molecules Review Review Molecular SimulationsSimulations ofof Disulfide-RichDisulfide-Rich VenomVenom Peptides withwith IonIon ChannelsChannels andand MembranesMembranes Evelyne Deplazes 1,2 Evelyne Deplazes 1,2 1 School of Biomedical Sciences, Curtin Health Innovation Research Institute, Curtin University, Perth, 1 School of Biomedical Sciences, Curtin Health Innovation Research Institute, Curtin University, WA 6102, Australia; [email protected] Perth, WA 6102, Australia; [email protected] 2 School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, 2 School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia QLD 4072, Australia Academic Editor: Roberta Galeazzi Academic Editor: Roberta Galeazzi Received: 8 February 2017; Accepted: 24 February 2017; Published: date Received: 8 February 2017; Accepted: 24 February 2017; Published: 27 February 2017 Abstract:Abstract: Disulfide-richDisulfide-rich peptides isolated isolated from from the the venom venom of of arthropods arthropods and and marine marine animals animals are are a arich rich source source of of potent potent and and selective selective modulators modulators of of ion ion channels. channels. This This makes these peptides valuable leadlead moleculesmolecules forfor thethe developmentdevelopment ofof newnew drugsdrugs toto treattreat neurologicalneurological disorders.disorders. Consequently,Consequently, much effort goes into understanding understanding their their mechanis mechanismm of of action. action. This This paper paper presents presents an an overview overview of ofhow how molecular molecular simulations simulations have have been beenused usedto study to studythe interactions the interactions of disulfide-rich of disulfide-rich venom peptides venom peptideswith ion channels with ion channelsand membranes. and membranes. The review The is reviewfocused is on focused the use on of thedocking, use of molecular docking, moleculardynamics dynamicssimulations, simulations, and free energy and free calculations energy calculations to (i) predict to the (i) predictstructure the of structure peptide-channel of peptide-channel complexes; complexes;(ii) calculate (ii) binding calculate free bindingenergies free including energies the including effect of peptide the effect modifications; of peptide modifications; and (iii) study and the (iii)membrane-binding study the membrane-binding properties of properties disulfide-rich of disulfide-rich venom peptides. venom peptides.The review The concludes review concludes with a withsummary a summary and outlook. and outlook. Keywords: venom peptides; ion channels; structure-basedstructure-based drug design;design; molecularmolecular dynamicsdynamics simulations; molecularmolecular docking;docking; molecularmolecular modelling;modelling; freefree energyenergy calculationscalculations 1. Introduction The venomvenom ofof arthropods arthropods (e.g., (e.g., spiders, spiders, scorpions, scorpion ands, and centipedes) centipedes) and and marine marine animals animals (e.g., (e.g., cone snails,cone snails, jellyfishes, jellyfishes, and and sea anemones)sea anemones) are are a rich a rich source source of of biologically biologically active active molecules. molecules. AA majormajor component of these venoms are disulfide-richdisulfide-rich peptides,peptides, also referred to as toxins.toxins. They are typically 10–6010–60 aminoamino acidsacids longlong andand foldfold intointo aa well-definedwell-defined secondarysecondary structurestructure thatthat isis stabilisedstabilised byby multiplemultiple highly conserved disulfidedisulfide bonds [[1].1]. The peptides are highly resistant to extremes of solvents, pH, and temperaturetemperature as as well well as as to to degradation degradation by by proteases. proteases. Figure Figure 11 depicts depicts the the structure structure of of three three examples examples of ofsuch such disulfide-rich disulfide-rich peptides: peptides: Charybdotoxin Charybdotoxin (ChTx) (ChTx) isolated isolated from the from venom the venom of the scorpion of the scorpion Leiurus Leiurusquinquestriatus quinquestriatus hebraeus hebraeus, Stichodactyla, Stichodactyla toxin toxin (ShK) (ShK) from from the the Caribbean Caribbean sea sea anemone anemone Stichodactyla helianthus,, andand Protoxin-IProtoxin-I (ProTx-I)(ProTx-I) fromfrom thethe PeruvianPeruvian green-velvetgreen-velvet tarantulatarantulaThrixopelma Thrixopelma pruriens.pruriens. Figure 1.1: StructuresStructures of of the disulfide-rich disulfide-rich venom peptidespeptides Charybotoxin (ChTx, PDB-id 2CRD), Stichodactyla toxin (ShK, PDB-id 1ROO), and Protoxin-IProtoxin-I (ProTx-I,(ProTx-I, PDB-idPDB-id 2M9L).2M9L). TheThe well-definedwell-defined secondarysecondary structurestructure isis stabilisedstabilised byby oneone oror moremore disulfidedisulfide bondsbonds (yellow).(yellow). Molecules 2017, 22, 362; doi:10.3390/molecules22030362 www.mdpi.com/journal/molecules Molecules 2017, 22, 362; doi:10.3390/molecules22030362 www.mdpi.com/journal/molecules Molecules 2017, 22, 362 2 of 16 Many disulfide-rich venom peptides are potent and selective inhibitors of ion channels and other membrane-bound receptors. Among the most common molecular targets are voltage-gated Molecules 2017, 22, 362 2 of 16 + + 2+ Na (NaV) and K (KV) channels, voltage-sensitive Ca channels, mechanosensitive channels, nicotinic acetylcholineMany disulfide-rich receptors, venom transient peptides receptor are potent potential and selective (TRP) inhibitors cation channels, of ion channels and acid and sensing ion channelsother membrane-bound (ASICs) [2–7 receptors.]. These Among channels the most and common receptors molecular are involved targets are in almostvoltage-gated all aspects Na+ of mammalian(NaV) and physiology K+ (KV) channels, and many voltage-sensitive of them are associated Ca2+ channels, with pathophysiologicalmechanosensitive channels, conditions nicotinic including autoimmuneacetylcholine disorders, receptors, cardiac transient diseases, receptor aspotent wellial as (TRP) neurological cation channels, and musculoskeletal and acid sensing disorders. ion Disulfide-richchannels (ASICs) venom [2–7]. peptides These channels are thus and valuable receptor pharmacologicals are involved in almost tools toall examineaspects of themammalian role of these physiology and many of them are associated with pathophysiological conditions including autoimmune ion channels and receptors in both physiological and pathological conditions [3,8] as well as lead disorders, cardiac diseases, as well as neurological and musculoskeletal disorders. Disulfide-rich molecules to develop new pharmaceuticals [2,4,6,7,9,10]. venom peptides are thus valuable pharmacological tools to examine the role of these ion channels andTranslating receptors venomin both peptidesphysiological into and therapeutically pathological conditions useful molecules [3,8] as well often as lead involves molecules the to use of structure-baseddevelop new andpharmaceuticals rational drug [2,4,6,7,9,10]. design approaches. For this, a detailed understanding of the structural,Translating chemical, venom and biophysical peptides into properties therapeuticall of they useful peptide molecules as well often as its involves interactions the use with of the targetstructure-based protein is required. and rational While drug the design specific approa interactionsches. For betweenthis, a detailed a peptide understanding and a given of the protein are unique,structural, many chemical, peptides and biophysical act via similar properties mechanisms of the peptide as illustrated as well as inits Figureinteractions2. Peptides with the that target protein is required. While the specific interactions between a peptide and a given protein are modulate voltage-gated ion channels (e.g., NaV and KV) can act as pore blockers or gating modifiers. Poreunique, blockers many bind peptides to the solvent-accessibleact via similar mechanisms pore domain as illustrated of the in channel Figure 2. and Peptides prevent that the modulate flow of ions voltage-gated ion channels (e.g., NaV and KV) can act as pore blockers or gating modifiers. Pore (Figure2a). Gating modifiers bind to the membrane-embedded voltage-sensing domains (VSDs) and blockers bind to the solvent-accessible pore domain of the channel and prevent the flow of ions thus alter the kinetics and gating behaviour of the channel (Figure2b). As the VSDs are partially (Figure 2a). Gating modifiers bind to the membrane-embedded voltage-sensing domains (VSDs) and embeddedthus alter into the the kinetics membrane, and gating the activity behaviour of someof the gatingchannel modifiers (Figure 2b). is relatedAs the VSDs to their are ability partially to bind to orembedded partition into into the the membrane, membrane the activity (Figure of2 c)some [ 11 gating,12]. Peptidesmodifiers is that related modulate to their ability ASICs to [bind8] mostly to or act by bindingpartition tointo the the large membrane extracellular (Figure 2c) domain [11,12]. Peptides where putativethat modulate proton-sensing ASICs [8] mostly residues act by binding are located (Figureto the2d). large extracellular domain where putative proton-sensing residues are located (Figure 2d). FigureFigure 2. Schematic 2. Schematic representation representation of of binding binding sites and and mechanisms mechanisms of ofaction action for fordisulfide-rich disulfide-rich venom venom peptidespeptides acting acting on voltage-gatedon voltage-gated ion