Crucial Amino Acid Residues Research Articles

Structural Bioinformatics Study Revealed Inhibition of Acute Myeloid Leukemia through Targeting Inhibition BTG2 Gene by Using Herbal Medicine

Acute myeloid leukemia (AML) is responsible for more than 40% of adult patients suffering from adverse effects leading to death around the world. The B-cell translocation gene 2 (BTG2) gene work as a tumor suppressor. In this study, a list of medicinal herb compounds and drugs was investigated for their pharmacokinetic properties and cytotoxicity by applying the SwissADME, pkCSM, and Molsoft LLC websites. The molecular docking between the medicinal herbs and AML-standard drugs against the human BTG2 gene was carried out by Auto-dock Vina. Furthermore, protein-protein interactions, gene ontology, and gene enrichment analysis were investigated to display the biological pathways related to BTG2. Also, molecular dynamics simulation was examined to study the behavior of the BTG2 protein and the protein-ligand complex. The present work exhibited that hesperidin displayed the highest binding affinity of −7.0 kcal/mol when interacting and docked against the BTG2 protein, while Cytarabinee and daunorubicin had binding affinity of 5.0 and 5.8 kcal/mol, respectively. The PPI highlighted 101 interactions with P-values less than 10 e-16., and the highest similarity score of 0.13 was found in P53 transcriptional gene network pathways. Interestingly, gene enrichment analysis illustrated that RNA degradation was the most significant enrichment pathway. Also, BTG2 contributes to the P53 signaling pathway in chronic myeloid leukemia. Via GADD45A gene. Molecular dynamics simulations were carried out for the highest binding docking (BTG2-hesperidin) complex, and the results revealed conformational alterations with more pronounced surface residue fluctuations in BTG2. The direct interaction of hesperidin with various crucial amino-acid residues like HIS 49, CYS 67, ARG 69, ASN 71, ASP 75, ARG 112, and THR 101 causes modifications in these residues, which ultimately attenuate the activity of the BTG-2 protein. The molecular dynamics determine the four numbers of H-bonds for executing the interaction between BTG2 and hesperidin. The best residue with high energy around all poses is Arg69. Finally, the present work highlighted that hesperidin was the highest phytochemical compound binding to BTG2 protein.

Synthesis, Molecular Docking, and Biological Evaluation of Novel Indole-triazole Conjugates.

Indole-triazole conjugates have emerged as promising candidates for new drug development. Their distinctive structural characteristics, coupled with a wide array of biological activities, render them a captivating and promising field of research for the creation of novel pharmaceutical agents. This study aimed to synthesize indole-triazole conjugates to investigate the influence of various substituents on the functional characteristics of indole-triazole hybrids. It also aimed to study the binding modes of new hybrids with the DNA Gyrase using molecular docking studies. A new set of indole-triazole hybrids was synthesized and characterized using various physicochemical and spectral analyses. All hybrids underwent in-silico pharmacokinetic prediction studies. The antimicrobial efficacy of the hybrids was assessed using tube dilution and agar diffusion methods. Additionally, the in-vitro antioxidant activity of synthesized compounds was determined using the 1,1-diphenyl-2-picryl-hydrazyl free radical scavenging assay. Furthermore, in silico molecular docking studies were performed to enhance our comprehension of how the synthesized compounds interact at the molecular level with DNA gyrase. Pharmacokinetic predictions of synthesized hybrids indicated favourable pharmacokinetic profiles, and none of the compounds violated the Lipinski rule of five. Notably, compound 6, featuring a cyclohexanol substituent, demonstrated superior antimicrobial and antioxidant activity (EC50 value = 14.23 μmol). Molecular docking studies further supported the in vitro antioxidant and antimicrobial findings, revealing that all compounds adeptly fit into the binding pocket of DNA Gyrase and engaged in interactions with crucial amino acid residues. In summary, our research underscores the efficacy of molecular hybridization in shaping the physicochemical, pharmacokinetic, and biological characteristics of novel indole-triazole derivatives.

Biosynthesis of Nonribosomal Peptides Chitinimides Reveal a Special Type of Thioesterase Domains.

Non-ribosomal peptide synthetases (NRPSs) and their tailored enzymes have diverse biological functions. In this study, we investigated the biosynthesis and function of chitinimides, which belong to the non-ribosomal peptide (NRP) subfamily featuring a pyrrolidine-containing part (X part) connected to the polypeptide chain via an ester bond. A conserved gene cassette, chmHIJK, is responsible for oxyacylation of the pyrrolidine moiety in the X part. The thioesterase (TE) domain of ChmC (ChmC-TE) catalyzes transesterification reactions with a free X part or methanol as a nucleophilic reagent to form different chitinimides. The crucial amino acid residues in the ChmC-TE domains responsible for the specific recognition of the X part were identified, and they were conserved in all the biosynthetic pathways of this NRP subfamily to form a signature motif, YNHNR, suggesting a special type of TE domain in NRPSs. Chitinimides demonstrate the biological function of promoting the swarming ability of the native producer. This study provides deep insights into the biosynthesis of this special NRP subfamily, and shows that the special TE domain could be used to generate diverse NRPs by combinatorial biosynthesis.

Catalytic selectivity and evolution of cytochrome P450 enzymes involved in monoterpene indole alkaloids biosynthesis.

Cytochrome P450 enzyme (CYP)-catalyzed functional group transformations are pivotal in the biosynthesis of metabolic intermediates and products, as exemplified by the CYP-catalyzed C7-hydroxylation and the subsequent C7-C8 bond cleavage reaction responsible for the biosynthesis of the well-known antitumor monoterpene indole alkaloid (MIA) camptothecin. To determine the key amino acid residues responsible for the catalytic selectivity of the CYPs involved in MIA biosynthesis, we characterized the enzymes CYP72A728 and CYP72A729 as stereoselective 7-deoxyloganic acid 7-hydroxylases (7DLHs). We then conducted a comparative analysis of the amino acid sequences and the predicted structures of the CYP72A homologs involved in camptothecin biosynthesis, as well as those of the CYP72A homologs implicated in the pharmaceutically significant MIAs biosynthesis in Catharanthus roseus. The crucial amino acid residues for the catalytic selectivity of the CYP72A-catalyzed reactions were identified through fragmental and individual residue replacement, catalytic activity assays, molecular docking, and molecular dynamic simulations analysis. The fragments 1 and 3 of CYP72A565 were crucial for its C7-hydroxylation and C7-C8 bond cleavage activities. Mutating fragments 1 and 2 of CYP72A565 transformed the bifunctional CYP72A565 into a monofunctional 7DLH. Evolutionary analysis of the CYP72A homologs suggested that the bifunctional CYP72A in MIA-producing plants may have evolved into a monofunctional CYP72A. The gene pairs CYP72A728-CYP72A610 and CYP72A729-CYP72A565 may have originated from a whole genome duplication event. This study provides a molecular basis for the CYP72A-catalyzed hydroxylation and C-C bond cleavage activities of CYP72A565, as well as evolutionary insights of CYP72A homologs involved in MIAs biosynthesis.

Unveiling crucial amino acid residues in the red clover necrotic mosaic virus movement protein for dynamic subcellular localization and viral cell-to-cell movement

Emerging evidence suggests that the localization of viral movement proteins (MPs) to both plasmodesmata (PD) and viral replication complexes (VRCs) is the key to viral cell-to-cell movement. However, the molecular mechanism that establishes the subcellular localization of MPs is not fully understood. Here, we investigated the PD localization pathway of red clover necrotic mosaic virus (RCNMV) MP and the functional regions of MP that are crucial for MP localization to PD and VRCs. Disruption analysis of the transport pathway suggested that RCNMV MP does not rely on the ER-Golgi pathway or the cytoskeleton for the localization to the PD. Furthermore, mutagenesis analysis identified amino acid residues within the alpha helix regions responsible for localization to the PD or VRCs. These α-helix regions were also essential for efficient viral cell-to-cell movement, highlighting the importance of these dynamic localization of the MPs for viral infection.

Computational Design of a Novel Inhibitor Against COVID

Background: In recent years, in silico computational approaches have tremendously guided computational medicinal chemists and research scientists to analyze protein structures, kinetics, functions, and molecular interactions of the administered drugs. Objective: This study aimed to identify a novel inhibitor against SARS-CoV-2 using human CD26 and modeled spike protein through suitable in silico approaches. Methods: In this work, molecular docking and molecular dynamics simulation experiments were conducted to gain insights into the binding affinity and stability, respectively. The docked complex of CD26 with modeled spike protein showed higher binding affinity than the complex of CD26 with resolved spike protein due to the existence of strong interactions with the crucial amino acid residues of the target proteins. Results: The results of the molecular dynamics simulation demonstrated that CD26 with the modeled spike protein docked complex showed good stability when compared with the resolved protein. Conclusion: From this computational finding, it was also suggested that the structure was stable and would rapidly guide the discovery of potential inhibitors against COVID-19.

Design, synthesis, and antifungal activity of novel pyrazole carboxamide derivatives containing benzimidazole moiety as potential SDH inhibitors.

To address the urgent need for new antifungal agents, a collection of novel pyrazole carboxamide derivatives incorporating a benzimidazole group were innovatively designed, synthesized, and evaluated for their efficacy against fungal pathogens. The bioassay results revealed that the EC50 values for the compounds A7 (3-(difluoromethyl)-1-methyl-N-(1-propyl-1H-benzo[d]imidazol-2-yl)-1H-pyrazole-4-carboxamide) and B11 (N-(1-(4-chlorobenzyl)-1H-benzo[d]imidazol-2-yl)-3-(difluoromethyl)-1-methyl-1H-pyrazole-4-carboxamide) against B. cinerea were notably low to 0.79µg/mL and 0.56µg/mL, respectively, demonstrating the potency comparable to that of the control fungicide boscalid, which has an EC50 value of 0.60µg/mL. Noteworthy is the fact that in vivo tests demonstrated that A7 and B11 showed superior protective effects on tomatoes and strawberries against B. cinerea infection when juxtaposed with the commercial fungicide carbendazim. The examination through scanning electron microscopy revealed that B11 notably alters the morphology of the fungal mycelium, inducing shrinkage and roughening of the hyphal surfaces. To elucidate the mechanism of action, the study on molecular docking and molecular dynamics simulations was conducted, which suggested that B11 effectively interacts with crucial amino acid residues within the active site of succinate dehydrogenase (SDH). This investigation contributes a novel perspective for the structural design and diversification of potential SDH inhibitors, offering a promising avenue for the development of antifungal therapeutics.

A ratiometric fluorescence sensor for detection of organophosphorus pesticides based on enzyme-regulated multifunctional Fe-based metal-organic framework

The residues of organophosphorus pesticides (OPs) are increasing environmental pollution and public health concerns. Thus, the development of simple, convenient and sensitive method for detection of OPs is crucial. Herein, a multifunctional Fe-based MOF with fluorescence, catalytic and adsorption, is synthesized by a simple one-pot hydrothermal method. The ratiometric fluorescence sensor for detection of OPs is constructed by using only one multifunctional sensing material. The NH2-MIL-101(Fe) is able catalyze the o-phenylenediamine (OPD) into 2,3-diaminophenazine (DAP) in the presence of H2O2. The generated DAP can significantly quench the intrinsic fluorescence of NH2-MIL-101(Fe) by the fluorescence resonance energy transfer (FRET) and internal filtration effect (IFE), while producing a new measurable fluorescence. Without immobilization or molecular imprinting, pyrophosphate ion (PPi) can inhibit the peroxidase-like activity of the NH2-MIL-101(Fe) by chelating with Fe3+/Fe2+ redox couple. Moreover, PPi can also be hydrolyzed by alkaline phosphatase (ALP), the presence of OPs inhibits the activity of ALP, resulting in the increase of extra PPi preservation and signal changes of ratiometric fluorescence, the interactions of ALP with different OPs are explored by molecular docking, the OPs (e.g., glyphosate) interact with crucial amino acid residues (Asp, Ser, Ala, Lys and Arg) are indicated. The proposed sensor exhibits excellent detection performance for OPs with the detection limit of 18.7 nM, which provides a promising strategy for detection of OPs.

In silico identification and mechanistic evaluation of novel tyrosinase inhibitory peptides derived from coconut proteins

Globulin proteins of coconut were in silico hydrolysis by proteinases for screening potential tyrosinase inhibitory peptides, of which their inhibitory mechanisms were investigated through molecular docking and molecular dynamics simulations. First, the coconut globulin was in silico hydrolyzed using the PeptideCutter online enzymatic digestion software. Second, prediction of toxicity of the hydrolyzed peptides was performed using ToxinPred, while Innovagen was employed for the determination of their water solubility. Third, the peptides were docked into tyrosinase to determine the binding site and its binding strength. Fourth, the inhibitory activity of the peptides against tyrosinase was experimentally validated. Finally, the inhibitory mechanism was investigated by molecular dynamics simulations and isothermal titration calorimetry. The results showed that the peptide Asp-Gly-Glu (DGE) exhibited an inhibitory effect on tyrosinase, with an IC50 value of 9.58 ± 0.01 mM. Moreover, His61, His296, Asn260, and Arg268 were the crucial amino acid residues enabling the binding of DGE to the pocket of tyrosinase. The present study demonstrates that the peptide DGE can be used as a tyrosinase inhibitor to prevent and ameliorate hyperpigmentation and other tyrosinase-related problems. This study provides a theoretical basis for the development of novel safe and effective tyrosinase inhibitory peptides.

Phenolic enriched fraction of Clerodendrum glandulosum Lindl. leaf extract ameliorates hyperglycemia and oxidative stress in streptozotocin-nicotinamide induced diabetic rats

BackgroundClerodendrum glandulosum Lindl. is an important ethnomedicinal shrub of Northeast India, used by traditional healers to control various ailments like diabetes, hypertension, arthritis, etc. ObjectivesThe present study was conducted to explore the anti-hyperglycemic and antioxidative effects of the polyphenol-rich fraction (PRF) of C. glandulosum leaf extract and identification of its major bioactive compounds. Further, an in-silico molecular docking study was also performed to understand the molecular interactions of the identified major compounds with some target proteins associated with diabetic complications. Materials and methodsPRF was purified from the hydromethanolic (80% MeOH) extract of leaves and subjected to assessment of in-vitro antioxidant and anti-diabetic properties. It was also subjected to evaluate the ameliorative effect during streptozotocin-nicotinamide-induced hyperglycemia in Wistar albino rats. An in-silico molecular docking study was also performed to complement the in-vitro/in-vivo studies. ResultsChemical analysis of PRF showed the presence of phenolics like caffeic acid, verbascoside, isoverbascoside, and apigenin, of which verbascoside (598.14 ± 1.24 mg/g) was found to be the principal compound. In-vitro studies showed potent antioxidant (IC50 of DPPH:32.45 ± 2.16 μg/mL; ABTS:39.08 ± 0.53 μg/mL) properties and excellent aldose reductase inhibition potential (IC50 2.18 ± 0.10 μg/mL). Treatment with PRF showed reduced blood glucose levels and increased plasma insulin levels. The results also indicate an improvement of endogenous antioxidants and suppression of inflammatory cytokines (IL-6 and TNF-α) comparable to the standard. Molecular docking studies predicted promising interactions between the identified molecules and the crucial amino acid residues of the enzymes involved in the development of hyperglycemia. ConclusionThis study revealed the antihyperglycemic and antioxidant potential of partially purified fraction PRF of C. glandulosum leaves.

Isoliquiritigenin retards starch digestion by increasing resistant starch content and inhibiting the activities of α-amylase and α-glucosidase

The inhibition mechanism of starch digestion by a natural plant active ingredient isoliquiritigenin was studied. The results indicated that isoliquiritigenin effectively decreased the starch hydrolysis through increasing the content of resistant starch, and inhibiting the activities of α-amylase and α-glucosidase. The content of resistant starch increased by 18.85% with the addition of isoliquiritigenin at 8% content. Multispectral analyses showed isoliquiritigenin combined with α-amylase or α-glucosidase to form stable complexes by non-covalent bonds, leading to the enzyme's structure to be loose, which was supported by the results of unstable conformations and an increase in the freedom of amino acid residues of the enzymes in molecular dynamics simulation. Molecular docking demonstrated that isoliquiritigenin bound to the amino acid residues 304–310 nearby the active pocket of α-amylase, and inserted the active site of α-glucosidase competing with the substrate to bind the crucial amino acid residues (Asp215, Asp352 and Glu411), thereby inhibiting α-amylase and α-glucosidase activity. These findings highlight the development potential of isoliquiritigenin as a hypoglycaemic dietary supplement.

Structural simulation and selective inhibitor discovery study for histone demethylases KDM4E/6B from a computational perspective

The methylation and demethylation of lysine and arginine side chains are fundamental processes in gene regulation and disease development. Histone lysine methylation, controlled by histone lysine methyltransferases (KMTs) and histone lysine demethylases (KDMs), plays a vital role in maintaining cellular homeostasis and has been implicated in diseases such as cancer and aging. This study focuses on two members of the lysine demethylase (KDM) family, KDM4E and KDM6B, which are significant in gene regulation and disease pathogenesis. KDM4E demonstrates selectivity for gene regulation, particularly concerning cancer, while KDM6B is implicated in inflammation and cancer. The study utilizes specific inhibitors, DA-24905 and GSK-J1, showcasing their exceptional selectivity for KDM4E and KDM6B, respectively. Employing an array of computational simulations, including sequence alignment, molecular docking, dynamics simulations, and free energy calculations, we conclude that although the binding cavities of KDM4E and KDM6B has high similarity, there are still some different crucial amino acid residues, indicating diverse binding forms between protein and ligands. Various interaction predominates when proteins are bound to different ligands, which also has significant effect on selective inhibition. These findings provide insights into potential therapeutic strategies for diseases by selectively targeting these KDM members.

D-Glucosamine is a Potential Urease Inhibitor from Middle Eastern Medicinal Plants for Combatting Helicobacter Pylori Infections; a Molecular Docking and Simulation Approach.

Helicobacter pylori stands as a significant risk factor for both peptic and stomach ulcers. Their resistance to the highly acidic host environment primarily stems from their capability to produce urease, an enzyme that rapidly converts urea into NH3 and CO2. These byproducts are crucial for the bacterium's survival under such harsh conditions. Given the pivotal role of medicinal plants in treating various ailments with minimal side effects, there is an urgent need for a natural drug that can effectively eliminate H. pylori by inhibiting urease. Hence, the current study aims to identify the most potent urease inhibitor among the natural compounds found in Middle Eastern medicinal plants, taking into consideration factors such as optimal affinity, drug-like properties, pharmacokinetic characteristics, and thermodynamic attributes. In total, 5599 ligand conformers from 151 medicinal plants were subjected to docking against the urease's active site. The top-ranking natural compounds, as determined by their high docking scores, were selected for further analysis. Among these compounds, D-glucosamine (PubChem code 439,213) exhibited the most interactions with the crucial amino acid residues in the urease's active site. Furthermore, D-glucosamine demonstrated superior absorption, distribution, metabolism, excretion, and toxicity properties compared to other top-ranked candidates. Molecular dynamics simulations conducted over 100 nanoseconds revealed stable root mean square deviations and fluctuations of the protein upon complexation with D-glucosamine. Additionally, the radius of gyration and solvent-accessible surface area values for the D-glucosamine-urease complex were notably lower than those observed in other typical urease-inhibitor complexes. In conclusion, this study provides valuable insights into the potential development of D-glucosamine as a novel urease inhibitor. This promising compound holds the potential to serve as an effective drug for combating H. pylori infections in the near future.

Biocatalytic Regioselective O-acylation of Sesquiterpene Lactones from Chicory: A Pathway to Novel Ester Derivatives.

We report the first biocatalytic modification of sesquiterpene lactones (STLs) found in the chicory plants, specifically lactucin (Lc), 11β,13-dihydrolactucin (DHLc), lactucopicrin (Lp), and 11β,13-dihydrolactucopicrin (DHLp). The selective O-acylation of their primary alcohol group was carried out by the lipase B from Candida antarctica (CAL-B) using various aliphatic vinyl esters as acyl donors. Perillyl alcohol, a simpler monoterpenoid, served as a model to set up the desired O-acetylation reaction by comparing the use of acetic acid and vinyl acetate as acyl donors. Similar conditions were then applied to DHLc, where five novel ester chains were selectively introduced onto the primary alcohol group, with conversions going from >99 % (acetate and propionate) to 69 % (octanoate). The synthesis of the corresponding O-acetyl esters of Lc, Lp, and DHLp was also successfully achieved with near-quantitative conversion. Molecular docking simulations were then performed to elucidate the preferred enzyme-substrate binding modes in the acylation reactions with STLs, as well as to understand their interactions with crucial amino acid residues at the active site. Our methodology enables the selective O-acylation of the primary alcohol group in four different STLs, offering possibilities for synthesizing novel derivatives with significant potential applications in pharmaceuticals or as biocontrol agents.

Mechanistic insight into the membrane disrupting properties of thymol in Candida species

Candida infection is a major problem in immunocompromised patients and has become a significant public health concern in recent years due to high toxicity, multidrug resistance and unfavourable side effects of conventional antifungal drugs. This study aims to investigate the antifungal efficacy of thymol, a natural monoterpenoid, on the membrane integrity of Candida albicans, Candida glabrata and Candida tropicalis. Minimum inhibitory concentrations (MICs) of thymol were 32 µg/ml, 63 µg/ml, and 125 µg/ml for C. albicans, C. tropicalis and C. glabrata, respectively. The minimum fungicidal concentrations (MFC) were 64 µg/ml, 110 µg/ml and 240 µg/ml, respectively. At MIC, thymol treated cells showed complete suppression of cell growth (growth kinetics, disc diffusion), altered morphology (scanning electron microscopy), leakage of intracellular macromolecules (absorption at 260 nm), significant reduction in ergosterol levels and inhibition of plasma membrane H+-ATPase (Pma1) activity. The disruption of the fungal membranes by thymol was further confirmed by propidium iodide uptake using flow cytometry and confocal microscopy. In silico studies with membrane-bound proteins (lanosterol 14-α demethylase (LDM) and Pma1), showed good binding affinity of −6.3 kcal/mol and −6.7 kcal/mol, respectively, and formed hydrogen bonds with crucial amino acid residues at the active site of target proteins. With low MIC values, negligible host toxicity, desirable ADME properties, thymol has immense potential as a potent antifungal drug that can be used for developing mechanism-based drugs as it has specific binding affinity for specific target proteins. Studies using animal models are required for further validation.

Novel pyrazole‐biphenyl‐carboxamides for SARS‐CoV2 entry‐level restriction and microbial infections

AbstractMicrobial diseases including viral infection are big issues globally. Effective medicinal discovery for them is the need for the day. In this study, we report pyrazole‐biphenyl‐carboxamides (4a‐l) validated for their SARS‐CoV2 entry‐level restriction effect over studying the protein–protein interaction of SARS‐CoV2 with human ACE protein. Their extended antimicrobial properties were also evaluated. Online and offline software tools predicted MD simulation and ADMET druggability in silico. The antimicrobial efficacy of all compounds was also evaluated against Gram+ve Streptococcus pneumoniae (MTCC 1936), Staphylococcus aureus (MTCC 737) and Gram‐ve Escherichia coli (MTCC 443), Pseudomonas aeruginosa (MTCC 424) (bacteria). In the results, compounds 4g and 4i were evenly active against both bacteria at a low concentration range (MIC: 1.00 to 9.5 μg/mL) and displayed lesser toxicity to tested mammalian cells (EC100 = 75 μg/mL). Furthermore, it was able to kill metabolically inactive bacterial cells and eradicate established biofilms of Methicillin‐resistant Staphylococcus aureus (MRSA). Both the compounds inhibited DNA gyrase well with an IC50 0.25 μM (96% relative activity) and 0.52 μM (97% relative activity) respectively. Compounds (4a‐l) showed restrictive efficiency of SARS‐CoV2 spike protein (SC2SP) and human angiotensin‐converting enzyme 2 (hACE2) entry‐level association in COVID‐19 in silico. To assess this ability, firstly, we identified the crucial amino acid residues involved in the interface of SARS‐CoV‐2 and hACE2 virtually. We recognized the ability of 4a‐l binding to the binding interface to SARS‐CoV2; thus, the interaction of SC2SP‐hACE2 was effectively inhibited.

In Silico and In vitro Analysis of Phenolic Acids for Identification of Potential DHFR Inhibitors as Antimicrobial and Anticancer Agents.

DHFR is an indispensable enzyme required for the survival of almost all prokaryotic and eukaryotic cells, making it an attractive molecular target for drug design. In this study, a combined in silico and in vitro approach was utilized to screen out potential anticancer and antimicrobial agents by using DHFR PDB ID 2W9S (for antimicrobial) and 1U72 (for anticancer). Computational work was performed using Maestro Schrodinger Glide software. The DHFR inhibitory activity of the selected compounds was assessed using the DHFR test kit (CS0340-Sigma- Aldrich). Exhaustive analysis of in silico results revealed that some natural phenolic acids have a good docking score when compared to standards, i.e., trimethoprim and methotrexate, and have astonishing interactions with crucial amino acid residues available in the binding pocket of DHFR, such as Phe 92, Asp 27, Ser 49, Asn 18, and Tyr 98. In particular, digallic acid and chlorogenic acid have amazing interactions with docking scores of -9.9 kcal/mol and -9.6 kcal/mol, respectively, for the targeted protein 2W9S. Docking scores of -10.3 kcal/mol and -10.2 kcal/mol, respectively, for targeted protein 1U72. The best hits were then tested in vitro to evaluate the DHFR inhibitory activity of the compounds. DHFR inhibition activity results are in correlation with molecular docking results. In silico and in vitro results confirmed the good binding and inhibitory activity of some phenolic acids to the modeled target proteins. Among all the studied natural phenolic acids, chlorogenic acid, digallic acid, and rosmarinic acid appeared to be the most potential leads for future chemical alteration. This study can provide significant speculative guidance for the design and development of potent DHFR inhibitors in the future by using these compounds as leads.

Computational Methods to Target Protein-Protein Interactions.

The chapter emphasizes the importance of understanding protein-protein interactions in cellular mechanisms and highlights the role of computational modeling in predicting these interactions. It discusses sequence-based approaches such as evolutionary trace (ET), correlated mutation analysis (CMA), and subtractive correlated mutation (SCM) for identifying crucial amino acid residues, considering interface conservation or evolutionary changes. The chapter also explores methods like differential ET, hidden-site class model, and spatial cluster detection (SCD) for interface specificity and spatial clustering. Furthermore, it examines approaches combining structural and sequential methodologies and evaluates modeled predictions through initiatives like critical assessment of prediction of interactions (CAPRI). Additionally, the chapter provides an overview of various software programs used for molecular docking, detailing their search, sampling, refinement and scoring stages, along with innovative techniques and tools like normal mode analysis (NMA) and adaptive Poisson-Boltzmann solver (APBS) for electrostatic calculations. These computational and experimental approaches are crucial for unraveling protein-protein interactions and aid in developing potential therapeutics for various diseases.

Explication of Pharmacological Proficiency of Phytoconstituents from Adansonia digitata Bark: An In Vitro and In Silico Approaches.

Compared to other drug discovery sources, traditional medicine has significantly contributed to developing innovative therapeutic molecules for preventive and curative medicine. The Baobab tree, also known as Adansonia digitata L., is significant in Africa due to its multitude of benefits and various parts that serve different purposes, providing economic support to rural communities. The analysis of a plant sample using Fourier transform infrared (FT-IR) spectroscopy detected multiple functional groups, such as carboxyl and aromatic groups. Additionally, gas chromatography-mass spectroscopy (GC-MS) was utilized to identify various compounds present in the sample, including tetrachloroethylene and octyl ester. The results of different assays, such as α-diphenyl-β-picrylhydrazyl (DPPH), superoxide, nitric oxide scavenging assays, and total antioxidant by thiobarbituric acid method (TBA) and ferric thiocyanate (FTC) method, demonstrated a substantial scavenging of free radicals and an effective antioxidant efficacy. The bark's antimicrobial activity was tested through agar diffusion, resulting in a range of zone of inhibition from 10.1 ± 0.36 mm to 20.85 ± 0.76 mm. The minimum inhibitory concentration (MIC) value was observed to be approximately 0.625 µg/mL. The biofilm inhibition percentage ranged from 9.89% to 57.92%, with the highest percentage being 57.92%. The GC-MS and FT-IR studies revealed phytocompounds, which were then analyzed for their potential therapeutic properties. Computational studies were conducted on the phytocompounds against Pseudomonas aeruginosa and C2 kinase (antioxidant). The study concluded that the Adansonia digitata bark extract and its phytocompound have potential therapeutic efficacy against the target proteins. The best docking scores were about -7.053 kcal/mol and -7.573 kcal/mol for Pseudomonas aeruginosa and C2 kinase (antioxidant), respectively. The interaction patterns with the crucial amino acid residues elucidate the inhibitory efficacy of the phytocompounds.

Identification and Characterization of a Nerol Synthase in Fungi.

Nerol, a linear monoterpenoid, is naturally found in essential oils of various plants and is widely used in the fragrance, food, and cosmetic industries. Nerol synthase, essential for nerol biosynthesis, has previously been identified only in plants that use NPP as the precursor. In this study, a novel fungal nerol synthase, named PgfB, was cloned and characterized from Penicillium griseofulvum. In vitro enzymatic assays showed that PgfB could directly convert the substrate GPP into nerol. Furthermore, the successful expression of PgfB and its homologous protein in Saccharomyces cerevisiae resulted in the heterologous production of nerol. Finally, crucial amino acid residues for PgfB's catalytic activity were identified through site-directed mutagenesis. This research broadens our understanding of fungal monoterpene synthases and presents precious gene resources for the industrial production of nerol.