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Fulltext Novel Complex of Zinc (II) Dichloroethylenediamine: Synthesis, Characterization, In-silico, and In-vitro Evaluation against Cervical Cancer Cells

Raya I, Kartina D, Wijaya RI, Irfandi R, Abdalrazaq EA, Prihantono P, et al.

Asian Pac J Cancer Prev, 2023 Dec 01;24(12):4155-4165.
PMID: 38156851 DOI: 10.31557/APJCP.2023.24.12.4155

OBJECTIVE: Cervical cancer is a malignancy originating from the cervix and often caused by oncogenic Human Papilloma Virus (HPV), specifically subtypes 16 and 18. Anticancer drugs are chemotherapeutic compounds used for cancer treatment. Therefore, this research aims to synthesize and characterize Zinc (II) dichloroethylenediamine (Zn(en)Cl2) complex, as well as determine its antiproliferative activity against HeLa cells. The Zn(en)Cl2 complex was successfully synthesized, and the antiproliferative activity was tested.
METHODS: The synthesis involved reacting ethylenediamine and KCl with Zn metal. The complex formed was characterized using a conductometer, UV-Vis spectroscopy, FT-IR spectroscopy, and XRD, while the activity was measured against HeLa cells.
RESULT: The synthesis yielded a 56.12% conversion with a melting point of 198-200 oC and a conductivity value of 2.02 mS/cm. The Zn(en)Cl2 complex showed potential activity against HeLa cells with an IC50 value of 898.35 µg/mL, which was evidenced by changes in the morphological structure of HeLa cells. Its interaction with DNA targets was investigated by employing molecular docking.
CONCLUSION: The observed data indicated that the Zn(en)Cl2 complex bound to DNA at the nitrogenous base Guanine (DG) by coordinate covalent bonds. Interestingly, DG maintained interaction with the complex until the end of the docking simulation. Additionally, molecular dynamics (MD) simulation was conducted, and the results showed that Zn(en)Cl2 remained bound to the DNA binding pocket all through the process.

Matched MeSH terms: Ligands
On-Demand Ligand-Base DNA Sensor with Electrochemical Impedance Spectroscopy

Han H, Sabani NB, Nobusawa K, Takei F, Nakatani K, Yamashita I

Anal Chem, 2023 Jul 04;95(26):9729-9733.
PMID: 37341999 DOI: 10.1021/acs.analchem.3c01126

We have developed a DNA sensor that can be finalized to detect a specific target on demand. The electrode surface was modified with 2,7-diamino-1,8-naphthyridine (DANP), a small molecule with nanomolar affinity for the cytosine bulge structure. The electrode was immersed in a solution of synthetic probe-DNA that had a cytosine bulge structure at one end and a complementary sequence to the target DNA at the other end. The strong binding between the cytosine bulge and DANP anchored the probe DNAs to the electrode surface, and the electrode became ready for target DNA sensing. The complementary sequence portion of the probe DNA can be changed as requested, allowing for the detection of a wide variety of targets. Electrochemical impedance spectroscopy (EIS) with the modified electrode detected target DNAs with a high sensitivity. The charge transfer resistance (Rct) extracted from EIS showed a logarithmic relationship with the concentration of target DNA. The limit of detection (LoD) was less than 0.01 μM. By this method, highly sensitive DNA sensors for various target sequences could be easily produced.

Matched MeSH terms: Ligands
Fulltext A Novel Protein Interaction between Nucleotide Binding Domain of Hsp70 and p53 Motif

Elengoe A, Naser MA, Hamdan S

Int J Genomics, 2015;2015:391293.
PMID: 26098630 DOI: 10.1155/2015/391293

Currently, protein interaction of Homo sapiens nucleotide binding domain (NBD) of heat shock 70 kDa protein (PDB: 1HJO) with p53 motif remains to be elucidated. The NBD-p53 motif complex enhances the p53 stabilization, thereby increasing the tumor suppression activity in cancer treatment. Therefore, we identified the interaction between NBD and p53 using STRING version 9.1 program. Then, we modeled the three-dimensional structure of p53 motif through homology modeling and determined the binding affinity and stability of NBD-p53 motif complex structure via molecular docking and dynamics (MD) simulation. Human DNA binding domain of p53 motif (SCMGGMNR) retrieved from UniProt (UniProtKB: P04637) was docked with the NBD protein, using the Autodock version 4.2 program. The binding energy and intermolecular energy for the NBD-p53 motif complex were -0.44 Kcal/mol and -9.90 Kcal/mol, respectively. Moreover, RMSD, RMSF, hydrogen bonds, salt bridge, and secondary structure analyses revealed that the NBD protein had a strong bond with p53 motif and the protein-ligand complex was stable. Thus, the current data would be highly encouraging for designing Hsp70 structure based drug in cancer therapy.

Matched MeSH terms: Ligands
Fulltext Advances in Aptamer-Based Biosensors and Cell-Internalizing SELEX Technology for Diagnostic and Therapeutic Application

Gan Z, Roslan MAM, Abd Shukor MY, Halim M, Yasid NA, Abdullah J, et al.

Biosensors (Basel), 2022 Oct 25;12(11).
PMID: 36354431 DOI: 10.3390/bios12110922

Aptamers are a group of synthetic single-stranded nucleic acids. They are generated from a random library of single-stranded DNA or RNA by a technology named systematic evolution of ligands by exponential enrichment (SELEX). SELEX is a repetitive process to select and identify suitable aptamers that show high affinity and specificity towards target cells. Great strides have been achieved in the design, construction, and use of aptamers up to this point. However, only a small number of aptamer-based applications have achieved widespread commercial and clinical acceptance. Additionally, finding more effective ways to acquire aptamers with high affinity remains a challenge. Therefore, it is crucial to thoroughly examine the existing dearth and advancement in aptamer-related technologies. This review focuses on aptamers that are generated by SELEX to detect pathogenic microorganisms and mammalian cells, as well as in cell-internalizing SELEX for diagnostic and therapeutic purposes. The development of novel aptamer-based biosensors using optical and electrical methods for microbial detection is reported. The applications and limitations of aptamers are also discussed.

Matched MeSH terms: Ligands
Machine learning and molecular simulation ascertain antimicrobial peptide against Klebsiella pneumoniae from public database

Al-Khdhairawi A, Sanuri D, Akbar R, Lam SD, Sugumar S, Ibrahim N, et al.

Comput Biol Chem, 2023 Feb;102:107800.
PMID: 36516617 DOI: 10.1016/j.compbiolchem.2022.107800

Antimicrobial peptides (AMPs) are short peptides with a broad spectrum of antimicrobial activity. They play a key role in the host innate immunity of many organisms. The growing threat of microorganisms resistant to antimicrobial agents and the lack of new commercially available antibiotics have made in silico discovery of AMPs increasingly important. Machine learning (ML) has improved the speed and efficiency of AMP discovery while reducing the cost of experimental approaches. Despite various ML platforms developed, there is still a lack of integrative use of ML platforms for AMP discovery from publicly available protein databases. Therefore, our study aims to screen potential AMPs with antibiofilm properties from databases using ML platforms, followed by protein-peptide molecular docking analysis and molecular dynamics (MD) simulations. A total of 5850 peptides classified as non-AMP were screened from UniProtKB and analyzed using various online ML platforms (e.g., CAMPr3, DBAASP, dPABBs, Hemopred, and ToxinPred). Eight potential AMP peptides against Klebsiella pneumoniae with antibiofilm, non-toxic and non-hemolytic properties were then docked to MrkH, a transcriptional regulator of type 3 fimbriae involved in biofilm formation. Five of eight peptides bound more strongly than the native MrkH ligand when analyzed using HADDOCK and HPEPDOCK. Following the docking studies, our MD simulated that a Neuropeptide B (Peptide 3) bind strongly to the MrkH active sites. The discovery of putative AMPs that exceed the binding energies of the native ligand underscores the utility of the combined ML and molecular simulation strategies for discovering novel AMPs with antibiofilm properties.

Matched MeSH terms: Ligands
Fulltext Multireceptor Analysis for Evaluating the Antidiabetic Efficacy of Karanjin: A Computational Approach

Nag S, Stany B, Mishra S, Kumar S, Mohanto S, Ahmed MG, et al.

Endocrinol Diabetes Metab, 2024 Jul;7(4):e509.
PMID: 38982323 DOI: 10.1002/edm2.509

BACKGROUND: Diabetes mellitus, notably type 2, is a rising global health challenge, prompting the need for effective management strategies. Common medications such as metformin, insulin, repaglinide and sitagliptin can induce side effects like gastrointestinal disturbances, hypoglycemia, weight gain and specific organ risks. Plant-derived therapies like Karanjin from Pongamia pinnata present promising alternatives due to their historical use, holistic health benefits and potentially fewer adverse effects. This study employs in silico analysis to explore Karanjin's interactions with diabetes-associated receptors, aiming to unveil its therapeutic potential while addressing the limitations and side effects associated with conventional medications.
METHODOLOGY: The research encompassed the selection of proteins from the Protein Data Bank (PDB), followed by structural refinement processes and optimization. Ligands such as Karanjin and standard drugs were retrieved from PubChem, followed by a comprehensive analysis of their ADMET profiling and pharmacokinetic properties. Protein-ligand interactions were evaluated through molecular docking using AutoDockTools 1.5.7, followed by the analysis of structural stability using coarse-grained simulations with CABS Flex 2.0. Molecular dynamics simulations were performed using Desmond 7.2 and the OPLS4 force field to explore how Karanjin interacts with proteins over 100 nanoseconds, focusing on the dynamics and structural stability.
RESULTS: Karanjin, a phytochemical from Pongamia pinnata, shows superior drug candidate potential compared to common medications, offering advantages in efficacy and reduced side effects. It adheres to drug-likeness criteria and exhibits optimal ADMET properties, including moderate solubility, high gastrointestinal absorption and blood-brain barrier penetration. Molecular docking revealed Karanjin's highest binding energy against receptor 3L2M (Pig pancreatic alpha-amylase) at -9.1 kcal/mol, indicating strong efficacy potential. Molecular dynamics simulations confirmed stable ligand-protein complexes with minor fluctuations in RMSD and RMSF, suggesting robust interactions with receptors 3L2M.
CONCLUSION: Karanjin demonstrates potential in pharmaceutical expansion for treating metabolic disorders such as diabetes, as supported by computational analysis. Prospects for Karanjin in pharmaceutical development include structural modifications for enhanced efficacy and safety. Nanoencapsulation may improve bioavailability and targeted delivery to pancreatic cells, while combination therapies could optimize treatment outcomes in diabetes management. Clinical trials and experimental studies are crucial to validate its potential as a novel therapeutic agent.

Matched MeSH terms: Ligands
Reporting multitargeted potency of Tiaprofenic acid against lung cancer: Molecular fingerprinting, MD simulation, and MTT-based cell viability assay studies

Ahmad S, Bano N, Khanna K, Gupta D, Raza K

Int J Biol Macromol, 2024 Sep;276(Pt 1):133872.
PMID: 39019378 DOI: 10.1016/j.ijbiomac.2024.133872

Lung Cancer (LC) is among the most death-causing cancers, has caused the most destruction and is a gender-neutral cancer, and WHO has kept this cancer on its priority list to find the cure. We have used high-throughput virtual screening, standard precision docking, and extra precise docking for extensive screening of Drug Bank compounds, and the uniqueness of this study is that it considers multiple protein targets of prognosis and metastasis of LC. The docking and MM\GBSA calculation scores for the Tiaprofenic acid (DB01600) against all ten proteins range from -8.422 to -5.727 kcal/mol and - 47.43 to -25.72 kcal/mol, respectively. Also, molecular fingerprinting helped us to understand the interaction pattern of Tiaprofenic acid among all the proteins. Further, we extended our analysis to the molecular dynamic simulation in a neutralised SPC water medium for 100 ns. We analysed the root mean square deviation, fluctuations, and simulative interactions among the protein, ligand, water molecules, and protein-ligand complexes. Most complexes have shown a deviation of <2 Å as cumulative understanding. Also, the fluctuations were lesser, and only a few residues showed the fluctuation with a huge web of interaction between the protein and ligand, providing an edge that supports that the protein and ligand complexes were stable. In the MTT-based Cell Viability Assay, Tiaprofenic Acid exhibited concentration-dependent anti-cancer efficacy against A549 lung cancer cells, significantly reducing viability at 100 μg/mL. These findings highlight its potential as a therapeutic candidate, urging further exploration into the underlying molecular mechanisms for lung cancer treatment.

Matched MeSH terms: Ligands
Structural basis for the recognition of anthelmintic activity of bioactive metabolite in watery rose apple leaf through in silico investigation

Suwendar S, Jantan I, Fakih TM, Priani SE, Mulyanti D, Patricia VM, et al.

J Biomol Struct Dyn, 2025 Feb;43(3):1539-1551.
PMID: 38084758 DOI: 10.1080/07391102.2023.2292294

This research is part of the research umbrella regarding the use of watery rose apple leaf [Eugenia aqueum (Burm. F) Alston] in the health sector. Infectious diseases of worms, are still a health problem with a high burden based on the incidence and mortality rates in Southeast Asian countries. Therefore, we tried to create a 3D structure of vital receptors of worms including Nicotinic Cholinergic Receptor (NCR), Acetylcholinesterase Enzymes (AE), and Phosphorylase Enzymes (PE) using homology modeling method through the SWISS-MODEL webserver, then conducted a molecular dynamics simulations using active metabolite of watery rose apple leaf i.e. 2',4'‑dihydroxy‑6'‑methoxy‑3',5'‑dimethylchalcone which was then compared with Piperazine Citrate and Pyrantel Pamoate which are anthelmintic drugs on the market. Based on the results of the study, the structure of the three receptors with high resolution was successfully obtained which was characterized by a good Ramachandran value, which was above 90%. Then the ligand structure was successfully modeled in a three-dimensional model and optimized geometrically using GaussView 5.0.8 and Gaussian09 software. In further, Root Mean Square Deviation (RMSD) and Root Mean Square Fluctuation (RMSF) analysis of molecular dynamics simulations ligand against the three receptors, compound 2',4'‑dihydroxy‑6'‑methoxy‑3',5'‑dimethylchalcone showed better stability than Piperazine Citrate and Pyrantel Pamoate at 50 ns simulation, although from the calculation of binding free energy Molecular Mechanics Poisson-Boltzmann Surface Area (MM/PBSA) is not better than the two comparisons. It can be concluded that the compound 2',4'‑dihydroxy‑6'‑methoxy‑3',5'‑dimethylchalcone from watery rose apple leaf showed potential as anthelmintic candidates.Communicated by Ramaswamy H. Sarma.

Matched MeSH terms: Ligands
E-pharmacophore based virtual screening of potent lead molecules against Cystic Fibrosis: An in silico study

Jeyaraman S, Sankar J, Wong LS, Muthusamy K

Comput Biol Chem, 2024 Dec;113:108249.
PMID: 39427605 DOI: 10.1016/j.compbiolchem.2024.108249

Cystic fibrosis is an autosomal recessive condition caused by mutations in the CFTR gene, which encodes the CFTR protein. Currently, CF is a life-limiting illness that has a limited cure. The present study aimed to identify top leads against CFTR protein with F508del in comparison with Lumacaftor. In this study, a homology model of the NBD domain of CFTR protein was developed using the available NBD domain crystal structure. The protein model was refined through apo dynamics. Energy-optimized pharmacophore mapping was carried out to identify essential features for CFTR, resulting in a model with a hydrogen-bond donor, two hydrogen-bond acceptors, and three aromatic ring sites. A screening of a compound from the NPASS database using these DAARRR six-point-pharmacophore features led to the identification of potential ligands that could act against CFTR protein. Further studies such as ADME/T, molecular dynamics, MM_GBSA, and DFT were performed to identify the top-hit compound from the NPASS database. The compound Anguibactin (NPC41982) has been identified as a top lead that exhibits higher binding affinity and stability than the reference compound Lumacaftor, suggesting their potential to bind to the active site of the CFTR protein. These compounds could serve as starting points for the development of drug-like molecules for treating cystic fibrosis.

Matched MeSH terms: Ligands
Computationally-Assisted Discovery and Assignment of a New Class of 6/6/5/5 Fused-Ring Diterpene Acting as Pregnane X Receptor Ligands from Isodon serra

Bian Z, Liu X, Hu S, Li H, Wood JS, Williamson RT, et al.

J Nat Prod, 2024 Oct 25;87(10):2459-2467.
PMID: 39315450 DOI: 10.1021/acs.jnatprod.4c00759

We report here the orchestration of molecular ion networking (MoIN) and a set of computationally assisted structural elucidation approaches in the discovery and assignment of a new class of rearranged 4,5-seco-abietane diterpenoids including serra A (1), which possesses an unusual 6/6/5/5 fused-ring skeleton system, together with two previously unreported diterpenoids serras B-C (2-3) and five known compounds were isolated from Isodon serra (I. serra). The structures were elucidated by spectroscopic analysis in conjunction with computationally assisted structure elucidation tools. In silico, serras A-C (1-3) bind well to PXR, suggesting their potential role in reducing inflammation. The results of serra A (1) with hPXR demonstrated agonist activity with an EC50 value of 15 μM. Serra A (1), graciliflorin F (4), gerardianin C (5), 11,12,15-trihydroxy-8,11,13-abietatrien-7-one (6), rabdosin D (7), and 15-hydroxysalprionin (8) exhibited promising anti-inflammatory activities in lipopolysaccharide (LPS)-induced RAW 267.4 cells, and their inhibition rates on NO production were more than 65% at 10 μM.

Matched MeSH terms: Ligands
Combinatorial treatment with β-glucanase enzyme and chlorhexidine induces cysticidal effects in Acanthamoeba cyst

Rased NM, Johari SATT, Zakeri HA, Ma NL, Razali SA, Hashim F

Parasitol Res, 2022 Nov;121(11):3105-3119.
PMID: 36102969 DOI: 10.1007/s00436-022-07650-0

Acanthamoeba cysts have a cellulose cell wall made up of a solid layer of β-glucan, which confers resistance to the dormant phase of this microorganism. The ability of Acanthamoeba to change to this dormant phase causes difficulties in treating its infection at the cyst stage as compared to the trophozoite stage. Therefore, targeting cyst total mortality can help to prevent re-infection in patients. To ensure cysticidal treatment, a β-glucanase enzyme was introduced in vitro to the Acanthamoeba cyst, followed by a chlorhexidine solution treatment. β-glucanase enzyme and chlorhexidine dose-response analysis was performed based on cell wall integrity measurement. The treatment was also performed on human corneal epithelial cells to confirm the safety of the treatment in vitro. The surface morphology of the cysts was observed using scanning electron microscopy (SEM), while the protein alterations were determined using 1D protein analysis. The interaction of the β-glucanase enzyme with cellulose linkages was investigated based on molecular dosimetry. Incubation of the cyst for 24 h at 8.75 units/ml of β-glucanase followed by 0.88 μg/ml of chlorhexidine resulted in a substantial reduction in the total chlorhexidine used, which made it safer for human corneal epithelial cells. Ultrastructural changes revealed the reduction of the thickness in ectocyst and endocyst layers with the loss of the internal structure of the cyst. After combination treatment of chlorhexidine and β-glucanase, a decrease in the cyst protein from the size of 37 to 25 kDa was observed. The enzyme-substrate interaction validated these results based on molecular docking between 1,4-β-D-glucan and 1,4- β-D-xylan with the β-glucanase enzyme. In silico analysis revealed that two catalytic glutamate residues (Glu160 and Glu267) are essential to catalysing the hydrolytic reaction. Molecular dynamic simulation analysis revealed that both ligands formed stable interactions throughout the simulation. This work concludes that the enzymatic approach combined with chlorhexidine is a novel and effective technique for ensuring the cysticidal effects against the Acanthamoeba cyst. The interaction of the chlorhexidine and β-glucanase enzyme on the surface of the cyst of amoeba resulted in the ecto-and endo cyst layer being damaged and confirmed the cysticidal effects.

Matched MeSH terms: Ligands
Fulltext Synthesis, characterization and biological evaluation of transition metal complexes derived from N, S bidentate ligands

Md Yusof EN, S A Ravoof TB, Tiekink ER, Veerakumarasivam A, Crouse KA, Mohamed Tahir MI, et al.

Int J Mol Sci, 2015 May 15;16(5):11034-54.
PMID: 25988384 DOI: 10.3390/ijms160511034

Two bidentate NS ligands were synthesized by the condensation reaction of S-2-methylbenzyldithiocarbazate (S2MBDTC) with 2-methoxybenzaldehyde (2MB) and 3-methoxybenzaldehyde (3MB). The ligands were reacted separately with acetates of Cu(II), Ni(II) and Zn(II) yielding 1:2 (metal:ligand) complexes. The metal complexes formed were expected to have a general formula of [M(NS)2] where M = Cu2+, Ni2+, and Zn2+. These compounds were characterized by elemental analysis, molar conductivity, magnetic susceptibility and various spectroscopic techniques. The magnetic susceptibility measurements and spectral results supported the predicted coordination geometry in which the Schiff bases behaved as bidentate NS donor ligands coordinating via the azomethine nitrogen and thiolate sulfur. The molecular structures of the isomeric S2M2MBH (1) and S2M3MBH (2) were established by X-ray crystallography to have very similar l-shaped structures. The Schiff bases and their metal complexes were evaluated for their biological activities against estrogen receptor-positive (MCF-7) and estrogen receptor-negative (MDA-MB-231) breast cancer cell lines. Only the Cu(II) complexes showed marked cytotoxicity against the cancer cell lines. Both Schiff bases and other metal complexes were found to be inactive. In concordance with the cytotoxicity studies, the DNA binding studies indicated that Cu(II) complexes have a strong DNA binding affinity.

Matched MeSH terms: Ligands*
An in silico approach towards the identification of novel inhibitors of the TLR-4 signaling pathway

Mahita J, Harini K, Rao Pichika M, Sowdhamini R

J Biomol Struct Dyn, 2016 Jun;34(6):1345-62.
PMID: 26264972 DOI: 10.1080/07391102.2015.1079243

Precise functioning and fine-tuning of Toll-like receptor 4 (TLR4) signaling is a critical requirement for the smooth functioning of the innate immune system, since aberrant TLR4 activation causes excessive production of pro-inflammatory cytokines and interferons. This can result in life threatening conditions such as septic shock and other inflammatory disorders. The TRIF-related adaptor molecule (TRAM) adaptor protein is unique to the TLR4 signaling pathway and abrogation of TRAM-mediated TLR4 signaling is a promising strategy for developing therapeutics aimed at disrupting TRAM interactions with other components of the TLR4 signaling complex. The VIPER motif from the vaccinia virus-producing protein, A46 has been reported to disrupt TRAM-TLR4 interactions. We have exploited this information, in combination with homology modeling and docking approaches, to identify a potential binding site on TRAM lined by the BB loop and αC helix. Virtual screening of commercially available small molecules targeting the binding site enabled to short-list 12 small molecules to abrogate TRAM-mediated TLR4 signaling. Molecular dynamics and molecular mechanics calculations have been performed for the analysis of these receptor-ligand interactions.

Matched MeSH terms: Ligands*
Smart electrical bi-layers lipopeptides: Novel peptidic chains like zigzag map esterified with phospho-glyceride as mono-layer moieties capable in forming a meso-sphere- envelop with scaffold- ability to cellular impurities

Saadi S, Saari N, Abdulkarim MS, Ghazali HM, Anwar F

J Control Release, 2018 03 28;274:93-101.
PMID: 29031897 DOI: 10.1016/j.jconrel.2017.10.011

Cell impurities are an emerging nucleating molecular barriers having the capability in disordering the metabolic chain reactions of proteolysis, glycolysis and lipolysis. Their massive effects induced by copolymer crystal growth in compaction with metal and mineral transients are extended as well as in damaging DNA and mRNA structure motif and other molecular assembly e.g. histones structure unites. Their polycrystalline packing modes, polydispersity and their tendency to surface and interface adhesion prompted us in structuring scaffold biomaterials enriched with biopeptides, layered by phospho-glycerides ester-forms. The interface tension of the formed map is flexible and dependent to the surface exposure and its collapse modes to the surrounding molecular ligands. Thus, the attempts in increasing surface exposure e.g. the viscoelastic of structured lipopeptides and types of formed network structures interplays an extra- conjugating biomolecules having a least cytotoxicity effects to cells constituents. Disulfides molecules are selected to be the key regulatory element in rejoining both lipidic and proteic moieties by disordering atoms status via chemical ionization using organic catalyst. The insertion of methionine based peptidic chain at the lateral surfaces of scaffold biomaterials enhances the electron-meta-static motions by raising a molecular disordering status at distinct regions of the map e.g. epimerization into a nonpolar side that helps the chemical conjunction of disulfide groups with the esterified phosphoglycerides mono-layers. These effects in turn are accomplished by the formation of meso-sphere nonpolar- vesicles. The oxidation of disulfide group would alter the ordering of initial molecules by raising a newly molecular disorders to the map with high polarity to surface regions. In the same time indicates a continuation in the crystallization growth factor via a low chemical lesions between the impurities and a supersaturation in the intra-atomic distances with maximum cross linking to the deformed ligand with scaffold biomaterials.

Matched MeSH terms: Ligands
Fulltext Molecular docking analysis of Carica papaya Linn constituents as antiviral agent

Radhakrishnan, N., Lam, K. W., Norhaizan, M. E.

International Food Research Journal, 2017;24(4):1819-1825.
MyJurnal

Carica papaya (papaya) fruits are available throughout the world and it is well accepted as food or as a quasi-drug. Aqueous papaya leaves extract have been used as treatment for dengue fever. This prompted us to carry out the docking study on these nine selected ligands (phyto-constituents of papaya) which are carpaine, dehydrocarpaine I and II, cardenolide, p-coumaric acid, chlorogenic acid, caricaxanthin, violaxanthin and zeaxanthin. These phytoconstituents were evaluated on the docking behaviour of dengue serotype 3 RNA-dependent RNA polymerase (RdRp); influenza A (H1N9) virus neuraminidase (NA); chikungunya virus glycoprotein (E3-E2-E1) and chikungunya virus non-structural protein2 (nsP2) protease using Discovery Studio Version 3.1. In addition, molecular physicochemical, drug-likeness, ADMET (Absorption, Distribution, Metabolism, Excretion and Toxicity) and TOPKAT (Toxicity Prediction by Komputer Assisted Technology) analyses were done. The molecular physicochemical analysis revealed that cardenolide and p-coumaric acid (2 ligands) complied with Lipinski’s rule of five. Dehydrocarpaine II, cardenolide, caricaxanthin, violaxanthin and zeaxanthin all the five ligands were predicted to have plasma protein binding (PPB) effect. Docking studies and binding free energy calculations revealed that p-coumaric acid exhibited very least binding energy irrespective of its target protein. Hence, the results of this present study exhibited the potential of these nine ligands as antiviral agent.

Matched MeSH terms: Ligands
In silico study of carvone derivatives as potential neuraminidase inhibitors

Jusoh N, Zainal H, Abdul Hamid AA, Bunnori NM, Abd Halim KB, Abd Hamid S

J Mol Model, 2018 Mar 15;24(4):93.
PMID: 29546582 DOI: 10.1007/s00894-018-3619-6

Recent outbreaks of highly pathogenic influenza strains have highlighted the need to develop new anti-influenza drugs. Here, we report an in silico study of carvone derivatives to analyze their binding modes with neuraminidase (NA) active sites. Two proposed carvone analogues, CV(A) and CV(B), with 36 designed ligands were predicted to inhibit NA (PDB ID: 3TI6) using molecular docking. The design is based on structural resemblance with the commercial inhibitor, oseltamivir (OTV), ligand polarity, and amino acid residues in the NA active sites. Docking simulations revealed that ligand A18 has the lowest energy binding (∆Gbind) value of -8.30 kcal mol-1, comparable to OTV with ∆Gbind of -8.72 kcal mol-1. A18 formed seven hydrogen bonds (H-bonds) at residues Arg292, Arg371, Asp151, Trp178, Glu227, and Tyr406, while eight H-bonds were formed by OTV with amino acids Arg118, Arg292, Arg371, Glu119, Asp151, and Arg152. Molecular dynamics (MD) simulation was conducted to compare the stability between ligand A18 and OTV with NA. Our simulation study showed that the A18-NA complex is as stable as the OTV-NA complex during the MD simulation of 50 ns through the analysis of RMSD, RMSF, total energy, hydrogen bonding, and MM/PBSA free energy calculations.

Matched MeSH terms: Ligands
Fulltext The Values of Receptor Activator Nuclear Kappa-B Ligand Expression in Stage III Giant Cell Tumor of the Bone

Ghani SA, Wan Ismail WF, Md Salleh MS, Yahaya S, Syahrul Fitri ZM

Indian J Orthop, 2018 2 9;52(1):31-34.
PMID: 29416167 DOI: 10.4103/ortho.IJOrtho_153_17

Background: Giant cell tumor (GCT) of bone is a benign locally aggressive primary bone tumor which is risky for local recurrences and pulmonary metastasis. Till date, there are still many uncertainties in predicting the aggressiveness of GCT. We aim to investigate whether receptor activator nuclear kappa-B ligand (RANKL) expression may determine the prognosis of the lesion.
Materials and Methods: We examined RANKL expression in 39 patients (21 males, 18 females) by immunohistochemistry. Four patients (10%) were presented with tumor recurrence, eight patients (20%) were complicated with lung metastasis, and two patients (5%) were presented with both recurrence and lung metastasis. Positive RANKL expression was assessed according to a scoring system evaluating the percentage of the immunostained epithelial area and the staining intensity. The cumulative score was calculated to determine the final score value. Data were analyzed using PASW version 18.0 and independent t-test between nonrecurrence/recurrence groups, and nonlung metastasis/lung metastasis groups. Significance was set at P < 0.05.
Results: Thirty-two patients (82%) scored 3 in RANKL-staining percentage from whole stromal cell population (>75%), 6 patients scored 2, and 1 patient scored 1. Nine patients (23%) scored 3 in RANKL-staining intensity (most intense), 19 patients (48%) scored 2, and 11 patients (29%) scored 1. Twenty six patients (67%) had strong RANKL expression (total score of 5-6), 12 patients (31%) showed moderate score (3-4) whereas only 1 patient (2%) showed weak RANKL expression. Together, the mean value of RANKL-staining percentage was 2.79, intensity 1.95 and the total score 4.77. The mean RANKL-staining percentage between recurrence and nonrecurrence groups was statistically significant (P = 0.009). There was no significant difference in the mean staining intensity and total score between nonrecurrence and recurrence groups, and staining percentage staining intensity and a total cumulative score of RANKL expression between lung metastasis and nonlung metastasis groups.
Conclusion: RANKL expression is generally high in Stage III GCT and is a reliable prognostic marker in predicting the risk of local recurrence however not in lung metastasis.

Matched MeSH terms: Ligands
Fulltext N-glycosylation and expression in human tissues of the orphan GPR61 receptor

Kozielewicz P, Alomar H, Yusof S, Grafton G, Cooper AJ, Curnow SJ, et al.

FEBS Open Bio, 2017 12;7(12):1982-1993.
PMID: 29226084 DOI: 10.1002/2211-5463.12339

A number of members of the G protein-coupled receptor class of cell surface receptors are 'orphans' with no known endogenous ligand. One of these orphan receptors is GPR61; there are little data about its expression in human cells and tissues. In this study, we investigated the post-translational modification of GPR61 by N-glycosylation at an identified consensus N-glycosylation site (N12) and the impact of this modification upon the subcellular expression of the protein. The N-glycosylation inhibitor tunicamycin reduced the apparent molecular weight of immunoreactivity associated with myc-tagged GPR61 by 1-2 kDa, which was comparable to the evident molecular weight of the myc-tagged N12S GPR61 mutant with disrupted consensus N-glycosylation site. Analysis of GPR61 expression demonstrated that tunicamycin treatment reduced considerably heterologous expression of GPR61 in the cell membrane despite the N12S GPR61 mutant being readily expressed at the cell surface. These results demonstrate that GPR61 is subject to N-glycosylation but suggest this is not a prerequisite for cell surface expression, although N-glycosylation of other proteins may be important for cell membrane expression of GPR61. Expression of GPR61 protein was demonstrated at the cellular level in human hippocampus and human peripheral blood mononuclear cells. In the latter, there was a significantly higher expression of GPR61 in the Th17 cell subset in comparison with resting CD4+ cells, which may point toward a potential role for the GPR61 receptor in autoimmune diseases. This is the first report that GPR61 protein is subject to post-translational modification and is expressed in immune cell subsets and the hippocampus. These findings will help guide studies to investigate the function of GPR61.

Matched MeSH terms: Ligands
Synthesis, structure, solution behavior, reactivity and biological evaluation of oxidovanadium(iv/v) thiosemicarbazone complexes

Saswati, Adão P, Majumder S, Dash SP, Roy S, Kuznetsov ML, et al.

Dalton Trans, 2018 Aug 21;47(33):11358-11374.
PMID: 30059099 DOI: 10.1039/c8dt01668b

The synthesis and characterization of an oxidovanadium(iv) [VIVO(L)(acac)] (1) and of two dioxidovanadium(v) [VVO2(L')] (2) and [VVO2(L)] (2a) complexes of the Schiff base formed from the reaction of 4-(p-fluorophenyl) thiosemicarbazone with pyridine-2-aldehyde (HL) are described. The oxidovanadium(iv) species [VIVO(L)(acac)] (1) was synthesized by the reaction of VIVO(acac)2 with the thiosemicarbazone HL in refluxing ethanol. The recrystallization of [VIVO(L)(acac)] (1) in DMF, CH3CN or EtOH gave the same product i.e. the dioxidovanadium(v) complex [VVO2(L)] (2a); however, upon recrystallization of 1 in DMSO a distinct compound [VVO2(L')] (2) was formed, wherein the original ligand L- is transformed to a rearranged one, L'-. In the presence of DMSO the ligand in complex 1 is found to undergo methylation at the carbon centre attached to imine nitrogen (aldimine) and transformed to the corresponding VVO2-species through in situ reaction. The synthesized HL and the metal complexes were characterized by elemental analysis, IR, UV-Vis, NMR and EPR spectroscopy. The molecular structure of [VVO2(L')] (2) was determined by single crystal X-ray crystallography. The methylation of various other ligands and complexes prepared from different vanadium precursors under similar reaction conditions was also attempted and it was confirmed that the imine methylation observed is both ligand and metal precursor specific. Complexes 1 and 2 show in vitro insulin-like activity against insulin responsive L6 myoblast cells, higher than VIVO(acac)2, with complex 1 being more potent. In addition, the in vitro cytotoxicity studies of HL, and of complexes 1 and 2 against the MCF-7 and Vero cell lines were also done. The ligand is not cytotoxic and complex 2 is significantly more cytotoxic than 1. DAPI staining experiments indicate that an increase in the time of incubation and an increase of concentration of the complexes lead to the increase in cell death.

Matched MeSH terms: Ligands
Fulltext Synthesis, characterisation and biological activities of Ru(III), Mo(V), Cd(II), Zn(II) and Cu(II) complexes containing a novel Nitrogen-Sulphur Macrocyclic Schiff base derived from Glyoxal

Chah, C.K., Ravoof, T.B.S.A., Veerakumarasivam, A.

Pertanika Journal of Science & Technology, 2018;26(2):653-670.
MyJurnal

A novel nitrogen-sulphur macrocyclic Schiff base, 4,11,20,27-tetrathioxo3,12,19,28-tetrathia-5,6,9,10,21,22,25,26-octaazatricyclo[28.2.2.214,17]hexatriaconta 1(33),6,8,14(36),15,17(35),22,24,30(34),31-decaene-2,13,18,29-tetraone (TGSB) derived from terephthaloyl-bis-dithiocarbazate (TDTC) and glyoxal (ethane-1,2-dione) is synthesised via condensation. Metal complexes are formed by reacting the Schiff base with various metal salts such as Ru(III), Mo(V), Cd(II), Zn(II) and Cu(II). The complexes are expected to have a general formula of M2L or M3L with a square planar or square pyramidal geometry. These compounds were characterised by various physicochemical and spectroscopic techniques. From the data, it is concluded that the azomethine nitrogen atom and the thiolate sulphur atom from the ligand are bonded to the metal ion. In the IR spectra of the complexes, the presence of the C=N band in the region of 1600 cm-1 indicates the successful formation of the Schiff base. The structures of the Schiff base and metal complexes are confirmed via FT-IR, GC-MS and NMR spectroscopic analysis. The magnetic susceptibility measurements, electronic spectral data and molar conductivity analysis support the desired geometry of the complexes. The Schiff base and its metal complexes are evaluated for their biological activities against the invasive human bladder carcinoma cell line (EJ-28) and the minimuminvasive human bladder carcinoma cell line (RT-112). The RuTGSB and CdTGSB complexes showed selective activity against RT-112.

Matched MeSH terms: Ligands

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