Plant-based analogues identified as potential inhibitor against tobacco mosaic virus: A biosimulation approach

TMV-CP based rational design and discovery of α-Amide phosphate derivatives as anti plant viral agents

The tobacco mosaic virus coat protein (TMV-CP) is indispensable for the virus's replication, movement and transmission, as well as for the host plant's immune system to recognize it. It constitutes the outermost layer of the virus particle, and serves as an essential component of the virus structure. TMV-CP is essential for initiating and extending viral assembly, playing a crucial role in the self-assembly process of Tobacco Mosaic Virus (TMV). This research employed TMV-CP as a primary target for virtual screening, from which a library of 43,417 compounds was sourced and SH-05 was chosen as the lead compound. Consequently, a series of α-amide phosphate derivatives were designed and synthesized, exhibiting remarkable anti-TMV efficacy. The synthesized compounds were found to be beneficial in treating TMV, with compound 3g displaying a slightly better curative effect than Ningnanmycin (NNM) (EC50 = 304.54 µg/mL) at an EC50 of 291.9 µg/mL. Additionally, 3g exhibited comparable inactivation activity (EC50 = 63.2 µg/mL) to NNM (EC50 = 67.5 µg/mL) and similar protective activity (EC50 = 228.9 µg/mL) to NNM (EC50 = 219.7 µg/mL). Microscale thermal analysis revealed that the binding of 3g (Kd = 4.5 ± 1.9 µM) to TMV-CP showed the same level with NNM (Kd = 5.5 ± 2.6 µM). Results from transmission electron microscopy indicated that 3g could disrupt the structure of TMV virus particles. The toxicity prediction indicated that 3g was low toxicity. Molecular docking showed that 3g interacted with TMV-CP through hydrogen bond, attractive charge interaction and π-Cation interaction. This research provided a novel α-amide phosphate structure target TMV-CP, which may help the discovery of new anti-TMV agents in the future.

Furofuran Lignans for Plant Protection: Discovery of Sesamolin and Its Derivatives as Novel Anti-Tobacco Mosaic Virus and Antibacterial Agents

Natural products have been a valuable source of efficient and low-risk pesticides. In this work, a series of novel sesamolin derivatives A0-A31 and B0-B4 were designed and synthesized via structural simplification of furofuran lignan phrymarolin II, and their antiviral and antibacterial activities were systematically evaluated. The bioassay results showed that compound A24 displayed remarkable inactivation activity against tobacco mosaic virus (TMV) with an EC₅₀ value of 130.4 μg/mL, which was superior to that of commercial ningnanmycin (EC₅₀ = 202.0 μg/mL). The antiviral mode of action assays suggested that compound A24 may obstruct self-assembly by binding to TMV coat protein (CP), thus resisting the TMV infection. In addition, compound A25 possessed prominent antibacterial activities, especially against Ralstonia solanacearum with an EC₅₀ value of 43.8 μg/mL, which is better than those of commercial bismerthiazol and thiodiazole copper. This research lays a solid foundation for the utilization of furofuran lignans in crop protection.

The coat protein of tobacco mosaic virus as an anti-tobacco mosaic virus: a molecular dynamics simulation

The Coat Protein (CP) of the Tobacco Mosaic Virus (TMV) executes an important duty in the protection of virus RNA. The interaction between the virus CP and host plant proteins induces infection in the host and creates dark and light green mosaics on crops, which disturb the growth and function of the plant. The interaction between the virus CP and the modified CP, expressed in transgenic plants, causes Coat Protein-Mediated Resistance (CP-MR), which reduces virus infection in transgenic plants. In this study, a model is suggested for resistance as "stop assembly of CP" in the virus. It is based on the fact that the CP, when mutated, acts as a dead-end in virus assembly. For evaluation of the model, we investigated the effect of four mutants including CBT28I, ABT42W, ABD77R, and ABT89W complexes on plant resistance against TMV infection by molecular dynamics simulation. Previous studies had shown the influence of such mutations on the CP-MR. The MD results of in the present study further confirmed the mentioned effect and demonstrated how the mutations could be the cause of CP-MR. The results are calculated by the RMSD, Rg, H-bond, and g-MMPBSA scripts. The change in binding energy between two chains is consistent with CP-MR such that with increase in binding energy, the affinity between two chains was reduced and the CP-MR increased. Based on this model, it is possible to design mutants with a high level of efficiency.Communicated by Ramaswamy H. Sarma.

Discovery of Novel α-Methylene-γ-Butyrolactone Derivatives Containing Vanillin Moieties as Antiviral and Antifungal Agents

On the basis of the structure of nicotlactone A (L1), a series of novel α-methylene-γ-butyrolactone derivatives B1-B43 were designed and synthesized by structure simplification and active fragment replacement strategies, and their antiviral and antifungal activities were evaluated. The bioassay studies indicated that many target compounds possessed good to excellent antiviral activity against tobacco mosaic virus (TMV) and some of these compounds exhibited specific antifungal activities against Valsa mali and Fusarium graminearum. Compound B32 exhibited the best anti-TMV activity (inactivation effect, 88.9%; protection effect, 65.8%; curative effect, 52.8%) in vivo at 500 mg/L, which is significantly higher than that of commercial virucides ribavirin and ningnanmycin. The inhibition effect of compound B32 was also visualized by the inoculation test using green fluorescent protein (GFP)-labeled TMV. The preliminary antiviral mechanism of compound B32 was investigated. Transmission electron microscopy (TEM) showed that compound B32 could destroy the integrity of virus particles. Then, molecular docking and isothermal titration calorimetry (ITC) analysis further demonstrated that compound B32 exhibited a strong binding affinity to the TMV coat protein with a dissociation constant (K_d) of 3.06 μM, superior to ribavirin. Thus, we deduced that compound B32 may interfere with the self-assembly of TMV particles by binding TMV coat protein (CP). In addition, compound B28 showed good in vitro activity against F. graminearum with an inhibition rate of 90.9% at 50 mg/L, which was greater than that of fluxapyroxad (59.1%) but lower than that of the commercial fungicide carbendazim (96.8%). The present study provides support for the application of these α-methylene-γ-butyrolactone derivatives as novel antiviral and antifungal agents in crop protection.

Structural insights into the RNA interaction with Yam bean Mosaic virus (coat protein) from Pachyrhizus erosus using bioinformatics approach

Plants are constantly threatened by a virus infection, i.e., Potyviruses, the second largest genus of plant viruses which results in several million-dollar losses in various essential crops globally. Yam bean (Pachyrhizus erosus) is considered to be one of the essential tuberous legume crops holding a great potential source of starch. Yam Bean Mosaic Virus (YBMV) of Potyvirus group belonging to the family potyviridae affects Yam bean and several angiosperms both in the tropical and sub-tropical regions causing large economical losses in crops. In this study, we attempted to understand the sequence-structure relationship and mode of RNA binding mechanism in YBMV CP using in silico integrative modeling and all-atoms molecular dynamics (MD) simulations. The assembly of coat protein (CP) subunits from YBMV and the plausible mode of RNA binding were compared with the experimental structure of CP from Watermelon mosaic virus potyvirus (5ODV). The transmembrane helix region is present in the YBMV CP sequence ranging from 76 to 91 amino acids. Like the close structural-homolog, 24 CPs monomeric sub-units formed YBMV a conserved fold. Our computational study showed that ARG124, ARG155, and TYR151 orient towards the inner side of the virion, while, THR122, GLN125, SER92, ASP94 reside towards the outer side of the virion. Despite sharing very low sequence similarity with CPs from other plant viruses, the strongly conserved residues Ser, Arg, and Asp within the RNA binding pocket of YBMV CP indicate the presence of a highly conserved RNA binding site in CPs from different families. Using several bioinformatics tools and comprehensive analysis from MD simulation, our study has provided novel insights into the RNA binding mechanism in YBMV CP. Thus, we anticipate that our findings from this study will be useful for the development of new therapeutic agents against the pathogen, paving the way for researchers to better control this destructive plant virus.

Antiviral Effect of Polyphenolic Substances in Geranium wilfordii Maxim against HSV-2 Infection Using in vitro and in silico Approaches

Background

Herpes simplex virus type 2 (HSV-2) infestation was the most widespread STD (sexually transmitted diseases) among humans and was the leading cause of infectious recurrent genital herpes. Existing therapies against HSV-2 did incompletely restrain the comeback of activated HSV-2 infestation. Geranium wilfordii Maxim had long been used as traditional Chinese medicine for treating the diseases owing to its anti-inflammatory and antiviral effects. Herein, the study was designed to investigate the antiviral activity of G.wilfordii and its potential effect in regulating the host's immune response.

Methods

To identify the stage of infection at which the compounds inhibited HSV-2, we performed virucidal, therapeutic, and prophylactic assays. The antiviral efficacy was evaluated by the analysis of viral components HSV-2 gD and VP16. The antiviral activities of these compounds were also evaluated by phenotypic analysis, such as cell proliferation and apoptosis. Molecular docking studies on candidate compounds were done to indicate binding interactions between the compounds and adopted compound targets.

Results

Quercetin, corilagin, and geraniin inhibited the replication of HSV-2, with geraniin showing greater TI. The obtained IC₅₀ value of quercetin was 204.7 μM and TI (IC₅₀/EC₅₀) was 5.1, whereas the obtained IC₅₀ value of corilagin was 118.0 μg/ml and TI was 4.05. Geraniin exhibited prominent antiviral activity with an IC₅₀ of 212.4 μM and an EC₅₀ of 18.37 μM, resulting in a therapeutic index (TI) of 11.56. Geraniin showed important in vitro virucidal activity through blocking viral attachment. Compared with the virus group, the apoptosis rates in quercetin-, corilagin-, and geraniin-treated groups were significantly decreased (p < 0.001).The expressions at the transcription genes of virus own replication key factors (including HSV-2 gD and VP16) and cytokines (including TBK1) of infected cells treated with quercetin, corilagin, and geraniin were inhibited. The in silico approaches demonstrated a high number of potential strong intermolecular interactions as hydrogen bonds between geraniin, corilagin, and the activity site of HSV-2 gD. Molecular docking studies demonstrated the effects of corilagin by targeting TBK1.

Conclusions

Together, these results highlighted the importance of G.wilfordii treatment in HSV-2 infection and underscored its therapeutic potential. However, additional in vitro and in vivo research was required to validate our findings.

Recent Research Progress: Discovery of Anti-Plant Virus Agents Based on Natural Scaffold

Plant virus diseases, also known as “plant cancers”, cause serious harm to the agriculture of the world and huge economic losses every year. Antiviral agents are one of the most effective ways to control plant virus diseases. Ningnanmycin is currently the most successful anti-plant virus agent, but its field control effect is not ideal due to its instability. In recent years, great progress has been made in the research and development of antiviral agents, the mainstream research direction is to obtain antiviral agents or lead compounds based on structural modification of natural products. However, no antiviral agent has been able to completely inhibit plant viruses. Therefore, the development of highly effective antiviral agents still faces enormous challenges. Therefore, we reviewed the recent research progress of anti-plant virus agents based on natural products in the past decade, and discussed their structure-activity relationship (SAR) and mechanism of action. It is hoped that this review can provide new inspiration for the discovery and mechanism of action of novel antiviral agents.

Insights into a rapid screening method for anti-cucumber mosaic virus compounds

Cucumber mosaic virus (CMV) is a detrimental plant virus in agricultural production. Traditionally, the half-leaf method using Nicotiana glutinosa has been used for screening agrochemicals to control CMV. However, this forms a time-consuming experimental bottleneck. In this study, we constructed a rapid screening model for anti-CMV compounds using CMV. In short, purified CMV particles were labeled through amine reactions and then subjected to binding studies with commercial compounds. The relative gene expression levels were then confirmed. Additionally, the rapid screening model results were verified using synthesized compounds. The commercial compounds ningnanmycin, ribavirin, and moroxydine hydrochloride bound to CMV with dissociation constants of 0.012, 2.870, and 0.069 μM, respectively, and they significantly inhibited expression of the gene for the CMV coat protein in CMV-infected tobacco leaves. This rapid screening model was assessed using our synthetic compounds N12, N16, and N18 through binding, which were shown to have dissociation constants 0.008, 0.025, and 70.800 μM, respectively, as well as via gene expression studies. Thus, a rapid method for screening anti-CMV commercial compounds and our synthetic compounds was constructed and confirmed.

Autoxidation Products of the Methanolic Extract of the Leaves of Combretum micranthum Exert Antiviral Activity against Tomato Brown Rugose Fruit Virus (ToBRFV)

Tomato brown rugose fruit virus (ToBRFV) is a new damaging plant virus of great interest from both an economical and research point of view. ToBRFV is transmitted by contact, remains infective for months, and to-date, no resistant cultivars have been developed. Due to the relevance of this virus, new effective, sustainable, and operator-safe antiviral agents are needed. Thus, 4-hydroxybenzoic acid was identified as the main product of the alkaline autoxidation at high temperature of the methanolic extract of the leaves of C. micranthum, known for antiviral activity. The autoxidized extract and 4-hydroxybenzoic acid were assayed in in vitro experiments, in combination with a mechanical inoculation test of tomato plants. Catechinic acid, a common product of rearrangement of catechins in hot alkaline solution, was also tested. Degradation of the viral particles, evidenced by the absence of detectable ToBRFV RNA and the loss of virus infectivity, as a possible consequence of disassembly of the virus coat protein (CP), were shown. Homology modeling was then applied to prepare the protein model of ToBRFV CP, and its structure was optimized. Molecular docking simulation showed the interactions of the two compounds, with the amino acid residues responsible for CP-CP interactions. Catechinic acid showed the best binding energy value in comparison with ribavirin, an anti-tobamovirus agent.

Molecular simulation probes the potency of resveratrol in regulating the toxic aggregation of mutant V30M TTR fibrils in Transthyretin mediated amyloidosis

Transthyretin (TTR) mediated amyloidosis is a highly ruinous illness that affects various organs by aggravating the deposition of misfolded or mutated TTR protein aggregates in tissues. Hence, hindering the formation of TTR amyloid aggregates could be a key strategy in finding an effective cure towards the aggravating disorder. In this analysis, we examined the subversive nature of point mutation, V30M, in TTR that promotes amyloidogenicity using discrete molecular dynamics (DMD) simulations. Besides, we probed the association of naturally occurring polyphenols: EGCG (a proven anti TTR aggregation agent as positive control), resveratrol and curcumin in mitigating the pathogenic repercussions of mutant TTR. Results from the computational studies endorsed that the resveratrol constitutes a restorative potential to subjugate TTR mediated amyloidosis, besides EGCG. Hence, this study could be a reminiscent aspect in understanding the inhibitory role of key polyphenols against the mutant TTR aggregates, which could be an aid towards structure-based drug design in the upcoming research era on familial amyloid disorders.

A network pharmacology analysis on drug-like compounds from Ganoderma lucidum for alleviation of atherosclerosis

Ganoderma lucidum (GL) is known as a potent alleviator against chronic inflammatory disease like atherosclerosis (AS), but its mechanisms against AS have not been unveiled. This research aimed to identify the key compounds(s) and mechanism(s) of GL against AS through network pharmacology. The compounds from GL were identified by gas chromatography-mass spectrum (GC-MS), and SwissADME screened their physicochemical properties. Then, the target(s) associated with the screened compound(s) or AS related targets were identified by public databases, and we selected the overlapping targets using a Venn diagram. The networks between overlapping targets and compounds were visualized, constructed, and analyzed by RStudio. Finally, we performed a molecular docking test (MDT) to explore key target(s), compound(s), on AutoDockVina. A total of 35 compounds in GL were detected via GC-MS, and 34 compounds (accepted by Lipinski's rule) were selected as drug-like compounds (DLCs). A total of 34 compounds were connected to the number of 785 targets, and DisGeNET and Online Mendelian Inheritance in Man (OMIM) identified 2,606 AS-related targets. The final 98 overlapping targets were extracted between the compounds-targets and AS-related targets. On Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment, the number of 27 signaling pathways were sorted out, and a hub signaling pathway (MAPK signaling pathway), a core gene (PRKCA), and a key compound (Benzamide, 4-acetyl-N-[2,6-dimethylphenyl]) were selected among the 27 signaling pathways via MDT. Overall, we found that the identified 3 DLCs from GL have potent anti-inflammatory efficacy, improving AS by inactivating the MAPK signaling pathway. PRACTICAL APPLICATIONS: Ganoderma lucidum (GL) has been used as a medicinal or edible mushroom for chronic inflammatory patients: diabetes mellitus and dyslipidemia, especially atherosclerosis (AS). Until now, the majority of mushroom research has been implemented regarding β-glucan derivatives with very hydrophilic physicochemical properties. It implies that β-glucan or its derivatives have poor bioavailability. Hence, we have involved GC-MS in identifying lipophilic compounds from GL, which filtered them in silico to sort drug-like compounds (DLCs). Then, we retrieved targets associated with the DLCs, and identified a key signaling pathway, key targets, and key compounds against AS. In this paper, we utilized bioinformatics and network pharmacology theory to understand the uncovered pharmacological mechanism of GL on AS. To sum things up, our analysis elucidates the relationships between signaling pathways, targets, and compounds in GL. Ultimately, this work provides biochemical evidence to identify the therapeutic effect of GL on AS, and a scientific basis for deciphering the key mechanism on DLCs of GL against AS.

Medicinal chemistry of anthranilic acid derivatives: A mini review

Anthranilic acid and its analogues present a privileged profile as pharmacophores for the rational development of pharmaceuticals deliberated for managing the pathophysiology and pathogenesis of various diseases. The substitution on anthranilic acid scaffold provides large compound libraries, which enable a comprehensive assessment of the structure activity relationship (SAR) analysis for the identification of hits and leads in a typical drug development paradigm. Besides, their widespread applications as anti-inflammatory fenamates, the amide and anilide derivatives of anthranilic acid analogues play a central role in the management of several metabolic disorders. In addition, these derivatives of anthranilic acid exhibit interesting antimicrobial, antiviral and insecticidal properties, whereas the derivatives based on anthranilic diamide scaffold present applications as P-glycoprotein inhibitors for managing the drug resistance in cancer cells. In addition, the anthranilic acid derivatives serve as the inducers of apoptosis, inhibitors of hedgehog signaling pathway, inhibitors of mitogen activated protein kinase pathway, and the inhibitors of aldo-keto reductase enzymes. The antiviral derivatives of anthranilic acid focus on the inhibition of hepatitis C virus NS5B polymerase to manifest considerable antiviral properties. The anthranilic acid derivatives reportedly present neuroprotective applications by downregulating the key pathways responsible for the manifestation of neuropathological features and neurodegeneration. Nevertheless, the transition metal complexes of anthranilic acid derivatives offer therapeutic applications in diabetes mellitus, and obesity by regulating the activity of α-glucosidase. The present review demonstrates a critical analysis of the therapeutic profile of the key derivatives of anthranilic acid and its analogues for the rational development of pharmaceuticals and therapeutic molecules.