Structure Of Target Protein Research Articles

Antiviral potential of some novel structural analogs of standard drugs repurposed for the treatment of COVID-19

SARS-CoV-2 pandemic has claimed millions of lives across the world. As of June 2020, there is no FDA approved antiviral therapy to eradicate this dreadful virus. In this study, drug re-purposing and computational approaches were employed to identify high affinity inhibitors of SARS-CoV-2 Main protease (3CLpro), Papain-like protease (PLpro) and the receptor domain of Spike protein. Molecular docking on 40 derivatives of standard drugs (Remdesivir, Lopinavir and Theophylline) led to the identification of R10, R2 and L9 as potential inhibitors of 3CLpro, PLpro and Spike protein, respectively. The binding affinity of R10, R2 and L9 towards 3CLpro, PLpro and Spike protein were 4.03 × 106, 3.72 × 104 and 1.31 × 104 M −1, respectively. These inhibitors interact with the active site or catalytic amino acid residues of 3CLpro, PLpro and Spike protein. We also examined the stability and dynamic behavior of protein-inhibitor complex by employing molecular dynamics simulation. RMSDs, RMSFs and variation in secondary structure of target proteins alone or in complex with their respective inhibitors were used to ascertain the integrity of proteins’ structure during simulation. Moreover, physicochemical and ADMET properties of R10, R2 and L9 along with Remdesivir, Lopinavir and Theophylline were determined. In vitro and In vivo studies are needed to further validate the potential of these derivatives before they can be developed into potential drug molecules. Communicated by Ramaswamy H. Sarma

Research progress on repositioning drugs and specific therapeutic drugs for SARS-CoV-2.

SARS-CoV-2 has been widely spread around the world and COVID-19 was declared a global pandemic by the World Health Organization. Limited clinically effective antiviral drugs are available now. The development of anti-SARS-CoV-2 drugs has become an urgent work worldwide. At present, potential therapeutic targets and drugs for SARS-CoV-2 are continuously reported, and many repositioning drugs are undergoing extensive clinical research, including remdesivir and chloroquine. On the other hand, structures of many important viral target proteins and host target proteins, including that of RdRp and Mpro were constantly reported, which greatly promoted structure-based drug design. This paper summarizes the current research progress and challenges in the development of anti-SARS-CoV-2 drugs, and proposes novel short-term and long-term drug research strategies.

Reckoning a fungal metabolite, Pyranonigrin A as a potential Main protease (Mpro) inhibitor of novel SARS-CoV-2 virus identified using docking and molecular dynamics simulation

The novel SARS-CoV-2 is the etiological agent causing the Coronavirus disease 2019 (COVID-19), which continues to become an inevitable pandemic outbreak. Over a short span of time, the structures of therapeutic target proteins for SARS-CoV-2 were identified based on the homology modelled structure of similar SARS-CoV transmission of 2003. Since the onset of the disease, the research community has been looking for a potential drug lead. Out of all the known resolved structures related to SARS-CoV, Main protease (Mpro) is considered an attractive anti-viral drug target on the grounds of its role in viral replication and probable non-interactive competency to bind to any viral host protein. To the best of our knowledge, till date only one compound has been identified and tested in-vivo as a potent inhibitor of Mpro protein, addressed as N3 (PubChem Compound CID: 6323191) and is known to bind irreversibly to Mpro suppressing its activity. Using computational approach, we intend to identify a probable natural fungal metabolite to interact and inhibit Mpro. After screening various small molecules for molecular docking and dynamics simulation, we propose Pyranonigrin A, a secondary fungal metabolite to possess potent inhibitory potential against the Main protease (Mpro) expressed in SARS-CoV-2 virus.

Pemodelan Homologi Komparatif Struktur 3d Protein dalam Desain dan Pengembangan Obat

One of the strategies applied in the initial steps of drug design and discovery is by utilizing the availability of 3D protein structures. However, most of functional protein structures have not been fully obtained experimentally to date. This is due to the difficulty of procedures, the high cost and the length of time required from structural biology experiments such as X-ray crystallography. Comparative homology modeling is a computational method that is proven to be accurate in predicting the structure of 3D target proteins with a ratio of 30% similarity to the arrangement of amino acids in the structure of the template proteins. This review attempts to explain comparative homology modeling methods such as MODELLER, PHYRE2, SWISS-MODEL, its iterative steps in predicting and building 3D protein target models, its evaluation and validation of protein models as well as the examples of their application in drug design and development targeting GPCR proteins, Zika virus RNA polymerase and HIV protease. With this, comparative homology modeling can be very useful to accelerate research on drug design and development in dealing with diseases and health problems that still exist in the society.

Structure Based Drug Design and Molecular Docking Studies of Anticancer Molecules Paclitaxel, Etoposide and Topotecan using Novel Ligands.

Tubulin is the biochemical target for several clinically used anticancer drugs as it helps in the formation of mitotic spindle during mitosis stage of cell division. Many of the anti-cancer drugs are known to interact with tubulin and microtubules including some plant alkaloids, such as paclitaxel, etoposide and topotecan. In silico drug design of these molecules were performed prior to testing these drugs in vitro. In silico drug design of these anti-cancer drugs becomes a challenge due to the complex structure of target protein. This challenge was overcome by predicting the structure of the target protein (tubulin) by homology modeling. In this study, computer aided drug designing approach was applied to predict the suitable docking site in target protein and the interaction of tubulin protein with paclitaxel, etoposide and topotecan was explored by molecular docking using Schrödinger software. Docking score and glide energy were determined with ligands to validate their anticancer properties. The results indicate that etoposide is the best drug for tubulin with a docking score of - 4.916 and glide energy of -46.470 kcal/mol compared to paclitaxel and topotecan. The testing of these drugs in silico provides an alternate to in vitro testing of these molecules on cancer cell lines which is a time and cost intensive process. The in silico study of parameters, such as docking score and glide energy, will help pharmacists in developing new molecules as targets for cancers in a time and cost-effective manner.

Dysregulated hydrogen sulfide metabolism links aberrant neuronal stress responses and neurodegeneration in Huntington's disease

Hydrogen sulfide (H2S) is a gaseous signaling molecule that plays central roles in a myriad of physiological processes ranging from response to oxidative stress and transcriptional regulation. Hydrogen sulfide is synthesized endogenously from the semi‐essential amino acid cysteine via the reverse transsulfuration pathway. Thus disrupted cysteine metabolism may also lead to aberrant H2S signaling. One of the modes by which hydrogen sulfide signals is by a posttranslational modification designated as sulfhydration/persulfidation, which occurs on reactive cysteine residues on target proteins, where the reactive SH group is converted to an SSH group. Sulfhydration is a highly prevalent modification which modifies the structure and/or activity of target proteins. Research on H2S and persulfidation is still in its infancy. We show here that H2S is generated in response to stress stimuli such as Golgi stress and oxidative stress in neurons, which modulates sulfhydration levels to modulate signaling pathways. We further show that these cytoprotective stress responses are compromised in striatal cell culture model and the R6/2 and Q175 mouse models of Huntington’s disease (HD). We have shown previously that the biosynthetic enzyme for cysteine and H2S in neurons, cystathionine g‐lyase (CSE) is depleted in HD and mediates neurodegeneraton. HD is a neurodegenerative disease which is triggered by expansion of polyglutamine repeats in the protein huntingtin, which causes it to aggregate and elicit multi‐system toxicity. Restoring H2S balance in cells mitigates neuronal dysfunction in neurodegenerative diseases such as HD. A screen for regulators of the transsulfuration pathway has resulted in identification of compounds that modulate cysteine balance and disease progression in HD.Support or Funding InformationUnited States Public Health Service (USPHS) grants DA000266 and MH18501 to S.H.S.

Role of Rhodopsin in Retinitis Pigmentosa

The ability of vertebrates, including humans, to see light relies on a visual transduction cascade in which rhodopsin’s ability to stimulate the nervous system plays a central role. Rhodopsin is a 348 amino acid protein composed of seven transmembrane alpha helices located within the rod photoreceptor cells of the retina. Rhodopsin is a member of the much broader protein superfamily, the G‐protein coupled receptors (GPCRs). GPCRs are cell surface signaling receptors that convert extracellular signals into intracellular signaling pathways through the activation of G proteins. There are about 800 different human GPCRs and members of this superfamily are responsible for our sense of smell, taste, and vision. The “wild type” rhodopsin uses its retinal pigment, a derivative of vitamin A, in conjunction with its G protein partner, transducin, to detect light, particularly in night vision. Retinal serves as the “cofactor” of rhodopsin that directly absorbs a photon, causing its isomerization and a change in the structure of rhodopsin that is sensed by transducin, leading to an intracellular signaling cascade that results in a signal being sent through the optic nerve to the brain that light has been detected. Any one of over 150 rhodopsin mutations already documented in humans are known to result in loss of rhodopsin’s light‐sensing function, leading to Retinitis Pigmentosa (RP). RP is a rare, slow, progressive, genetic disease which damages the retina leading to loss of vision, particularly among young adults. The most common cause of RP is a mutation‐induced misfolding of rhodopsin. The many forms of proposed treatment of RP are largely focused on improving folding of rhodopsin and inducing proteostasis, the process in the cell that promotes correct folding and quantities of proteins. Pharmacological chaperones, such as retinoids or non‐isomerrizable retinoid analogues directly target protein structure and have produced lab results that show enhanced folding and protection of other cells from the effects of mutated rhodopsin. However, replicating this in living organisms has not been possible yet. Nutritional supplements, histone deacetylase inhibitors, such as Valproate, and molecular chaperone inducers have also been tested, but only produce laboratory results that positively affect only a few aspects of mutated rhodopsin and have not yet yielded promising results in humans. Seemingly, the most promising forms of treatment for RP and rhodopsin mutations are gene therapy and CRISPR Cas‐9 genome editing to correct the genetic defects that underlie RP. However, whether any of these approaches will eventually form the basis for effective treatment or cure of RP is not yet known. The Walton High School MSOE Center for Biomolecular Modeling SMART Team has designed a 3‐D model of rhodopsin to further investigate and examine the structure‐function relationship of the protein.Support or Funding InformationMSOE Center for Biomolecular Modeling

Network Biology Approaches to Identify the Drug Lead Molecule for Neurodevelopmental Disorders in Human

Aims: To identify most novel drug target and lead molecule for neurodevelopmental disorder Autism, Intellectual Disability (ID) and Attention Deficit Hyperactivity Disorder (ADHD) diseases through system biology approaches Background: Neurodevelopmental disorders (NNDs) are disabilities associated chiefly with the functioning of the neurological system and brain. Children with neurodevelopmental disorders have difficulties with speech, behaviour, learning and other neurological functions. Systems biology is a holistic approach to enciphering the complexity of biological systems and their interactions. It opens the way to a more successful discovery of novel therapeutics. Objective: To identify most novel drug target and lead molecule for neurodevelopmental disorder Autism, Intellectual Disability (ID) and Attention Deficit Hyperactivity Disorder (ADHD) diseases through system biology approaches. Methods: A list of genes was collected from NCBI database for Autism, Intellectual Disability (ID) and Attention Deficit Hyperactivity Disorder (ADHD) diseases. STRING database and Cytoscape software was used for construction and interpreting molecular interaction in the network. 3D structure of target protein, was build and validated.The phytochemicals were identified through various research articles and filtered out by virtual screening through Molinspiration. Molecular docking analyses of known phytochemical with target proteins were performed usingAutoDock tool. Result: AKT1 for Autism, SNAP25 for Intellectual Disability (ID) and DRD4 for Attention Deficit Hyperactivity Disorder (ADHD) were identified as most potential drug target through network study. further the modelled structure of obtained target were undergo molecular docking study with kown phytochemicals. Based on lowest binding energy, Huperzine A for Autism and ID, Valerenic acid for ADHD found to be the most potential therapeutic molecules. Conclusion: Huperzine A against Autism and ID, Valerenic acid against ADHD found to be the most potential therapeutic molecules and expected to be effective in the treatment of NNDs. Phytochemicals do not have side effects so extract of these can be taken in preventive form too as these disorders occur during developmental stages of the child. Further the obtained molecule if experimentally validated would play promising role for the treatment of NDDs in human.

Study of the mechanism of antibacterial action of 1,4-di- and 1,4,5-trisubstituted 1Н-1,2,3-triazoles by molecular modeling

The target for antibacterial action of 1,4-di- and 1,4,5-trisubstituted 1H-1,2,3-triazoles against E. coli ATCC 25922 and S. aureus ATCC 6538 was proposed. Structures of target proteins and investigated triazoles were built using molecular modeling. Binding mechanism was suggested according to conducted docking studies. Suggested binding models and affinity for a binding site of 1,4-disubstituted 1H-1,2,3-triazoles correlated with their experimental activity. Further functionalization directions for continuation of a search for a novel effective antibacterial agents were discovered.

Identification and In-silico Prediction of Hermetiaillucens Larval Protein that Inhibits the Progression of Cervical Cancer

The aim of the current research is to assess the anticancer activity of the proteins identified from the crude protein extract derived from Hermetiaillucens larvae by computational methods. Bioinformatics methods were used to identify the protein sequence and virtual screening for the prediction of protein structure, their physico-chemical characteristics and functional aspects, that aid in exploring the anti-cancer interaction that is inclined to inhibit the oncoprotein activity. Due to the pathological process transpired by HPV, an array of genetic alterations, including the overexpression of oncoproteins or the inactivation of tumor suppressor proteins like TP53, BCL2, MDM2, ARF and BAX occur. The altered protein signaling pathways convulse to cervical cancer. In this research, we identified proteins, from the crude extract derived from Hermetiaillucens by LC-MS method. Further Computational screening of the selected proteins were employed to assess the functional units which has anticancer activity. We predicted four proteins Metallothionine, Defensin like precursor 1 protein, Heat shock protein 90 and NADH dehydrogenase and eluted the protein sequence from NCBI GenBank database. These sequences were used to predict physicochemical properties and protein structure prediction. Pharmacophore analysis of the peptide sequences as potential targets for cancer treatment was evaluated. Molecular docking of peptide sequences with target protein structure was carried out. To screen the best active potential molecule for cancer treatment the Molecular dynamics of docked protein-peptide structures were administered. The molecular docking of the peptides with onco-proteins has been predicted and virtually screened based on RMSD values. The resultant protein sequence was evaluated further by amino acid sequencing, extensive scrutiny of the proteins, advanced computational imaging, molecular docking examination and assessed the results for clinical interpretation. To summate, bioinformatics assessment enabled us to identify four key proteins derived from Hermetiaillucens larvae that have strong inhibitory function against proteins that cause cervical cancer.

User guide for the discovery of potential drugs via protein structure prediction and ligand docking simulation.

Due to accumulating protein structure information and advances in computational methodologies, it has now become possible to predict protein-compound interactions. In biology, the classic strategy for drug discovery has been to manually screen multiple compounds (small scale) to identify potential drug compounds. Recent strategies have utilized computational drug discovery methods that involve predicting target protein structures, identifying active sites, and finding potential inhibitor compounds at large scale. In this protocol article, we introduce an in silico drug discovery protocol. Since multi-drug resistance of pathogenic bacteria remains a challenging problem to address, UDP-N-acetylmuramate-L-alanine ligase (murC) of Acinetobacter baumannii was used as an example, which causes nosocomial infection in hospital setups and is responsible for high mortality worldwide. This protocol should help microbiologists to expand their knowledge and research scope.

SOLATION, CHARACTERIZATION, AND DOCKING STUDIES OF ISOLATED COMPOUNDS AS ANTIDIABETIC MOLECULES FROM CRESSA CRETICA

Objective: The purpose of this study was to investigate the diabetic effect of phytocompounds isolated from Cressa cretica Linn. using spectroscopic analysis and molecular docking studies.
 Methods: Coarse powder of the whole plant of C. cretica was extracted with methanol, extracted part was subjected to silica column isolation, and two compounds: 2-Isopropyl-4-(1-methyl-dodeca-2,4-dienyloxy)-benzene-1,3,5-triol (Compound CN-01) and 11-Methyl-dodeca-2,4,6,8,10-pentenoic acid 2,3-dihydroxy-5-methyl-phenyl ester (Compound CN-02) were isolated in pure form. The three-dimensional structure of target protein was downloaded from PDB (www.rcsb.org) Protein Data Bank, Ligand file CN – 01 and CN – 02 were converted to MDL Molfile (V2000) format using ChemSketch 2017.2.1. These files could not be used directly in AutoDock 4.0 tools; thus, they were first converted to PDB files using an open babel tool.
 Results: Compounds were revealed through spectroscopic analysis and screened using AutoDock 4.0 tools. Docking study recommended that CN – 01 and CN – 02 an existing phytochemical from the plant of C. cretica had the highest fitness docking score and hence could be a potent antidiabetic drug.
 Conclusion: In this investigation, we docked the receptor (glycogen phosphorylase protein) holds a promising lead target formation against diabetes based on molecular docking analysis (minimum hydrogen bond length and maximum docked score). Thus, these compounds can be effectively used as drugs for treating diabetes which is predicted on the basis of docking scores.

Frankincense essential oil extraction and lead compound analysis into cancer cells using molecular docking

Oil was extracted from Frankincense (Boswellia Sacra) by the soxhlet extraction method and various bioactive compounds were identified using gas chromatography (GC).These compounds can be developed as active pharmacophores.The present study involves the extraction and identification of bioactive compounds and their in-vitro study on the interaction of these compounds to target proteins. Frankincense oil collected from Boswelia Sacra species was subjected to Soxhlet extraction using Hexane solvent and essential oil (EO) was separated using vacuum distillation. Chemical profiling of essential oil was done using GC-MS. Various biological databases like PubChem, Protein Data Bank and software like Argus Lab, Rasmol were used to retrieve and analyze the structural and molecular interactions of bioactive compounds from Frankincense oil with receptor proteins. The target protein structure was retrieved from Protein data bank ligand structures that were downloaded from Pubchem, which was visualized using Rasmol Software. Protein-ligand interaction was studied using Argus Lab software by docking simulations and various docking poses were analyzed.The energy values of docking conformations were analyzed for obtaining the best docking pose & score.

Design and synthesis of anti-convulsant and anti-bacterial activity of new hydrazone derivatives

Synthesis of new hydrazone derivatives, starting from 2-(3, 4-Dichloro-benzoyl)-benzoic acid to 2-(3, 4-dichloro-benzoyl) - benzoic acid ethyl ester than converted into 2- (3, 4-Dichloro-benzoyl)-benzoic acid hydrazide with a substituted aldehyde. The structure of newly synthesized compounds was confirmed by analytical and spectral analysis IR, 1HNMR and MASS. For docking study, we took structures of ligand compounds (i.e. AK-series Compounds) and target protein structures into ‘pdb’ file format. Three compounds as possible anti-convulsant AK-1, AK-2 &Ak-4 were considered for compounds Ak-1 was not found suitable for anti-convulsant activity; while AK-2 & AK-4 have the capacity to show anti-convulsant activity with lesser affinity than controls. As an overall conclusion, except Ak-1, other compounds can be further used for anti- convulsant activity. Anti-convulsant activities were performed on rats by using maximal Electroshock Seizure test and minimal Neurotoxicity. Compound 2- (3, 4 – Dichloro-benzoyl)-benzoic acid (4- chloro-benzylidene) (AK-2) shows good anti-convulsant activity. The in-vitro antibacterial strains Escherichia coli MTCC 1573), and staphylococcus aureus (MTCC 1430), were used. Compound 2-(3, 4-Dichloro-benzoyl)-benzoic acid (2-notro-benzylidene-hydrazide (AK-1) gives the highest activity against Escherichia coli (MTCC 1573) and Staphylococcus aureus (MTCC-1430).

Mechanisms Inspired Targeting Peptides.

Peptides, as a large group of molecules, are composed of amino acid residues and can be divided into linear or cyclic peptides according to the structure. Over 13,000 molecules of natural peptides have been found and many of them have been well studied. In artificial peptide libraries, the number of peptide diversity could be up to 1 × 1013. Peptides have more complex structures and higher affinity to target proteins comparing with small molecular compounds. Recently, the development of targeting cancer immune checkpoint (CIP) inhibitors is having a very important role in tumor therapy. Peptides targeting ligands or receptors in CIP have been designed based on three-dimensional structures of target proteins or directly selected by random peptide libraries in biological display systems. Most of these targeting peptides work as inhibitors of protein-protein interaction and improve CD8+ cytotoxic T-lymphocyte (CTL) activation in the tumor microenvironment, for example, PKHB1, Ar5Y4 and TPP1. Peptides could be designed to regulate CIP protein degradation in vivo, such as PD-LYSO and PD-PALM. Besides its use in developing therapeutic drugs for targeting CIP, targeting peptides could be used in drug's targeted delivery and diagnosis in tumor immune therapy.

A De-Novo drug design and ADMET study to design small molecule stabilisers targeting mutant (V210I) human prion protein against familial Creutzfeldt-Jakob disease (fCJD)

The purpose of our project was to computationally design small molecule stabilisers targeting mutant (V210I) human prion protein (HuPrP) using combined De-novo pharmacophore based drug design and virtual molecular docking. The newly designed molecules were also analysed so it might qualify as a new cure for the familial Creutzfeldt-Jakob disease (fCJD). We collected the target protein structure from protein data bank (RCSB PDB). and minimised the energy using Yasara energy minimisation webserver and validated the structure using RAMPAGE webserver. We used KV Finder, a plug-in of Pymol to identify the drug binding pockets in the target protein. The pocket information was used for de-novo ligand design using the e-LEA3D webserver. Those ligands were used to generate a pharmacophore using LigandScout for the selected pockets. The pharmacophores were used as the search templates using Pharmit for the virtual screening of small molecules from Pubchem database followed by the docking of the screened small molecules in the pockets using Autodock Vina. Best five molecules were selected for ADMET properties using SwissADME. All the five small molecules were proven to be the ideal candidates for further drug development.

A De-Novo drug design and ADMET study to design small molecule stabilisers targeting mutant (V210I) human prion protein against familial Creutzfeldt-Jakob disease (fCJD)

The purpose of our project was to computationally design small molecule stabilisers targeting mutant (V210I) human prion protein (HuPrP) using combined De-novo pharmacophore based drug design and virtual molecular docking. The newly designed molecules were also analysed so it might qualify as a new cure for the familial Creutzfeldt-Jakob disease (fCJD). We collected the target protein structure from protein data bank (RCSB PDB). and minimised the energy using Yasara energy minimisation webserver and validated the structure using RAMPAGE webserver. We used KV Finder, a plug-in of Pymol to identify the drug binding pockets in the target protein. The pocket information was used for de-novo ligand design using the e-LEA3D webserver. Those ligands were used to generate a pharmacophore using LigandScout for the selected pockets. The pharmacophores were used as the search templates using Pharmit for the virtual screening of small molecules from Pubchem database followed by the docking of the screened small molecules in the pockets using Autodock Vina. Best five molecules were selected for ADMET properties using SwissADME. All the five small molecules were proven to be the ideal candidates for further drug development.

Glutamine-walking: Creating reactive substrates for transglutaminase-mediated protein labeling.

Chemically modified proteins are increasingly being tested and approved as therapeutic products. Batch-to-batch homogeneity is crucial to ensure safety and quality of therapeutic products. Highly selective protein modification may be achieved using enzymatic routes. Microbial transglutaminase (mTG) is a robust, easy to use and well-established enzyme that is used at a very large scale in the food industry such that its efficacy and its safety for human consumption are well established. In the context of therapeutic protein modification, mTG should crosslink one or more glutamines on the target protein with an aminated moiety such as a solubilizer, a tracer or a cytotoxic moiety. mTG has the advantage of being unreactive toward the majority of surface-exposed glutamines on most proteins, reducing sample heterogeneity. The caveat is that there may be no reactive glutamine on the target protein, or else a reactive glutamine may be found in a location where its modification compromises function of the target protein. Here we describe the glutamine-walk (Gln-walk), a straightforward method to create a glutamine-substrate site that is reactive to mTG in a target protein. Iterative substitution of single amino acids to a glutamine is followed by facile identification of reactivity with mTG, where covalent labeling of the target with an aminated fluorophore allows visualization of the most reactive modified targets. The approach is empirical; knowledge of the target protein structure and functional regions facilitates application of the method.

Preparation and Characterisation of Polyphenol-HP-β-Cyclodextrin Inclusion Complex that Protects Lamb Tripe Protein against Oxidation.

Grape seed extract (GSE) displays strong antioxidant activity, but its instability creates barriers to its applications. Herein, three HP-β-CD/GSE inclusion complexes with host–guest ratios of 1:0.5, 1:1, and 1:2 were successfully prepared by co-precipitation method to improve stability. Successful embedding of GSE in the HP-β-CD cavity was confirmed by fourier-transform infrared spectroscopy (FTIR), X-ray diffraction (XRD), differential scanning calorimetry (DSC), and scanning electron microscopy (SEM) analyses. The Autodock Tools 1.5.6 was used to simulate the three-dimensional supramolecular structure of the inclusion complex of 2-hydroxypropyl-β-cyclodextrin and grape seed extract (HP-β-CD/GSE) by molecular docking. The MALDI-TOF-MS technology and chemical database Pubchem, and structural database PDB were combined to reconstitute the three-dimensional structure of target protein. The binding mode of the HP-β-CD/GSE inclusion complex to target protein was studied at the molecular level, and the antioxidant ability of the resulting HP-β-CD/GSE inclusion complexes was investigated by measuring 2,2-diphenyl-1-picrylhydrazyl (DPPH) free radical scavenging. The effects of HP-β-CD/GSE on myofibrillar protein from lamb tripe were also investigated under oxidative conditions. The positions and interactions of the binding sites of HP-β-CD/GSE inclusion complexes and target protein receptors were simulated by molecular docking. The results showed that HP-β-CD/GSE inclusion complexes were successfully prepared, optimally at a molar ratio of 1:2. At low (5 μmol/g) to medium (105 μmol/g) concentrations, HP-β-CD/GSE inclusion complexes decreased the carbonyl content, hydrophobicity, and protein aggregation of myofibrillar protein from lamb tripe, and increased the sulphydryl content. Furthermore, high concentration (155 μmol/g) of HP-β-CD/GSE inclusion complexes promoted protein oxidation.

The application of differential scanning fluorimetry in exploring bisubstrate binding to protein arginine N-methyltransferase 1.

Protein arginine N-methyltransferases (PRMTs) are a family of 9 enzymes that catalyze mono- or di-methylation of arginine residues using S-adenosyl-l-methionine (SAM). Arginine methylation is an important post-translational modification that can regulate the activity and structure of target proteins. Altered PRMT activity can lead to a variety of health issues including neurodevelopmental disease, autoimmune disorders, cancer, and cardiovascular disease. Thus, developing a robust mechanistic understanding of PRMT function may provide insight into these various disease states and enable the development of potential therapeutic agents. Although PRMTs have been studied for nearly two decades, a consensus regarding the mechanism of action for this class of enzymes has remained noticeably elusive. To address this shortcoming, differential scanning fluorimetry (DSF) was used to gain mechanistic insight into the order of PRMT substrate and cofactor binding. This methodology confirms that PRMT cofactor binding precedes target substrate binding and supports the use of DSF to study bisubstrate enzymatic reaction mechanisms.