein detoxification protocols and compounds that had signals of benefit and acceptable safety profiles. We found abundant evidence that SARS-CoV-2 spike protein may cause damage in the cardiovascular, hematological, neurological, respiratory, gastrointestinal, and immunological systems. Viral and vaccine-encoded spike proteins have been shown to play a direct role in cardiovascular and thrombotic injuries from both SARS-CoV-2 and vaccination. Detection of spike protein for at least 6-15 months after vaccination and infection in those with post-acute sequelae indicates spike protein as a possible primary contributing factor to long COVID. We rationalized that these findings give support to the potential benefit of spike protein detoxification protocols in those with long-term post-infection and/or vaccine-induced complications. We propose a base spike detoxification protocol, composed of oral nattokinase, bromelain, and curcumin. This approach holds immense promise as a base of clinical care, upon which additional therapeutic agents are applied with the goal of aiding in the resolution of post-acute sequelae after SARS-CoV-2 infection and COVID-19 vaccination. Large-scale, prospective, randomized, double-blind, placebo-controlled trials are warranted in order to determine the relative risks and benefits of the base spike detoxification protocol.

Computational studies on the interaction of Omicron subvariants (BA.1, BA.2, and BA.3) with ACE2 and polyphenols

INTRODUCTION

The SARS-CoV-2 Omicron variant BA.2 is spreading widely across the globe. The World Health Organization (WHO) designated BA.2 as a variant of concern due to its high transmission rate and pathogenicity. To elucidate the structural changes caused by mutations, we conducted a comparative analysis of BA.2 with variants BA.1 and BA.3.

OBJECTIVE

In the present study, we aimed to investigate the interactions of the spike glycoprotein receptor-binding domain (SGp RBD) of Omicron variants BA.1, BA.2, and BA.3 with the human receptor hACE2. Further, a library of 233 polyphenols was screened by molecular docking with the SGp RBDs of Omicron variants BA.1, BA.2, and BA.3.

METHODS

Protein-protein and protein-ligand molecular docking simulations were performed with AutoDock Vina and the ClusPro 2.0 server, respectively. The protein-ligand interactions were evaluated by BIOVIA Discovery Studio and ChimeraX 1.4. The molecular dynamics simulations for 100 ns were performed using GROMACS 2021.

RESULTS

Compared to other variants of concern, the structural changes in Omicron caused by mutations at key positions improved its ability to cause infection. Despite multiple mutations, many important polyphenols bind effectively at the RBDs of Omicron variants, with the required pharmacokinetic and ADME features and obeying the Lipinski rule.

CONCLUSION

Even though Omicron variants have multiple mutations and their transmission rate is relatively high, the computed binding affinities of lead polyphenols like epigallocatechin-3-O-gallate (EGCG) and luteolin-7-O-glucuronide (L7G) indicate that traditional medicines and proper immunity booster diets may be useful in the long-term fight against SARS-CoV-2.

An Abies Extract Containing Nonvolatile Polyphenols Shows Virucidal Activity against SARS-CoV-2 That Is Enhanced in Increased pH Conditions

Researching the beneficial health properties of wood byproducts can prevent wastage by turning them into valuable resources. In this study, the virucidal activity of two extracts from Abies sachalinensis byproducts, ASE1, and ASE2, against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was investigated. ASE1 is rich in monoterpenoid volatile compounds, whereas ASE2 contains nonvolatile polyphenols. SARS-CoV-2 solutions were mixed with ASE1 or ASE2, and viral titer reduction was evaluated. At their original acidic pH, ASE2 showed stronger virucidal activity than ASE1. The virucidal activity of ASE2 was also significantly enhanced when pH was increased to neutral or basic, which was not the case for ASE1. At a neutral pH, ASE2 induced statistically significant viral titer reduction in 1 min. HCl and NaOH solutions, which had a pH close to that of acidic and basic ASE2 test mixtures, respectively, exhibited no virucidal activity against SARS-CoV-2. Among the SARS-CoV-2 variants, Omicron showed the highest vulnerability to ASE2. Western blotting, RT-PCR, and electron microscopic analysis revealed that neutral ASE2 interacts with SARS-CoV-2 spike proteins and moderately disrupts the SARS-CoV-2 genome and viral envelope. These findings reveal the virucidal potential of ASE2.

Evaluation of therapeutic potentials of selected phytochemicals against Nipah virus, a multi-dimensional in silico study

The current study attempted to evaluate the potential of fifty-three (53) natural compounds as Nipah virus attachment glycoprotein (NiV G) inhibitors through in silico molecular docking study. Pharmacophore alignment of the four (4) selected compounds (Naringin, Mulberrofuran B, Rutin and Quercetin 3-galactoside) through Principal Component Analysis (PCA) revealed that common pharmacophores, namely four H bond acceptors, one H bond donor and two aromatic groups were responsible for the residual interaction with the target protein. Out of these four compounds, Naringin was found to have the highest inhibitory potential ( - 9.19 kcal mol^-1) against the target protein NiV G, when compared to the control drug, Ribavirin ( - 6.95 kcal mol^-1). The molecular dynamic simulation revealed that Naringin could make a stable complex with the target protein in the near-native physiological condition. Finally, MM-PBSA (Molecular Mechanics-Poisson-Boltzmann Solvent-Accessible Surface Area) analysis in agreement with our molecular docking result, showed that Naringin ( - 218.664 kJ mol^-1) could strongly bind with the target protein NiV G than the control drug Ribavirin ( - 83.812 kJ mol^-1).

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-023-03595-y.

Therapeutic potential of curcumin in ARDS and COVID-19

Curcumin is a safe, non-toxic, readily available and naturally occurring compound, an active constituent of Curcuma longa (turmeric). Curcumin could potentially treat diseases, but faces poor physicochemical and pharmacological characteristics. To overcome these limitations, we developed a stable, water-soluble formulation of curcumin called cyclodextrin-complexed curcumin (CDC). We have previously shown that direct delivery of CDC to the lung following lipopolysaccharides exposure reduces acute lung injury (ALI) and effectively reduces lung injury, inflammation and mortality in mice following Klebsiella pneumoniae. Recently, we found that administration of CDC led to a significant reduction in angiotensin-converting enzyme 2 and signal transducer and activator of transcription 3 expression in gene and protein levels following pneumonia, indicating its potential in treating coronavirus disease 2019 (COVID-19). In this review, we consider the clinical features of ALI and acute respiratory distress syndrome (ARDS) and the role of curcumin in modulating the pathogenesis of bacterial/viral-induced ARDS and COVID-19.

Indian food habit & food ingredients may have a role in lowering the severity & high death rate from COVID-19 in Indians: findings from the first nutrigenomic analysis

Background & objectives

During the COVID-19 pandemic, the death rate was reportedly 5-8 fold lower in India which is densely populated as compared to less populated western countries. The aim of this study was to investigate whether dietary habits were associated with the variations in COVID-19 severity and deaths between western and Indian population at the nutrigenomics level.

Methods

In this study nutrigenomics approach was applied. Blood transcriptome of severe COVID-19 patients from three western countries (showing high fatality) and two datasets from Indian patients were used. Gene set enrichment analyses were performed for pathways, metabolites, nutrients, etc., and compared for western and Indian samples to identify the food- and nutrient-related factors, which may be associated with COVID-19 severity. Data on the daily consumption of twelve key food components across four countries were collected and a correlation between nutrigenomics analyses and per capita daily dietary intake was investigated.

Results

Distinct dietary habits of Indians were observed, which may be associated with low death rate from COVID-19. Increased consumption of red meat, dairy products and processed foods by western populations may increase the severity and death rate by activating cytokine storm-related pathways, intussusceptive angiogenesis, hypercapnia and enhancing blood glucose levels due to high contents of sphingolipids, palmitic acid and byproducts such as CO2 and lipopolysaccharide (LPS). Palmitic acid also induces ACE2 expression and increases the infection rate. Coffee and alcohol that are highly consumed in western countries may increase the severity and death rates from COVID-19 by deregulating blood iron, zinc and triglyceride levels. The components of Indian diets maintain high iron and zinc concentrations in blood and rich fibre in their foods may prevent CO2 and LPS-mediated COVID-19 severity. Regular consumption of tea by Indians maintains high high-density lipoprotein (HDL) and low triglyceride in blood as catechins in tea act as natural atorvastatin. Importantly, regular consumption of turmeric in daily food by Indians maintains strong immunity and curcumin in turmeric may prevent pathways and mechanisms associated with SARS-CoV-2 infection and COVID-19 severity and lowered the death rate.

Interpretation & conclusions

Our results suggest that Indian food components suppress cytokine storm and various other severity related pathways of COVID-19 and may have a role in lowering severity and death rates from COVID-19 in India as compared to western populations. However, large multi-centered case-control studies are required to support our current findings.

Plants as Biofactories for Therapeutic Proteins and Antiviral Compounds to Combat COVID-19

The outbreak of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) had a profound impact on the world's health and economy. Although the end of the pandemic may come in 2023, it is generally believed that the virus will not be completely eradicated. Most likely, the disease will become an endemicity. The rapid development of vaccines of different types (mRNA, subunit protein, inactivated virus, etc.) and some other antiviral drugs (Remdesivir, Olumiant, Paxlovid, etc.) has provided effectiveness in reducing COVID-19's impact worldwide. However, the circulating SARS-CoV-2 virus has been constantly mutating with the emergence of multiple variants, which makes control of COVID-19 difficult. There is still a pressing need for developing more effective antiviral drugs to fight against the disease. Plants have provided a promising production platform for both bioactive chemical compounds (small molecules) and recombinant therapeutics (big molecules). Plants naturally produce a diverse range of bioactive compounds as secondary metabolites, such as alkaloids, terpenoids/terpenes and polyphenols, which are a rich source of countless antiviral compounds. Plants can also be genetically engineered to produce valuable recombinant therapeutics. This molecular farming in plants has an unprecedented opportunity for developing vaccines, antibodies, and other biologics for pandemic diseases because of its potential advantages, such as low cost, safety, and high production volume. This review summarizes the latest advancements in plant-derived drugs used to combat COVID-19 and discusses the prospects and challenges of the plant-based production platform for antiviral agents.

An in-silico pharmacophore-based molecular docking study to evaluate the inhibitory potentials of novel fungal triterpenoid Astrakurkurone analogues against a hypothetical mutated main protease of SARS-CoV-2 virus

BACKGROUND

The main protease is an important structural protein of SARS-CoV-2, essential for its survivability inside a human host. Considering current vaccines' limitations and the absence of approved therapeutic targets, Mpro may be regarded as the potential candidate drug target. Novel fungal phytocompound Astrakurkurone may be studied as the potential Mpro inhibitor, considering its medicinal properties reported elsewhere.

METHODS

In silico molecular docking was performed with Astrakurkurone and its twenty pharmacophore-based analogues against the native Mpro protein. A hypothetical Mpro was also constructed with seven mutations and targeted by Astrakurkurone and its analogues. Furthermore, multiple parameters such as statistical analysis (Principal Component Analysis), pharmacophore alignment, and drug likeness evaluation were performed to understand the mechanism of protein-ligand molecular interaction. Finally, molecular dynamic simulation was done for the top-ranking ligands to validate the result.

RESULT

We identified twenty Astrakurkurone analogues through pharmacophore screening methodology. Among these twenty compounds, two analogues namely, ZINC89341287 and ZINC12128321 showed the highest inhibitory potentials against native and our hypothetical mutant Mpro, respectively (-7.7 and -7.3 kcal mol-1) when compared with the control drug Telaprevir (-5.9 and -6.0 kcal mol-1). Finally, we observed that functional groups of ligands namely two aromatic and one acceptor groups were responsible for the residual interaction with the target proteins. The molecular dynamic simulation further revealed that these compounds could make a stable complex with their respective protein targets in the near-native physiological condition.

CONCLUSION

To conclude, Astrakurkurone analogues ZINC89341287 and ZINC12128321 can be potential therapeutic agents against the highly infectious SARS-CoV-2 virus.