Binding Energy Calculation of Patchouli Alcohol Isomer Cyclooxygenase Complexes Suggested as COX-1/COX-2 Selective Inhibitor

Enantioselectivity regulation of antibody against chiral herbicide metolachlor based on interaction at chiral center

Enantioselective antibodies have emerged as great potential biomaterials in the fields of immunoassays and chiral separation. However, cross-reactivity of antibodies to the distomer may severely restrict the application. Comprehending the interaction mechanism between antibodies and enantiomers could be beneficial to produce superior enantioselective antibodies. In this study, a pair of recombinant antibodies (RAbs) against metolachlor enantiomers at chiral carbon (αSS-MET and αSR-MET) were generated and characterized. The αSS-MET-RAb and αSR-MET-RAb showed comparable sensitivity and specificity to the parental monoclonal antibodies by icELISA, with IC50 values of 3.45 and 223.77 ng/mL, respectively. Moreover, the complex structures of RAbs and corresponding eutomer were constructed and analyzed, and site-specific mutagenesis was utilized to verify the reliability of the enantioselective mechanism elucidated. It demonstrated that the strength of the interaction between the chiral center region of eutomer and the antibody was the key factor for the enantioselectivity of antibody. Increasing this interaction could limit the conformational adjustment of the distomer in a specific chiral recognition cavity, thus decreasing the affinity of the antibody to the distomer. This work provided the in-depth analysis of enantioselective mechanism for two RAbs and paved the way to regulate antibody enantioselective performance for immunoassays of chiral compounds.

QSAR, Docking, and Molecular Dynamics Simulation Studies of Sigmacidins as Antimicrobials against Streptococci

Streptococci are a family of bacterial species significantly affecting human health. In addition, environmental Streptococci represent one of the major causes of diverse livestock diseases. Due to antimicrobial resistance, there is an urgent need for novel antimicrobial agent discovery against Streptococci. We discovered a class of benzoic acid derivatives named sigmacidins inhibiting the bacterial RNA polymerase-σ factor interaction and demonstrating excellent antimicrobial activity against Streptococci. In this work, a combinational computer approach was applied to gain insight into the structural basis and mechanism of action of sigmacidins as antimicrobials against Streptococcus pneumoniae. Both two- and three-dimensional quantitative structure-active relationships (2D and 3D QSAR) of sigmacidins displayed good predictive ability. Moreover, molecular docking and molecular dynamics simulation studies disclosed possible contacts between the inhibitors and the protein. The results obtained in this study provided understanding and new directions to the further optimizations of sigmacidins as novel antimicrobials.

An Insight of Co-Encapsulation Nigella sativa and Cosmos caudatus Kunth Extracts as Anti-Inflammatory Agent Through In Silico Study

This study analyzes anti-inflammatory activity from extracts of Nigella sativa and Cosmos caudatus Kunth co-encapsulated through in silico molecular docking. The LC-MS results revealed that extracts of N. sativa mostly contained thymoquinone and alpha-hederin, whereas quercetin and kaempferol were the major compounds in C. caudatus K. Nevertheless, the bioactive compounds are usually susceptible to degradation by exposure to light, heat, oxygen, which may limit its biological activity. Therefore, encapsulation is one of the promising techniques to protect bioactive compounds. Ligands were encapsulated with chitosan and sodium tripolyphosphate as wall materials. Cyclooxygenase-1 (COX-1) and cyclooxygenase-2 (COX-2) as the target enzymes were docked with a combination of these active compounds (non-encapsulated and encapsulated), using the HEX 8.0 program, and visualized using the Discovery studio visualizer software v16.1.0.15350. Interestingly, docking results of the combination of encapsulated ligands showed no interactions to COX-1 but interacted with COX-2. Therefore, co-encapsulation of extracts combinations has been suggested to act as anti-inflammatory agents targeted specifically to the COX-2 enzyme. The total energy of the encapsulated of combination of extract compounds to COX-2 were -1425.88 (mol/cal) for thymoquinone + quercetin; -1435.87 (mol/cal) for thymoquinone + kaempferol; 1175.97 (mol/cal) for quercetin + alpha hederin; -957.74 (mol/cal) for kaempferol + alpha hederin; and -283.3 (mol/cal) for diclofenac sodium, as a control NSAID drug. These suggest that encapsulated active compounds in N. sativa and C. caudatus K. have potency as a drug candidate for the selective NSAIDs category, which can be subjected to further in vitro and in vivo studies.

Synergistic Effects of Curcumin and 5-Fluorouracil on the Hepatocellular Carcinoma In vivo and vitro through regulating the expression of COX-2 and NF-κB

Curcumin (CU) has shown broad anti-cancer effects. 5-fluorouracil (5-FU) has been a conventional chemotherapeutic agent for hepatocellular carcinoma. Unfortunately, the nonspecific cytotoxicity and multidrug resistance caused by long-term use limited the clinical efficacy of 5-FU. This study was aimed to investigate whether the combination of CU and 5-FU could generate synergistic effect in inhibiting the human hepatocellular carcinoma. The results of cytotoxicity test showed that compared with applying single drugs, the combination of CU and 5-FU (1:1, 1:2, 1:4, 2:1 and 4:1, mol/mol) presented stronger cytotoxicity in SMMC-7721, Bel-7402, HepG-2 and MHCC97H cells, while the combination groups are relatively insensitive to normal hepatocytes (L02). Among them, the molar ratio of 2:1 combination group showed strong synergistic effect in SMMC-7721cells. Then, western blotting assay further verified that the mechanism of the synergistic effect may be related to the inhibition of the expression of NF-κB (overall) and COX-2 protein. In addition, the synergistic effect was also validated in the xenograft mice in vivo. This research not only provides a novel and effective combination strategy for the therapy of hepatocellular carcinoma but also provides an experimental basis for the development of CU and 5-FU compound preparation.

Site-directed mutations of anti-amantadine scFv antibody by molecular dynamics simulation: prediction and validation

A recombinant single-chain variable fragment (scFv) antibody was produced from a hybridoma cell strain secreting the monoclonal antibody for amantadine (AMD), and then its recognition mechanisms for AMD were studied using the molecular docking and molecular dynamics. Complex dockings revealed that three regions are involved in antibody recognition; framework 2 of the VL chain (LFR2) GLU40 and TYR42, complementarity-determining region of the VL chain (LCDR3) TYR116, and framework 2 of the VH chain (HFR2) HIS40 and TRP52 were the key amino acid residues. The results of molecular dynamics show that the most important amino acid residues in the interaction between AMD and scFv are HIS40 and TYR116. On the basis of the results of virtual mutation, the scFv antibody was evolved by directional mutagenesis of amino acid residue GLY107 to PHE. Indirect competitive ELISA (icELISA) results indicated that the scFv mutant had highly increased affinity for AMD with up to 3.9-fold improved sensitivity. Thus, the scFv antibody can be applied for mechanistic studies of intermolecular interactions, and our work offered affinity maturated antibodies by site mutations, which were beneficial for valuable anti-AMD antibody design and preparation in future.

Virtual Prediction of the Delphinidin-3-O-glucoside and Peonidin-3-O-glucoside as Anti-inflammatory of TNF-α Signaling

INTRODUCTION

Anthocyanin is the bioactive compound in black rice, which promotes some health benefits for human body. Present study revealed that black rice anthocyanins improve the biomarker of the metabolic syndrome, such as tumor necrosis factor alpha (TNF-α). However, the mechanism of anthocyanin in preventing metabolic syndrome has not been elucidated.

AIM

This study was performed to identify the interaction of six types of black rice anthocyanin towards TNF-α protein and TNF-α receptor through in silico studies, to assess the molecular properties and bioactivity of black rice anthocyanin.

METHODS

We retrieved the black rice anthocyanin compounds from the PubChem database and the proteins (TNF-α protein and TNF-α receptor) from Protein Data Bank (PDB) database. Protein and ligands were docked using Hex 8.0 software and visualized by Discovery Studio 4.1 program.

RESULTS

This study found the possibility that black rice anthocyanins interacted with TNF-α have no influence into TNF-α and TNF-α receptor interaction. The binding of delphinidin-3-O-glucoside & peonidin-3-O-glucoside to TNF-α receptor inhibited the TNF-α and TNF-α receptor signaling. The black rice anthocyanins had low activity as a drug. Interestingly, black rice anthocyanins had a potency as an antioxidant due to the hydrogen donor or acceptor in their structure, as protein kinase inhibitor, nuclear receptor ligand, and enzyme kinase inhibitor.

CONCLUSION

This study suggests that delphinidin-3-O-glucoside and peonidin-3-O-glucoside might have function as anti-inflammatory factor related with TNF-α signaling.

Molecular Dynamic Screening Sesquiterpenoid Pogostemon Herba as Suggested Cyclooxygenase Inhibitor

OBJECTIVE

Virtual molecular dynamic sesquiterpenoid Pogostemon Herba (CID56928117, CID94275, CID107152, and CID519743) have screening as cyclooxygenase (COX-1/COX-2) selective inhibitor.

METHODS

Molecular interaction studies sesquiterpenoid compounds with COX-1 and COX-2 were using the molecular docking tools by Hex 8.0 and interactions were further visualized using by Discovery Studio Client 3.5 software tool and Virtual Molecular Dynamic 1.9.1 software. The binding energy calculation of molecular dynamic interaction was calculated by AMBER12 software.

RESULT

The analysis of the sesquiterpenoid compounds showed that CID56928117, CID94275, CID107152, and CID519743 have suggested as inhibitor of COX-1 and COX-2.

CONCLUSION

Collectively, the scoring binding energy calculation (with PBSA Model Solvent) sesquiterpenoid compounds: CID519743 had suggested as candidate for non-selective inhibitor; CID56928117 and CID94275 had suggested as candidate for a selective COX-1 inhibitor; and CID107152 had suggested as candidate for a selective COX-2 inhibitor.