Interacting Amino Acid Residues Research Articles

Intracellular bactericidal activity and action mechanism of MDP1 antimicrobial peptide against VRSA and MRSA in human endothelial cells.

Staphylococcus aureus is a prominent cause of postoperative infections, often persisting within host cells, leading to chronic infections. Conventional antibiotics struggle to eliminate intracellular S. aureus due to poor cell penetration. Antimicrobial peptides are a new hope for tackling intracellular bacteria. Accordingly, this study examines the antimicrobial peptide MDP1, derived from melittin, for its efficacy against intracellular S. aureus. In this study, the physiochemical properties (Prediction of three-dimensional structure, circular dichroism and helical wheel projection analysis) were investigated. Extracellular antibacterial activity and cytotoxicity of MDP1 were also assessed. The mechanism of interaction of MDP1 with S. aureus was evaluated by molecular dynamic simulation, atomic force and confocal microscopy. Bacterial internalization into an endothelial cell model was confirmed through culture and transmission electron microscopy. The effect of the peptide on intracellular bacteria was investigated by culture and epi-fluorescence microscopy. 3D structural prediction proved the conformation of MDP1 as an α-helix peptide. Helical-wheel projection analysis indicated the proper orientation of hydrophobic amino acid residues for membrane interaction. CD spectroscopy of MDP1 showed that MDP1 in SDS 10 and 30 mM adopted 87 and 91% helical conformation. Atomic force and confocal microscopy assessments as well as molecular dynamics studies revealed the peptide-bacterial membrane interaction. MDP1, at the concentration of 0.32 μg mL-1, demonstrated a fold reduction of 21.7 ± 1.8, 1.7 ± 0.2, and 7.3 ± 0.8 in intracellular bacterial load for ATCC, VRSA, and MRSA, respectively. Molecular dynamics results demonstrate a preferential interaction of MDP1 with POPG/POPE membranes, primarily driven by electrostatic forces and hydrogen bonding. In POPC systems, two out of four MDP1 interacted effectively, while all four MDP1 engaged with POPG/POPE membranes. Gathering all data together, MDP1 is efficacious in the reduction of intracellular VRSA and MRSA proved by culture and epi-fluorescent microscopy although further studies should be performed to increase the intracellular activity of MDP1.

Molecular docking of ferulic acid, bakuchiol and niazirin on peroxisome proliferator-activated receptor gamma (PPAR-γ) as anti-diabetic agents

Background: Diabetes mellitus remains one of the most dangerous illnesses worldwide. The PPAR-gamma protein plays a crucial role in lipid and carbohydrate metabolism, making it a key target for diabetes therapy. Research into plant-derived active compounds for diabetes treatment is increasingly important. Objective: This study aims to evaluate and analyze the interaction of ferulic acid, niazirin, and bakuchiol with the peroxisome proliferator-activated receptor gamma (PPAR-γ) protein using molecular docking. Methods: Molecular docking was employed to assess the interactions between ferulic acid, niazirin, bakuchiol, and the PPAR-γ protein (PDB ID: 2PRG). The analysis focused on binding free energy values, amino acid residue interactions, the number of hydrogen bonds, and bond distances, comparing these results to those of the native ligand and pioglitazone, a known anti-diabetic drug targeting PPAR-γ. Results: The binding free energies for the ferulic acid-PPAR-γ, bakuchiol-PPAR-γ, niazirin-PPAR-γ, native ligand-PPAR-γ, and pioglitazone-PPAR-γ complexes were -5.54 kcal/mol, -8.47 kcal/mol, -6.56 kcal/mol, -10.08 kcal/mol, and -9.94 kcal/mol, respectively. The amino acid residue similarity percentages with the native ligand were 18.18% for ferulic acid, 27.27% for bakuchiol, 18.18% for niazirin, and 81.82% for pioglitazone. The native ligand-2PRG and pioglitazone-2PRG complexes exhibited superior hydrogen bond numbers and shorter bond distances compared to the other compounds. Conclusion: Although bakuchiol showed the most promising interaction among the tested compounds, none surpassed the binding affinity and stability of the native ligand or pioglitazone. Further research is needed to optimize these compounds for potential anti-diabetic therapy.

Exploration of dynamic interaction between β-lactoglobulin and casein micelles during UHT milk process

The protein aggregation induced by UHT treatment shortens the shelf life of UHT milk. However, the mechanism of β-Lg induced casein micelle aggregation remains unclear. Herein, the dynamic interaction between β-Lg and casein micelles during UHT processing was investigated by experimental techniques and molecular dynamics simulations. Results showed that β-Lg decreased the stability of casein micelles, increased their size and zeta potential. Raman and FTIR spectra analysis suggested that hydrogen and disulfide bonds facilitated their interaction. Cryo-TEM showed that the formation of the casein micelle/β-Lg complex involved rigid binding, flexible linking, and severe cross-linking aggregation during UHT processing. SAXS and MST demonstrated β-Lg bound to κ-casein on micelle surfaces with a dissociation constant (Kd) of 3.84 ± 1.14 μm. Molecular docking and dynamic simulations identified the interacting amino acid residues and clarified that electrostatic and van der Waals forces drove the interaction. UHT treatment increased hydrogen bonds and decreased total binding energy. The non-covalent binding promoted the formation of disulfide bonds between β-Lg and casein micelles under heat treatment. Ultimately, it was concluded that non-covalent interaction and disulfide bonding resulted in casein micelle/β-Lg aggregates. These findings provided scientific insights into protein aggregation in UHT milk.

Direct Interaction of Minocycline to p47phox Contributes to its Attenuation of TNF-α-Mediated Neuronal PC12 Cell Death: Experimental and Simulation Validation.

Minocycline, a repurposed approved medication, shows promise in treating neurodegeneration. However, the specific pathways targeted by minocycline remain unclear despite the identification of molecular targets. This study explores minocycline's potential protective effects against TNF-α-mediated neuronal death in PC12 cells, with a focus on unraveling its interactions with key molecular targets. The study begins by exploring minocycline's protective role against TNF-α-mediated neuronal death in PC12 cells, showcasing a substantial reduction in cleaved caspase-3 expression, DNA fragmentation, and intracellular ROS levels following minocycline pretreatment. Subsequently, a comprehensive analysis utilizing pull-down assays, computational docking, mutation analysis, molecular dynamics simulations, and free energy calculations is conducted to elucidate the direct interaction between minocycline and p47phox-the organizer subunit of NADPH oxidase-2 (NOX2) complex. Computational insights, including a literature survey and analysis of key amino acid residues, reveal a potential binding site for minocycline around Trp193 and Cys196. In silico substitutions of Trp193 and Cys196 further confirm their importance in binding with minocycline. These integrated findings underscore minocycline's protective mechanisms, linking its direct interaction with p47phox to the modulation of NOX2 activity and attenuation of NOX-derived ROS generation. Minocycline demonstrates protective effects against TNF-α-induced PC12 cell death, potentially linked to its direct interaction with p47phox. This interaction leads to a reduction in NOX2 complex assembly, ultimately attenuating NOX-derived ROS generation. These findings hold significance for researchers exploring neuroprotection and the development of p47phox inhibitors.

Mechanistic Insight into Binding of Graphene Towards Multiple Therapeutic Target of SARS-CoV-2 by Molecular Docking and Dynamics Studies

Background: Even after more than three years of emergence of coronavirus diseases 2019 (COVID-19), it remains incurable, despite the use of emergency-approved vaccines. The impact of the emergency-approved vaccines against it is not highly certain. The entire world may face surge of new wave of the infection, and therefore, its reoccurrence cannot be denied. Causalities and economic losses may happen in the future. In this situation, it is need of the hour to explore some suitable therapeutic agents against this highly infectious and challenging disease. Organic molecules, inactivated virus etc were largely focused to derive the vaccines, however, nanomaterials still remain untested for it. Interaction of nanomaterials like graphene against proteins of the coronavirus to inhibit its activity is yet to be tested computationally. Method: In this computational research work, graphene is tested for interaction with the viral proteins, as the dimension of the novel coronavirus also belongs to nano-scale (diameter 65-125 nm). A detailed study ondocking structures and molecular dynamics between viral proteins and graphene, is undertaken. Autodock and Discovery Studio packages were used for docking calculations and interaction analysis, respectively. Molecular dynamics simulation was performed using NAMD software and obtained results were visualized using VMD software. Results: Range of proteins of the coronavirus including spike proteins (both open and closed form), Main Protease (MPRO), Receptor-Binding Domain (RBD), RNA-dependent RNA polymerase (RdRp), and Angiotensin Converting Enzyme 2 (ACE2) have been individually evaluated for their docking and dynamics with graphene, so as to inactivate the virus. Details of interacting amino acid residues of coronavirus with graphene is found in the study. Conclusion: Computationally, it is observed that most of these proteins were found interactive through their amino acid residues with graphene. Number of interacting amino acid residues is considerable enough to collectively acquire high binding energy. It can be envisaged that cumulative perturbations of all the interactions of each protein caused by graphene can lower down or inactivate the virus.

Potential bioactive compound and hub gene identification of endometrial carcinoma using systems biology

Endometrial carcinoma is a frequent cancer of the female genital tract. Endometrial carcinoma accounts for 97% of all uterine malignancies and 3 % of sarcomas that develop from the endometrium’s glands. Endometrial cancer is frequently found in its early stages since most women quickly report postmenopausal vaginal hemorrhage. The need for more advanced medications to improve survival in such situations is still unfulfilled. As a result, there is growing interest in employing an herbal treatment to treat endometriosis, which seems to be an effective strategy. We have discovered a few unintended targets (ligands) in our investigation that are active components of common therapeutic herbs. The differentially expressed genes (DEG - target protein) for endometrial cancer were found using the NCBI and CIViC databases. In our investigation, the protein used for docking and simulation was PDB ID: 3THW. Using the Cytoscape server, the gene-encoding protein network has been identified. It was discovered that the Protein 3THW's binding energy to the bioactive substance (Asarone) was −7.15 Kcal/mol. It was discovered that the crucial interacting amino acid residues were ILE648, PHE650, ILE651, VAL802, TYR815, VAL817. The properties of the pharmaceutical target are further investigated by employing a molecular simulation study for 100 ns with NAMD software. Low RMSD and SASA (Solvent accessible surface area), high RMSF, High hydrogen bonds, between Asarone and MSH2 demonstrated their potency as endometrial cancer inhibitor compounds. Based on these analyses we infer that the bioactive substances originating from medicinal plants may be an effective treatment for endometrial cancer. Communicated by Ramaswamy H. Sarma

Next generation sequencing shows diversity of Omicron sub-lineages of SARS-COV2 circulating in Jeddah, Saudi Arabia

The ever-evolving Omicron variant of the SARS-CoV-2 and its sub-lineages have prompted Saudi Arabia to continuously track circulating lineages. We focused on the presence of diverse SARS-CoV-2 circulation in Saudi Arabia and presented the whole genome sequencing study of 94 positive SARS-CoV-2 specimens procured between February and April 2022 in the city of Jeddah, Saudi Arabia. Following whole-genome sequencing, bioinformatics analysis was undertaken. The SARS-CoV-2 variant Omicron clades 21K and 21L constituted the entirety of sequenced specimens, belonging to BA.2 (n = 56) and BA.1.1 (n = 20), respectively, and low-frequency sub-lineages were BA.2.3 (n = 6), BA.1 (n = 4), BA.2.40.1 (n = 2), BA.1.14 (n = 1), BA.2.10 (n = 1), BA2.32 (n = 1), BA.2.57 (n = 1), BA2.64 (n = 1), and BA2.5 (n = 1). Mutational patterns were identified, as well as possible consequences for the spread of the virus. Comparative molecular docking of Omicron-specific Nucleocapsid protein harboring the mutations P13L, R203K, G204R, as well as S413R, and the deletions E31-, R32-, and S33- showed reduced interaction with human RIG-I protein with 8 interacting amino acid residues and 10 polar interactions, while the SARS-CoV-2 Nucleocapsid protein exhibited 15 interacting amino acid residues and 26 polar interactions. Ongoing monitoring is essential for assessing the genomic epidemiological consequences of tourist travel and pilgrimage in Jeddah and across Saudi Arabia, as well as the prompt identification of emerging variants for further investigation.

PH dependent physicochemical signatures of amino acids in aqueous buffers: Thermodynamic analysis

The physicochemical signatures such as apparent molar volume (V2,Φ), isoentropic compressibilities (KS,2,φ), and dilution enthalpies of a series of amino acids (AAs) glycine (Gly), L-alanine (Ala), DL-α-amino-n-butyric acid (ABA), L-valine (Val) and L-leucine (Leu) have been measured at various pH values (pH = 2, 5 7 and 9) at a buffer molality of 0.1 mol kg−1 of water at 298.15 K. The data obtained from high sensitivity densimeter and sound analyser along with ultrasensitive isothermal titration calorimetry has been analyzed to evaluate the values of standard partial molar quantities such as for volume at infinite dilution (V2,m0), compressibility KS, 2,m0 and dilution enthalpy (ΔdilH0) of the AAs together with standard partial molar quantities of transfer of these solutes from water to aqueous buffer systems at these pH values. The linear correlation of V2,m0 for this series of AAs against number of carbon atoms in their alkyl chain has been used to evaluate the contribution of zwitterionic end groups (NH3+, COO–), the CH2 group, and other parts of alkyl chains of the AAs to the overall value of V2,m0. The results of standard partial molar transfer properties on volumes, compressibilities and enthalpies of dilution from water to aqueous buffer systems at various pH values have been connected and explained in terms of ion-polar, ion-hydrophilic, hydrophobic-hydrophobic and ion-hydrophobic interactions of the participating groups. These thermodynamic signatures when compared at different pH values suggest that at electrostriction of water dominates at pH 2. Such physicochemical properties of constituents of proteins such as amino acids have not been reported earlier. Thus, the results demonstrate that the interaction of individual amino acid residues with the buffer components does not lead to significant change in their physicochemical properties thereby permitting their use in obtaining mechanistic insights into systems of biological interest consisting of these constituents.

Unraveling the underlying mechanism of interactions between astaxanthin geometrical isomers and bovine serum albumin

The health benefits of astaxanthin (AST) are related to its geometric isomers. Generally, functional activity is realized by the interactions between active substances and transporters. Hereto, bovine serum albumin (BSA), as a model-binding protein and transporter, is able to recognize and transport isomers of active substances through binding with them. However, differences in the binding mechanism of isomers to BSA may affect the functional activities of isomers through the “binding-transport-activity” chain reaction. Thus, this study sought to elucidate the interactions between AST geometrical isomers and BSA using multi-spectroscopy, surface plasmon resonance and molecular docking. The results showed that Z-AST displayed more interacting amino acid residues and lower thermodynamic parameters than all-E-AST. Meanwhile, the order of binding affinity to BSA was 13Z-AST (1.56 × 10−7 M) > 9Z-AST (2.70 × 10−7 M) > all-E-AST (4.01 × 10−7 M), indicating that Z-AST possessed stronger binding ability to BSA. Moreover, AST isomers were located at the junction between subdomains ⅡA and ⅢA of BSA, and showed the same interaction forces (hydrogen bond and van der Waals force) as well as kinetic processes (slow combination, slow dissociation). These interaction parameters provide valuable insights into their pharmacokinetics in vivo, and it was of great significance to explain the potential differences among AST isomers in functional activities.

Quinolone Tethered 1,2,3-triazole Conjugates: Design, Synthesis, and Computational Docking Studies on New Heterocycles as Potent Antimicrobial Targets

Abstract: The synthesis and biological properties of molecules simultaneously comprising various heterocycles, such as fused 2-quinolones and 1,2,3-triazoles, have been evaluated as a part of our ongoing research in medicinal and organic chemistry. We were successful in developing a synthetic procedure for 1,2,3-triazole substituted quinolone derivatives. Infrared, proton, and carbon nuclear magnetic resonance, mass spectroscopy and elemental analysis were used to characterise the structures of the recently synthesised triazole derivatives. From screening results, all the compounds demonstrated increased antibacterial action against both Gram-positive and Gram-negative bacteria. Moreover, 1,2,3-triazoles linked to tert-butyl benzyl (3a), trifluoromethyl benzyl (3b), 3-chlorobenzyl (3c), 4- hydroxy-3-nitrobenzyl (6b), 4-hydroxy-4-trifluoromethylbenzyl (6d), and 4-hydroxy-2,4- difluorobenzyl (6e) compounds showed promising antibacterial and antifungal activities with MICs values of 1.07-4.33 μg/mL. The prepared ligand 4-hydroxy-2,4-difluoro benzyl-1,2,3-triazole (6e) exhibited the highest docking score of -6.34 kcal/mol and showed interacting amino acid residues ArgB:1122, MetB:1121, AspB:1083, TryB:1087, AlaB:1118, AlaB:1120, GluB:1088, GlyB:1117, SerB:1084, and AlaB:1119 within the active site of 2XCT. Final scaffolds were further evaluated for their ADMET and physicochemical properties by using ADMETlab2.0 and SwissADME web servers as good oral bioavailability drugs.

Aminochalcones Attenuate Neuronal Cell Death under Oxidative Damage via Sirtuin 1 Activity.

Encouraged by the lack of effective treatments and the dramatic growth in the global prevalence of neurodegenerative diseases along with various pharmacological properties of chalcone pharmacophores, this study focused on the development of aminochalcone-based compounds, organic molecules characterized by a chalcone backbone (consisting of two aromatic rings connected by a three-carbon α,β-unsaturated carbonyl system) with an amino group attached to one of the aromatic rings, as potential neuroprotective agents. Thus, the aminochalcone-based compounds in this study were designed by bearing a -OCH3 moiety at different positions on the ring and synthesized by the Claisen-Schmidt condensation. The compounds exhibited strong neuroprotective effects against hydrogen peroxide-induced neuronal death in the human neuroblastoma (SH-SY5Y) cell line (i.e., by improving cell survival, reducing reactive oxygen species production, maintaining mitochondrial function, and preventing cell membrane damage). The aminochalcone-based compounds showed mild toxicity toward a normal embryonic lung cell line (MRC-5) and a human neuroblastoma cell line, and were predicted to have preferable pharmacokinetic profiles with potential for oral administration. Molecular docking simulation indicated that the studied aminochalcones may act as competitive activators of the well-known protective protein, SIRT1, and provided beneficial knowledge regarding the essential key chemical moieties and interacting amino acid residues. Collectively, this work provides a series of four promising candidate agents that could be developed for neuroprotection.

Genome-wide study of Cerrena unicolor 87613 laccase gene family and their mode prediction in association with substrate oxidation

BackgroundLaccases are green biocatalysts with wide industrial applications. The study of efficient and specific laccase producers remains a priority. Cerrena species have been shown to be promising basidiomycete candidates for laccase production. Although two sets of Cerrena genome data have been publicly published, no comprehensive bioinformatics study of laccase gene family in C. unicolor has been reported, particularly concerning the analysis of their three-dimensional (3D) structures and molecular docking to substrates, like ABTS and aflatoxin B1 (AFB1).ResultsIn this study, we conducted a comprehensive genome-wide analysis of laccase gene family in C. unicolor 87613. We identified eighteen laccase genes (CuLacs) and classified them into three clades using phylogenetic analysis. We characterized these laccases, including their location in contig 5,6,9,12,15,19,26,27, gene structures of different exon-intron arrangements, molecular weight ranging from 47.89 to 141.41 kDa, acidic pI value, 5–15 conserved protein motifs, signaling peptide of extracellular secretion (harbored by 13 CuLacs) and others. In addition, the analysis of cis-acting element in laccase promoters indicated that the transcription response of CuLac gene family was regulatable and complex under different environmental cues. Furthermore, analysis of transcription pattern revealed that CuLac8, 12 and CuLac2, 13 were the predominant laccases in response to copper ions or oxidative stress, respectively. Finally, we focused on the 3D structure analysis of CuLac proteins. Seven laccases with extra transmembrane domains or special sequences were particularly interesting. Predicted structures of each CuLac protein with or without these extra sequences showed altered interacting amino acid residues and binding sites, leading to varied affinities to both ABTS and AFB1. As far as we know, it is the first time to discuss the influence of the extra sequence on laccase’s affinity to substrates.ConclusionsOur findings provide robust genetic data for a better understanding of the laccase gene family in C. unicolor 87613, and create a foundation for the molecular redesign of CuLac proteins to enhance their industrial applications.

In silico analysis of Diosmetin as an effective chemopreventive agent against prostate cancer: molecular docking, validation, dynamic simulation and pharmacokinetic prediction-based studies

Prostate cancer is the second most dangerous cancer type worldwide. While various treatment options are present i.e. agonists and antagonists, their utilization leads to adverse effects and due to this resistance developing, ultimately the outcome is remission. So, to overcome this issue, we have undertaken an in-silico investigation to identify promising and unique flavonoid candidates for combating prostate cancer. Using GOLD software, the study assessed the effectiveness of 560 natural secondary polyphenols against CDKN2. Protein Data Bank was used to retrieve the 3D crystal structure of CDKN2 (PDB Id: 4EK3) and we retrieved the structure of selected secondary polyphenols from the PubChem database. The compound Diosmetin shows the highest GOLD score with the selected Protein i.e. CDKN2 which is 58.72. To better understand the 2-dimensional and 3-dimensional interactions, the interacting amino acid residues were visualised using Discovery Studio 3.5 and Maestro 13.5. Using Schrodinger-Glide, the Diosmetin and CDKN2 were re-docked, and decoy ligands were docked to CDKN2, which was used to further ascertain the study. The ligands with the highest Gold score were forecasted for pharmacokinetics characteristics, and the results were tabulated and analysed. Utilising the Gromacs software and Desmond packages, 100 ns of Diosmetin molecular dynamics simulations were run to evaluate the structural persistence and variations of protein-ligand complexes. Additionally, our investigation revealed that Diosmetin had a better binding affinity with CDKN2 measuring 58.72, and it also showed remarkable stability across a 100-ns simulation. Thus, following in-vitro and in-vivo clinical studies, diosmetin might lead to the Prostate regimen. Communicated by Ramaswamy H. Sarma

Simulated Docking of alpha-Conotoxin Interactions with Nicotinic Acetylcholine Receptors

The nicotinic acetylcholine receptors (nAChRs) are linked to several biological processes and neurological conditions. The α-conotoxins represent an essential resource for ligands with which to explore structure-function correlations for a variety of nAChR subtypes. With the multitude of nAChR subtypes occurring in vivo, it is imperative to search for subtype-selective ligands to effectively utilize their modulatory functions for their target receptors. In this work,docking simulations using PatchDock showed that either the replacement of Ala10 with the more hydrophobic Leu in PnIA to PnIA[A10L] or the presence of a sulfated tyrosine in the structural scaffold of PnIA[Y15Y] or PnIB[Y15Y] (Y stands for sulfated tyrosine) is sufficient to alter the interactions of α-conotoxins PnIA and PnIB for their target nAChR receptor subtypes – α7and α3β2. The employed protocol can be utilized to screen for ligand docking and amino acid residue interactions of α-conotoxins to certain nAChR subtypes. This was tested on α-conotoxinLoIA, which was predicted to preferentially bind to the α3β2 nAChR over α7 nAChR. The present work is supportive of the idea that the conserved α-conotoxin structural scaffold can be further investigated to guide the synthesis of novel nAChR ligands with greater specificity.The results of this study will be useful in the rational design of selective nAChR antagonists for potential peptide therapeutics.

Molecular docking analysis of MCL-1 inhibitors for breast cancer management.

Myeloid leukemia 1 (MCL-1), a BCL-2 protein family member, acts as an anti-apoptotic protein by interacting with pro-apoptotic BCL-2 proteins. Its overexpression is frequently observed in numerous cancer types including breast cancer, and is closely linked to the initiation and progression of tumors as well as poor prognosis and resistance to therapeutic interventions. Here, a database of 3402 chemicals with established therapeutic activity against various diseases was chosen and systematically screened against the MCL-1 protein. Visual inspection and binding energy analysis revealed that the compounds OSU-03012, Raltitrexed, Ostarine (MK-2866), Dovitinib (TKI-258), and Varespladib (LY315920) had strong binding affinity for the MCL-1 protein. Notably, their binding affinity was higher than that of the control compounds. These compounds exhibited strong interactions with critical amino acid residues of the MCL-1 protein. Furthermore, these compounds shared several common amino acid residue interactions with the control compounds. These findings suggest that these compounds may be useful as MCL-1 inhibitors in the treatment of breast cancer. However, additional experimental validation is required to confirm these findings.

Detection of Nonsynonymous Single Variants in Human HLA-DRB1 Exon 2 Associated with Renal Transplant Rejection.

Background: HLA-DRB1 is the most polymorphic gene in the human leukocyte antigen (HLA) class II, and exon 2 is critical because it encodes antigen-binding sites. This study aimed to detect functional or marker genetic variants of HLA-DRB1 exon 2 in renal transplant recipients (acceptance and rejection) using Sanger sequencing. Methods: This hospital-based case-control study collected samples from two hospitals over seven months. The 60 participants were equally divided into three groups: rejection, acceptance, and control. The target regions were amplified and sequenced by PCR and Sanger sequencing. Several bioinformatics tools have been used to assess the impact of non-synonymous single-nucleotide variants (nsSNVs) on protein function and structure. The sequences data that support the findings of this study with accession numbers (OQ747803-OQ747862) are available in National Center for Biotechnology Information (GenBank database). Results: Seven SNVs were identified, two of which were novel (chr6(GRCh38.p12): 32584356C>A (K41N) and 32584113C>A (R122R)). Three of the seven SNVs were non-synonymous and found in the rejection group (chr6(GRCh38.p12): 32584356C>A (K41N), 32584304A>G (Y59H), and 32584152T>A (R109S)). The nsSNVs had varying effects on protein function, structure, and physicochemical parameters and could play a role in renal transplant rejection. The chr6(GRCh38.p12):32584152T>A variant showed the greatest impact. This is because of its conserved nature, main domain location, and pathogenic effects on protein structure, function, and stability. Finally, no significant markers were identified in the acceptance samples. Conclusion: Pathogenic variants can affect intramolecular/intermolecular interactions of amino acid residues, protein function/structure, and disease risk. HLA typing based on functional SNVs could be a comprehensive, accurate, and low-cost method for covering all HLA genes while shedding light on previously unknown causes in many graft rejection cases.

Molecular docking analysis of PPARγ antagonists for obesity associated diabetes management.

Obesity is a major metabolic disorder in developed countries, with an increasing number of people affected globally. PPARγ is primarily expressed in adipose tissue with a lesser extent in other tissues. PPARγ is an important mediator in several metabolic processes such as insulin sensitivity and adipogenesis. Because of its critical role in these processes, PPARγ is regarded as a critical target for therapeutic intervention in obesity treatment. A library of 2,320 bioactive compounds was screened insilico to identify compounds that strongly interact with the PPARγ protein. The compounds Z1982689600, Z2235802137, Z2235801970, and Z2037275165, demonstrated notable binding affinity values towards the PPARγ protein with values of -12.1, -11.7, -11.4, and -11.4 kcal/mol, respectively, which were higher than the binding affinity value observed for the control compound (-10.5 kcal/mol). These compounds bind tightly to PPARγ and have several amino acid residue interactions in common with the control compound. In addition, these compounds meet the ADMET criteria. These compounds could aid in the development of PPARγ antagonists for the management of obesity associated diabetes. However, additional research is needed to optimize their efficacy in wet laboratory conditions.

PENAMBATAN MOLEKUL SIANIDIN Ipomoea batatas L. SEBAGAI INHIBITOR HUMAN EPIDERMAL RECEPTOR 2 (HER-2) PADA KANKER PAYUDARA

HER-2 (Human Epidermal Receptor 2) is a receptor on the cell surface that affects cell proliferation, this receptor support controls healthy cell growth,divide and repair cells when they are damaged. When HER-2 had overexpressed will not controlled cancer cell division. Overexpressed HER-2 could inhibited with cyanidine compound flavonoid derivatives from Ipomoea batatas L. (purple sweet potato). This study aim to measured potential of Ipomoea batatas L. cyanidin compounds in inhibited overexpressed HER-2 using computational chemistry methods specifically is molecular docking. Stages of molecular docking receptor HER-2 is ligand set up with drew structure cyanidine with Marvin Sketch then optimized by Autodock Tools and Discovery Studio, lapatinib as a comparison ligand downloaded on PubChem website. HER-2 (3PP0) prepared with downloaded on Protein Data Bank website then optimized by Autodock Tools. Molecular Docking validated with docked protein target with native ligand by PyMOL to secured RMSD (root mean square deviation). Protein Targeted HER-2 docked with test ligand cyanidine, lapatinib, and native ligand by Autodock VINA, analysed energy bond and amino acid residue interactions by LigPlot+. Cyanidine had potency inhibitor of receptor HER-2 overexpressed from docked is had bound energy -7.1 ccal/mol up to -8.6 ccal/mol wich is also had amino acid residue interactions Met 801 equal to native ligand

Screening, characterization of trace α-glucosidase inhibitors from the root of Pueraria lobata and evaluation of their hypoglycemic activity

Pueraria lobata (Willd.) Ohwi (Gegen) is a nutritious medicine food homology plant that has been recorded in many ancient remedies for diabetes. However, its hypoglycemic active components and related mechanisms have not been fully elucidated. In this study, potential α-glucosidase inhibitors in Pueraria lobata were investigated by liquid-liquid refined extraction, high-resolution profiling and their hypoglycemic activity were evaluated. Ten compounds showing α-glucosidase inhibitory bioactivity were separated and identified, including two new compounds, 8-geranyl-7, 3′, 4′-trihydroxy-isoflavone (4) and 8-geranyl-7, 2′, 4′-trihydroxy-isoflavone (6), and eight known compounds. All screened compounds showed potential hypoglycemic activity, in which compounds 4, 6, 7, 8, 9 and 10 showed strong inhibitory activity (IC50 < 8 μM). Furthermore, molecular docking simulation revealed binding energy and interacting amino acid residues of the screened compounds with α-glucosidase, strongly supporting their potential as α-glucosidase inhibitors.

Structural Basis of Dual Specificity of Sinorhizobium meliloti Clr, a cAMP and cGMP Receptor Protein.

In bacteria, the most prevalent receptor proteins of 3',5'-cyclic AMP (cAMP) and 3',5'-cyclic GMP (cGMP) are found among transcription factors of the Crp-Fnr superfamily. The prototypic Escherichia coli catabolite activator protein (CAP) represents the main Crp cluster of this superfamily and is known to bind cAMP and cGMP but to mediate transcription activation only in its cAMP-bound state. In contrast, both cyclic nucleotides mediate transcription activation by Sinorhizobium meliloti Clr, mapping to cluster G of Crp-like proteins. We present crystal structures of Clr-cAMP and Clr-cGMP bound to the core motif of the palindromic Clr DNA binding site (CBS). We show that both cyclic nucleotides shift ternary Clr-cNMP-CBS-DNA complexes (where cNMP is cyclic nucleotide monophosphate) to almost identical active conformations, unlike the situation known for the E. coli CAP-cNMP complex. Isothermal titration calorimetry measured similar affinities of cAMP and cGMP binding to Clr in the presence of CBS core motif DNA (equilibrium dissociation constant for cNMP (KDcNMP], ~7 to 11 μM). However, different affinities were determined in the absence of this DNA (KDcGMP, ~24 μM; KDcAMP, ~6 μM). Sequencing of Clr-coimmunoprecipitated DNA as well as electrophoretic mobility shift and promoter-probe assays expanded the list of experimentally proven Clr-regulated promoters and CBS. This comprehensive set of CBS features conserved nucleobases that are consistent with the sequence readout through interactions of Clr amino acid residues with these nucleobases, as revealed by the Clr-cNMP-CBS-DNA crystal structures. IMPORTANCE Cyclic 3',5'-AMP (cAMP) and cyclic 3',5'-GMP (cGMP) are both long known as important nucleotide secondary messengers in eukaryotes. This is also the case for cAMP in prokaryotes, whereas a signaling role for cGMP in this domain of life has been recognized only recently. Catabolite repressor proteins (CRPs) are the most ubiquitous bacterial cAMP receptor proteins. Escherichia coli CAP, the prototypic transcription regulator of the main Crp cluster, binds both cyclic mononucleotides, but only the CAP-cAMP complex promotes transcription activation. In contrast, Crp cluster G proteins studied so far are activated by cGMP or by both cAMP and cGMP. Here, we report a structural analysis of the cAMP- and cGMP-activatable cluster G member Clr from Sinorhizobium meliloti, how binding of cAMP and cGMP shifts Clr to its active conformation, and the structural basis of its DNA binding site specificity.