In silico protein engineering shows that novel mutations affecting NAD+ binding sites may improve phosphite dehydrogenase stability and activity

Pseudomonas stutzeri phosphite dehydrogenase (PTDH) catalyzes the oxidation of phosphite to phosphate in the presence of NAD, resulting in the formation of NADH. The regeneration of NADH by PTDH is greater than any other enzyme due to the substantial change in the free energy of reaction (G°' = - 63.3 kJ/mol). Presently, improving the stability of PTDH is for a great importance to ensure an economically viable reaction process to produce phosphite as a byproduct for agronomic applications. The binding site of NAD⁺ with PTDH includes thirty-four residues; eight of which have been previously mutated and characterized for their roles in catalysis. In the present study, the unexplored twenty-six key residues involved in the binding of NAD⁺ were subjected to in silico mutagenesis based on the physicochemical properties of the amino acids. The effects of these mutations on the structure, stability, activity, and interaction of PTDH with NAD⁺ were investigated using molecular docking, molecular dynamics simulations, free energy calculations, and secondary structure analysis. We identified seven novel mutations, A155I, G157I, L217I, P235A, V262I, I293A, and I293L, that reduce the compactness of the protein while improving PTDH stability and binding to NAD⁺.

Structure and inhibition mechanism of some synthetic compounds and phenolic derivatives as tyrosinase inhibitors: review and new insight

Safety concerns are the primary consideration to identify and detection of enzyme inhibitors. In this regard, safe and potent tyrosinase inhibitors play important role in enhancing nutritional quality, health promotion and also prevent further damages. The present review focuses on the recent and efficient tyrosinase inhibitors discovered from both synthetic sources and synthesized phenolic compounds, including flavonoid, carvacrol, thymol, cinnamic acid and resorcinol derivatives. The inhibitory activity of these compounds was analyzed according to chemical structure, IC₅₀, K_i and their binding energy. Further, inhibition mechanism and the biological effects of some these inhibitors with potential application in food, agricultural, cosmetic and pharmaceutical industries were briefly discussed. Molecular docking procedure was performed on some derivatives and demonstrated favorable binding affinity with amino acid residues of mushroom tyrosinase (PDB ID: 2Y9X). The information offered showed that the substitution pattern of hydroxyl groups at the phenyl ring is an important factor of tyrosinase inhibitory activity. The results confirmed that understanding structural modification of inhibitors is a key role in finding novel and efficacious tyrosinase inhibitors.Communicated by Ramaswamy H. Sarma.

Bioactivities and Mode of Actions of Dibutyl Phthalates and Nocardamine from Streptomyces sp. H11809

Dibutyl phthalate (DBP) produced by Streptomyces sp. H11809 exerted inhibitory activity against human GSK-3β (Hs GSK-3β) and Plasmodiumfalciparum 3D7 (Pf 3D7) malaria parasites. The current study aimed to determine DBP’s plausible mode of action against Hs GSK-3β and Pf 3D7. Molecular docking analysis indicated that DBP has a higher binding affinity to the substrate-binding site (pocket 2; −6.9 kcal/mol) than the ATP-binding site (pocket 1; −6.1 kcal/mol) of Hs GSK-3β. It was suggested that the esters of DBP play a pivotal role in the inhibition of Hs GSK-3β through the formation of hydrogen bonds with Arg96/Glu97 amino acid residues in pocket 2. Subsequently, an in vitro Hs GSK-3β enzymatic assay revealed that DBP inhibits the activity of Hs GSK-3β via mixed inhibition inhibitory mechanisms, with a moderate IC₅₀ of 2.0 µM. Furthermore, the decrease in K_m value with an increasing DBP concentration suggested that DBP favors binding on free Hs GSK-3β over its substrate-bound state. However, the antimalarial mode of action of DBP remains unknown since the generation of a Pf 3D7 DBP-resistant clone was not successful. Thus, the molecular target of DBP might be indispensable for Pf survival. We also identified nocardamine as another active compound from Streptomyces sp. H11809 chloroform extract. It showed potent antimalarial activity with an IC₅₀ of 1.5 μM, which is ~10-fold more potent than DBP, but with no effect on Hs GSK-3β. The addition of ≥12.5 µM ferric ions into the Pf culture reduced nocardamine antimalarial activity by 90% under in vitro settings. Hence, the iron-chelating ability of nocardamine was shown to starve the parasites from their iron source, eventually inhibiting their growth.

Novel derivatives of arabinogalactan, pullulan & lactobionic acid for targeting asialoglycoprotein receptor: Biomolecular interaction, synthesis & evaluation

Targeted-drug administration to liver reduces side effects by minimising drug distribution to non-target organs and increases therapeutic efficacy by boosting drug concentration in target cells. In this study, arabinogalactan-(AG), pullulan-(PL) and lactobionic acid-(LA) were selected as natural ligands to target asialoglycoprotein receptor-(ASGPR-1) present on hepatocytes. In silico docking studies were performed and binding affinities of novel ligands viz. palmitoylated AG-(PAG), lauroylated AG-(LAG), palmitoylated PL-(PPL), lauroylated PL-(LPL) and lactobionic acid-adipic acid dihydrazide conjugate-(LAD) were compared with AG, PL and LA. These novel ligands were successfully synthesized and characterized. The ligands were incorporated into drug loaded nanostructured lipid carriers-(NLCs) for surface functionalization. HepG2 cellular internalization of hepatocyte-targeted NLCs was studied using fluorescence microscopy and LAD-decorated-drug loaded NLCs giving maximum cellular uptake were studied using confocal microscopy. Toxicity potential of LAD-decorated NLCs was assessed in vivo. Molecular docking results suggested that among the ligands, order of binding affinity was found to be LAD>PAG > PPL > LPL > LAG. Acute toxicity studies revealed hemocompatibility and absence of organ toxicity for ligand LAD. Additionally, the results establish proof-of-concept of enhanced targeting efficacy of novel ASGPR targeting ligands. These ligands can be used for surface modification of nanocarriers for future targeted delivery in treating various liver disorders.

Evaluation of quercetin omega-6 and -9 esters on activity and structure of mushroom tyrosinase: Spectroscopic and molecular docking studies

Quercetin is one of the most ubiquitous dietary flavonoids widely distributed in plants and foods of plant origin, and is a potent tyrosinase inhibitor. Quercetin fatty esters could lead to an improve in quercetin lipophilicity which could positively affect its pharmacological activity. In this study, the inhibitory effect of two novel esters of quercetin-linoleic acid (ligand A) and quercetin-oleic acid (ligand B) has been investigated on structure and diphenolase activity of mushroom tyrosinase (MT) by experimental and molecular docking techniques. The inhibitory kinetics study using UV-visible spectrophotometry in the presence of its substrate 3,4-dihydroxyphenylalanine (L-dopa), revealed that both esters successfully inhibit the activity of tyrosinase and reduce the formation of dopaquinone. Results showed that the binding of ligands to MT induced rearrangement and conformational changes of the enzyme. Thermodynamic parameters of these interactions (K_a , ∆G°, ∆H° and ∆S°) were obtained at pH = 6.8 and temperatures of 298 and 310 K. Molecular docking studies further was applied to calculation of binding energies (ΔG_bA  = -21.84 kJ/mol, ΔG_bB  = -20.92 kJ/mol), inhibition constant values (K_IA  = 160 µM, K_IB  = 220 µM) and the special binding site. It can be deduced that ligands act as a potential tyrosinase inhibitor and it was found that the best possible interaction condition with binding modes visualize was achieved by ligand A and exhibited the potent tyrosinase inhibitory activity. These findings may be helpful to understand the inhibition mechanism of quercetin fatty acids esters on tyrosinase and provide a convenient screening method to differentiate phenolic tyrosinase inhibitors. PRACTICAL APPLICATIONS: Bioavailability and antioxidant activity of conjugated fatty acids with their bioequivalence in several biological effects and metabolic processes such as beta-oxidation from various forms has been reported to be highly variable and useful. Quercetin shows beneficial role in human health, but its biological effects in vivo is limited by poor bioavailability, low skin permeability and solubility. This study design new tyrosinase inhibitors which helpful to functional research of unsaturated fatty acid esters in the treatment of inflammatory diseases and hyperpigmentation disorders. In addition, undesirable enzymatic browning of plant derived-foods by tyrosinase causes a decrease in market value and economic loss of food products. The results suggest that the conjugation of quercetin with linoleic and oleic acids resulted in novel stronger tyrosinase inhibitors which may have therapeutic applications and replacement of toxic tyrosinase inhibitors and contribute as anti- browning agents in food, cosmetic and pharmaceutical industry.

Novel Quercetin Derivative of 3,7-Dioleylquercetin Shows Less Toxicity and Highly Potent Tyrosinase Inhibition Activity

Quercetin is a well-known plant flavonol and antioxidant; however, there has been some debate regarding the efficacy and safety of native quercetin as a skin-whitening agent via tyrosinase inhibition. Several researchers have synthesized quercetin derivatives as low-toxicity antioxidants and whitening agents. However, no suitable quercetin derivatives have been reported to date. In this study, a novel quercetin derivative was synthesized by the S_N2 reaction using quercetin and oleyl bromide. The relationship between the structures and activities of quercetin derivatives as anti-melanogenic agents was assessed using in vitro enzyme kinetics, molecular docking, and quenching studies; cell line experiments; and in vivo zebrafish model studies. Novel 3,7-dioleylquercetin (OQ) exhibited a low cytotoxic concentration level at >100 µg/mL (125 µM), which is five times less toxic than native quercetin. The inhibition mechanism showed that OQ is a competitive inhibitor, similar to native quercetin. Expression of tyrosinase, tyrosinase-related protein 1 (TRP-1) and tyrosinase-related protein 2 (TRP-2), and microphthalmia-associated transcription factor was inhibited in B16F10 melanoma cell lines. mRNA transcription levels of tyrosinase, TRP-1, and TRP-2 decreased in a dose-dependent manner. Melanin formation was confirmed in the zebrafish model using quercetin derivatives. Therefore, OQ might be a valuable asset for the development of novel skin-whitening agents.