Ensemble-based molecular docking and spectrofluorometric analysis of interaction between cytotoxin and tumor necrosis factor receptor 1.

Cytotoxin (CTX) is a three-finger toxin presents predominantly in cobra venom. The functional site of the toxin is located at its three hydrophobic loop tips. Its actual mechanism of cytotoxicity remains inconclusive as few conflicting hypotheses have been proposed in addition to direct cytolytic effects. The present work investigated the interaction between CTX and death receptor families via ensemble-based molecular docking and fluorescence titration analysis. Multiple sequence alignments of different CTX isoforms obtained a conserved CTX sequence. The three-dimensional structure of the conserved CTX was later determined using homology modelling, and its quality was validated. Ensemble-based molecular docking of CTX was performed with different death receptors, such as Fas-ligand and tumor necrosis factor receptor families. Our results showed that tumor necrosis factor receptor 1 (TNFR1) was the best receptor interacting with CTX attributed to the interaction of all three functional loops and evinced with low HADDOCK, Z-score and RMSD value. The interaction between CTX and TNFR1 was also supported by a concentration-dependent reduction of fluorescence intensity with increasing binding affinity. The possible intermolecular interactions between CTX and TNFR1 were Van der Waals forces and hydrogen bonding. Our findings suggest a possibility that CTX triggers apoptosis cell death through non-covalent interactions with TNFR1.Communicated by Ramaswamy H. Sarma.

[1]  H. Jin,et al.  The effects of Naja sumatrana venom cytotoxin, sumaCTX on alteration of the secretome in MCF-7 breast cancer cells following membrane permeabilization. , 2021, International journal of biological macromolecules.

[2]  M. Nikzad,et al.  On the Use of Molecular Dynamics Simulations for Elucidating Fine Structural, Physico-Chemical and Thermomechanical Properties of Lignocellulosic Systems: Historical and Future Perspectives , 2021, Journal of Composites Science.

[3]  R. Kontermann,et al.  Selective Targeting of TNF Receptors as a Novel Therapeutic Approach , 2020, Frontiers in Cell and Developmental Biology.

[4]  J. Pande,et al.  Hydrophobic residues of melittin mediate its binding to αA−crystallin , 2019, Protein science : a publication of the Protein Society.

[5]  Jean-Charles Carvaillo,et al.  TTClust: A Versatile Molecular Simulation Trajectory Clustering Program with Graphical Summaries , 2018, J. Chem. Inf. Model..

[6]  M. Tavares,et al.  Multi-Spectroscopic and Theoretical Analysis on the Interaction between Human Serum Albumin and a Capsaicin Derivative—RPF101 , 2018, Biomolecules.

[7]  H. Rashedi,et al.  Molecular dynamic of curcumin/chitosan interaction using a computational molecular approach: Emphasis on biofilm reduction. , 2018, International journal of biological macromolecules.

[8]  David Ramírez,et al.  Is It Reliable to Take the Molecular Docking Top Scoring Position as the Best Solution without Considering Available Structural Data? , 2018, Molecules.

[9]  O. Firuzi,et al.  Molecular dynamics simulation and molecular docking studies of 1,4-Dihydropyridines as P-glycoprotein’s allosteric inhibitors , 2018, Journal of biomolecular structure & dynamics.

[10]  Radka Svobodová Vařeková,et al.  PDBsum: Structural summaries of PDB entries , 2017, Protein science : a publication of the Protein Society.

[11]  Alexandre M. J. J. Bonvin,et al.  PRODIGY: a web server for predicting the binding affinity of protein-protein complexes , 2016, Bioinform..

[12]  G C P van Zundert,et al.  Sense and simplicity in HADDOCK scoring: Lessons from CASP‐CAPRI round 1 , 2016, Proteins.

[13]  Ben M. Webb,et al.  Comparative Protein Structure Modeling Using MODELLER , 2016, Current protocols in bioinformatics.

[14]  Silvio C. E. Tosatto,et al.  The RING 2.0 web server for high quality residue interaction networks , 2016, Nucleic Acids Res..

[15]  G C P van Zundert,et al.  The HADDOCK2.2 Web Server: User-Friendly Integrative Modeling of Biomolecular Complexes. , 2016, Journal of molecular biology.

[16]  H. Vatanpour,et al.  Cobra venom cytotoxins; apoptotic or necrotic agents? , 2015, Toxicon : official journal of the International Society on Toxinology.

[17]  Thomas J Lane,et al.  MDTraj: a modern, open library for the analysis of molecular dynamics trajectories , 2014, bioRxiv.

[18]  Berk Hess,et al.  GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers , 2015 .

[19]  I. Shrivastava,et al.  Naja naja oxiana Cobra Venom Cytotoxins CTI and CTII Disrupt Mitochondrial Membrane Integrity: Implications for Basic Three-Fingered Cytotoxins , 2015, PloS one.

[20]  Chen Zeng,et al.  Molecular Dynamics Simulation Reveals Insights into the Mechanism of Unfolding by the A130T/V Mutations within the MID1 Zinc-Binding Bbox1 Domain , 2015, PloS one.

[21]  Leandro Martínez,et al.  Automatic Identification of Mobile and Rigid Substructures in Molecular Dynamics Simulations and Fractional Structural Fluctuation Analysis , 2015, PloS one.

[22]  K. Ebrahim,et al.  Anticancer Activity of Cobra Venom Polypeptide, Cytotoxin-II, against Human Breast Adenocarcinoma Cell Line (MCF-7) via the Induction of Apoptosis , 2014, Journal of breast cancer.

[23]  B. Berne,et al.  Role of Desolvation in Thermodynamics and Kinetics of Ligand Binding to a Kinase , 2014, Journal of chemical theory and computation.

[24]  G. Folkers,et al.  Proteins feel more than they see: fine-tuning of binding affinity by properties of the non-interacting surface. , 2014, Journal of molecular biology.

[25]  S. Sim,et al.  Pharmacokinetics of Naja sumatrana (Equatorial Spitting Cobra) Venom and Its Major Toxins in Experimentally Envenomed Rabbits , 2014, PLoS neglected tropical diseases.

[26]  S. Sim,et al.  Toxicokinetics of Naja sputatrix (Javan spitting cobra) venom following intramuscular and intravenous administrations of the venom into rabbits. , 2013, Toxicon : official journal of the International Society on Toxinology.

[27]  A. Gomes,et al.  Inhibition of leukemic U937 cell growth by induction of apoptosis, cell cycle arrest and suppression of VEGF, MMP-2 and MMP-9 activities by cytotoxin protein NN-32 purified from Indian spectacled cobra (Naja naja) venom. , 2013, Toxicon.

[28]  R. Efremov,et al.  Structure and dynamics of cardiotoxins. , 2012, Current protein & peptide science.

[29]  Zesheng Li,et al.  Molecular dynamics studies of the 3D structure and planar ligand binding of a quadruplex dimer , 2011, Journal of molecular modeling.

[30]  C. Chien,et al.  Taiwan cobra cardiotoxin III inhibits Src kinase leading to apoptosis and cell cycle arrest of oral squamous cell carcinoma Ca9-22 cells. , 2010, Toxicon : official journal of the International Society on Toxinology.

[31]  C. Chien,et al.  Down-regulation of the JAK2/PI3K-mediated signaling activation is involved in Taiwan cobra cardiotoxin III-induced apoptosis of human breast MDA-MB-231 cancer cells. , 2010, Toxicon : official journal of the International Society on Toxinology.

[32]  A. Bonvin,et al.  The HADDOCK web server for data-driven biomolecular docking , 2010, Nature Protocols.

[33]  G. Gores,et al.  Life and death by death receptors , 2009, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

[34]  Wei Zhao,et al.  Validation of Molecular Docking Programs for Virtual Screening against Dihydropteroate Synthase , 2009, J. Chem. Inf. Model..

[35]  Sheng-Huei Yang,et al.  INVOLVEMENT OF BOTH ENDOPLASMIC RETICULUM‐ AND MITOCHONDRIA‐DEPENDENT PATHWAYS IN CARDIOTOXIN III‐INDUCED APOPTOSIS IN HL‐60 CELLS , 2008, Clinical and experimental pharmacology & physiology.

[36]  Rodrigo Lopez,et al.  Clustal W and Clustal X version 2.0 , 2007, Bioinform..

[37]  Liangyu Zhang,et al.  A cytotoxin isolated from Agkistrodon acutus snake venom induces apoptosis via Fas pathway in A549 cells. , 2007, Toxicology in vitro : an international journal published in association with BIBRA.

[38]  Andrej Sali,et al.  Minimalist representations and the importance of nearest neighbor effects in protein folding simulations. , 2006, Journal of molecular biology.

[39]  C. Chien,et al.  CARDIOTOXIN III INDUCES APOPTOSIS IN K562 CELLS THROUGH A MITOCHONDRIAL‐MEDIATED PATHWAY , 2005, Clinical and experimental pharmacology & physiology.

[40]  P. Krammer,et al.  Death receptor signaling , 2005, Journal of Cell Science.

[41]  David S. Wishart,et al.  SuperPose: a simple server for sophisticated structural superposition , 2004, Nucleic Acids Res..

[42]  R. Abagyan,et al.  Identification of protein-protein interaction sites from docking energy landscapes. , 2004, Journal of molecular biology.

[43]  R. Kini,et al.  Molecular moulds with multiple missions: Functional sites in three‐finger toxins , 2002, Clinical and experimental pharmacology & physiology.

[44]  A. Denicola,et al.  Protein tryptophan accessibility studied by fluorescence quenching , 2002 .

[45]  A. Sali,et al.  Statistical potentials for fold assessment , 2009 .

[46]  L. Nilsson,et al.  Structure and Dynamics of the TIP3P, SPC, and SPC/E Water Models at 298 K , 2001 .

[47]  K. Kuwano,et al.  Signal transduction pathways of apoptosis and inflammation induced by the tumor necrosis factor receptor family. , 2000, American journal of respiratory cell and molecular biology.

[48]  G. Gores,et al.  Death receptors in liver biology and pathobiology , 1999, Hepatology.

[49]  V. Dixit,et al.  Death receptors: signaling and modulation. , 1998, Science.

[50]  C. Yu,et al.  Snake venom cardiotoxins-structure, dynamics, function and folding. , 1997, Journal of biomolecular structure & dynamics.

[51]  W. L. Jorgensen,et al.  Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids , 1996 .

[52]  Berk Hess,et al.  P-LINCS:  A Parallel Linear Constraint Solver for Molecular Simulation. , 2008, Journal of chemical theory and computation.

[53]  M. Peter,et al.  The death receptors. , 1999, Results and problems in cell differentiation.