Nature-inspired Enzyme engineering and sustainable catalysis: biochemical clues from the world of plants and extremophiles

The use of enzymes to accelerate chemical reactions for the synthesis of industrially important products is rapidly gaining popularity. Biocatalysis is an environment-friendly approach as it not only uses non-toxic, biodegradable, and renewable raw materials but also helps to reduce waste generation. In this context, enzymes from organisms living in extreme conditions (extremozymes) have been studied extensively and used in industries (food and pharmaceutical), agriculture, and molecular biology, as they are adapted to catalyze reactions withstanding harsh environmental conditions. Enzyme engineering plays a key role in integrating the structure-function insights from reference enzymes and their utilization for developing improvised catalysts. It helps to transform the enzymes to enhance their activity, stability, substrates-specificity, and substrate-versatility by suitably modifying enzyme structure, thereby creating new variants of the enzyme with improved physical and chemical properties. Here, we have illustrated the relatively less-tapped potentials of plant enzymes in general and their sub-class of extremozymes for industrial applications. Plants are exposed to a wide range of abiotic and biotic stresses due to their sessile nature, for which they have developed various mechanisms, including the production of stress-response enzymes. While extremozymes from microorganisms have been extensively studied, there are clear indications that plants and algae also produce extremophilic enzymes as their survival strategy, which may find industrial applications. Typical plant enzymes, such as ascorbate peroxidase, papain, carbonic anhydrase, glycoside hydrolases and others have been examined in this review with respect to their stress-tolerant features and further improvement via enzyme engineering. Some rare instances of plant-derived enzymes that point to greater exploration for industrial use have also been presented here. The overall implication is to utilize biochemical clues from the plant-based enzymes for robust, efficient, and substrate/reaction conditions-versatile scaffolds or reference leads for enzyme engineering.

Identification of potential phytochemicals from Citrus Limon against main protease of SARS-CoV-2: molecular docking, molecular dynamic simulations and quantum computations

The outbreak of coronavirus disease (COVID-19) caused by a novel RNA virus emerged at the end of 2019. Most of the patient's symptoms are mild to moderate, and influenza, acute respiratory distress syndrome (ARDS) and multi-organ failure are common. The disease is mild to moderate in most patients and is reported in many cases such as pneumonia, ARDS and multi-organ dysfunction. This study's objective is to evaluate 25 natural compounds from Citrus limon (CL) used by comprehensive molecular docking, density functional theory (DFT) and molecular dynamics analysis against SARS-CoV-2 main protease (M^pro). Among all the experimental compounds, diosmetin has shown the best docking values against the M^pro of SARS-CoV-2 compared to the standard antiviral drug. In DFT calculations, the order associated with biochemical reactivity is as follows: eriodictoyl > quercetin > spinacetin > diosmetin > luteolin > apigenin, whereas the regions of oxygen and hydrogen atoms from the selected isolated compounds are appropriate for electrophilic and nucleophilic attacks, respectively. Also, HOMO-LUMO and global descriptors values indicated a promising result of these compounds. Moreover, a molecular dynamics simulation study revealed the stable conformation and binding pattern in a stimulating environment of natural compounds CL. Considering molecular docking, simulation, and DFT analysis of the selected compounds, notably eriodictoyl, quercetin, and diosmetin showed good potential against SARS-CoV-2 M^pro. Our in silico study revealed promising antiviral activity, which may be considered a potential key factor or a therapeutic target for COVID-19.Communicated by Ramaswamy H. Sarma.

A Comprehensive Review of the Potential Use of Green Tea Polyphenols in the Management of COVID-19

Green tea is produced from Camellia sinensis (L.) buds and leaves that have not gone through the oxidation and withering processes used to produce black and oolong teas. It was originated in China, but its cultivation and production have expanded to other Eastern Asian countries. Several polyphenolic compounds, including flavandiols, flavonols, flavonoids, and phenolic acids, are found in green tea and may constitute greater than 30% of the dry weight. Flavonols, especially catechins, represent the majority of green tea polyphenols. Green tea polyphenolic compounds have been reported to confer several health benefits. This review describes the potential use of green tea polyphenols in the management of coronavirus disease 2019 (COVID-19). The immunomodulatory, antibacterial, antioxidant, and anti-inflammatory effects of green tea polyphenols have also been considered in this review. In addition to describing the bioactivities associated with green tea polyphenols, this review discusses the potential delivery of these biomolecules using a nanoparticle drug delivery system. Moreover, the bioavailability and toxicity of green tea polyphenols are also evaluated.

Potential of Plant Bioactive Compounds as SARS-CoV-2 Main Protease (Mpro) and Spike (S) Glycoprotein Inhibitors: A Molecular Docking Study

Since the outbreak of the COVID-19 (coronavirus disease 19) pandemic, researchers have been trying to investigate several active compounds found in plants that have the potential to inhibit the proliferation of SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2). The present study aimed to evaluate bioactive compounds found in plants using a molecular docking approach to inhibit the main protease (Mpro) and spike (S) glycoprotein of SARS-CoV-2. The evaluation was performed on the docking scores calculated using AutoDock Vina (AV) as a docking engine. A rule of five (Ro5) was calculated to determine whether a compound meets the criteria as an active drug orally in humans. The determination of the docking score was performed by selecting the best conformation of the protein-ligand complex that had the highest affinity (most negative Gibbs' free energy of binding/ΔG). As a comparison, nelfinavir (an antiretroviral drug), chloroquine, and hydroxychloroquine sulfate (antimalarial drugs recommended by the FDA as emergency drugs) were used. The results showed that hesperidin, nabiximols, pectolinarin, epigallocatechin gallate, and rhoifolin had better poses than nelfinavir, chloroquine, and hydroxychloroquine sulfate as spike glycoprotein inhibitors. Hesperidin, rhoifolin, pectolinarin, and nabiximols had about the same pose as nelfinavir but were better than chloroquine and hydroxychloroquine sulfate as Mpro inhibitors. This finding implied that several natural compounds of plants evaluated in this study showed better binding free energy compared to nelfinavir, chloroquine, and hydroxychloroquine sulfate, which so far are recommended in the treatment of COVID-19. From quantum chemical DFT calculations, the ascending order of chemical reactivity of selected compounds was pectolinarin > hesperidin > rhoifolin > morin > epigallocatechin gallate. All isolated compounds' C=O regions are preferable for an electrophilic attack, and O-H regions are suitable for a nucleophilic attack. Furthermore, Homo-Lumo and global descriptor values indicated a satisfactory remarkable profile for the selected compounds. As judged by the RO5 and previous study by others, the compounds kaempferol, herbacetin, eugenol, and 6-shogaol have good oral bioavailability, so they are also seen as promising candidates for the development of drugs to treat infections caused by SARS-CoV-2. The present study identified plant-based compounds that can be further investigated in vitro and in vivo as lead compounds against SARS-CoV-2.

Phytogenic Products and Phytochemicals as a Candidate Strategy to Improve Tolerance to Coronavirus

Coronaviruses are the causative agents of many infectious diseases in human and animals. These included severe acute respiratory syndrome (SARS), avian infectious bronchitis (IBV) in poultry, Middle East respiratory syndrome (MERS), and coronavirus disease 2019 (COVID-19) in humans. These results had considerable death burdens and negative influences on social-economic life. Since the appearance of the outbreak of the COVID-19 pandemic, continuous investigations have been carried out by researchers to find active compounds, mainly from plants, as natural sources, that could inhibit or stop the proliferation of the causative agent of COVID-19 (SARS-CoV-2). The most common symptoms caused by infections with COVID-19 can include cough, fever, and sore throat. Nevertheless, there is a shortage of active antiviral compounds for treating different strains of coronavirus. Herbal medicine is a class of medication that originates from nature and is aimed at decreasing the use of preservatives, excipients, or other additives and, consequently, lesser side effects. The rapid spread of COVID-19 infection besides the lack of knowledge about any treatments and the growing concern of the public from the virus directed us toward writing this review article in an aim to provide alternatives to the allopathic medicine use. There is a wealth of chemical diversity in the naturally existing compounds, including their antiviral activities, which may encourage their utilization as therapeutics against viral infections, including coronaviruses. The majority of publications on the herbal remedies of coronavirus, MERS, or SARS focused primarily on the use of polar compounds. These substances displayed encouraging inhibitory influences on coronavirus in humans. These include psoralidin, scutellarein, silvestrol, tryptanthrin, caffeic acid, quercetin, myricetin, saikosaponin B2, griffithsin (lectins), and isobavachalcone. Some other agents like lycorine may be useful, if the antiviral activity is obtained by concentrations below the toxic plasma levels. According to the available literatures, the most promising inhibitors of coronaviruses are polyphenolic compounds, which are small molecules with conjugated fused ring structures.

Encapsulated Methionine γ-Lyase: Application in Enzyme Prodrug Therapy of Pseudomonas aeruginosa Infection

Lung disease caused by Pseudomonas aeruginosa is the leading reason for death in cystic fibrosis patients. Therapeutic efficacy of the pharmacological pairs, the naked/encapsulated mutant form of Citrobacter freundii methionine γ-lyase and the substrates, sulfoxides of S-substituted l-cysteine, generating thiosulfinates, was evaluated on the murine model of experimental sepsis caused by the multidrug-resistant P. aeruginosa 203-2 strain. The pairs containing the naked enzyme and substrates did not have antibacterial activity. The treatment of mice with the pair encapsulated enzyme and S-methyl-l-cysteine sulfoxide, generating dimethyl thiosulfinate, led to a complete recovery of the animals of the model, with the infecting dose equal to LD₅₀. The pair generating diallyl thiosulfinate (allicin) proved to be less effective. So, the substituents, attached to the thiosulfinate moiety, affect the antibacterial activity of thiosulfinates against P. aeruginosa.

Potential of Plant Bioactive Compounds as SARS-CoV-2 Main Protease (Mpro) and Spike (S) Glycoprotein Inhibitors: A Molecular Docking Study

Since the outbreak of the COVID-19 (coronavirus disease 19) pandemic, researchers have been trying to investigate several active compounds found in plants that have the potential to inhibit the proliferation of SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2). The present study aimed to evaluate bioactive compounds found in plants using a molecular docking approach to inhibit the main protease (M^pro) and spike (S) glycoprotein of SARS-CoV-2. The evaluation was performed on the docking scores calculated using AutoDock Vina (AV) as a docking engine. A rule of five (Ro5) was calculated to determine whether a compound meets the criteria as an active drug orally in humans. The determination of the docking score was performed by selecting the best conformation of the protein-ligand complex that had the highest affinity (most negative Gibbs' free energy of binding/ΔG). As a comparison, nelfinavir (an antiretroviral drug), chloroquine, and hydroxychloroquine sulfate (antimalarial drugs recommended by the FDA as emergency drugs) were used. The results showed that hesperidin, nabiximols, pectolinarin, epigallocatechin gallate, and rhoifolin had better poses than nelfinavir, chloroquine, and hydroxychloroquine sulfate as spike glycoprotein inhibitors. Hesperidin, rhoifolin, pectolinarin, and nabiximols had about the same pose as nelfinavir but were better than chloroquine and hydroxychloroquine sulfate as M^pro inhibitors. This finding implied that several natural compounds of plants evaluated in this study showed better binding free energy compared to nelfinavir, chloroquine, and hydroxychloroquine sulfate, which so far are recommended in the treatment of COVID-19. From quantum chemical DFT calculations, the ascending order of chemical reactivity of selected compounds was pectolinarin > hesperidin > rhoifolin > morin > epigallocatechin gallate. All isolated compounds' C=O regions are preferable for an electrophilic attack, and O-H regions are suitable for a nucleophilic attack. Furthermore, Homo-Lumo and global descriptor values indicated a satisfactory remarkable profile for the selected compounds. As judged by the RO5 and previous study by others, the compounds kaempferol, herbacetin, eugenol, and 6-shogaol have good oral bioavailability, so they are also seen as promising candidates for the development of drugs to treat infections caused by SARS-CoV-2. The present study identified plant-based compounds that can be further investigated in vitro and in vivo as lead compounds against SARS-CoV-2.