Protein conformation and cryptic pockets

Drug-binding sites are usually pockets or grooves located on the surface of the target protein (Vajda et al., Reference Vajda, Beglov, Wakefield, Egbert and Whitty2018) accessible even in the absence of the drug (Vajda et al., Reference Vajda, Beglov, Wakefield, Egbert and Whitty2018). However, since proteins are dynamic objects, ‘hidden’ binding sites may appear in the presence of an interacting compound (Oleinikovas et al., Reference Oleinikovas, Saladino, Cossins and Gervasio2016; Vajda et al., Reference Vajda, Beglov, Wakefield, Egbert and Whitty2018). These cryptic pockets are often not apparent on the unbound protein surface, only transiently opening up as rare events or shaping themselves in the presence of a ligand (Fig. 1). Cryptic sites can provide unforeseen tractable drug target sites, thus expanding the druggable proteome considerably (Vajda et al., Reference Vajda, Beglov, Wakefield, Egbert and Whitty2018; Hopkins and Groom, Reference Hopkins and Groom2002). On one hand, cryptic pockets offer the prospect to design allosteric drugs (Wenthur et al., Reference Wenthur, Gentry, Mathews and Lindsley2014), a strategy that could be exploited as a therapeutic path towards treating cancer (Zhong et al., Reference Zhong, Li, Xiong, Wang, Wu, Yuan, Yang, Tian, Miao, Wang and Yang2021), diabetes (Wang et al., Reference Wang, Yang, Cheng, Yang, Wang, Dai, Cai, Zhang, Yuliantie, Liu, Jiang, Liu, Wang and Yang2021a), and more recently, SARS-CoV-2 infections (Zimmerman et al., Reference Zimmerman, Porter, Ward, Singh, Vithani, Meller, Mallimadugula, Kuhn, Borowsky, Wiewiora, Hurley, Harbison, Fogarty, Coffland, Fadda, Voelz, Chodera and Bowman2021). On the other hand, cryptic pockets commonly occur at protein–protein interfaces [PPI; (see section ‘Drugs targeting protein–protein interactions’)]. Therefore, the ability to discover and target cryptic pockets would also enable the design of compounds targeting PPIs en route to new therapeutic formulations (Wells and McClendon, Reference Wells and McClendon2007; Shan et al., Reference Shan, Mysore, Leffler, Kim, Sagawa and Shaw2022).

Fig. 1.

Schematic representation of a GPCR (PDB IDs 5XEZ & 6LMK) in inactive (left) and active (right) conformations with an allosteric and peptide ligand bound, respectively. Large conformational changes occur upon binding of the peptide ligand and G_s-protein binding intracellularly, which represent possible dynamics that could be observed with Martin combined with Gō-models. The allosteric pocket in the transmembrane domain exemplifies the possibility to use Martini models for identifying transmembrane pockets, allosteric or cryptic, in various complex membrane compositions. Once a ligand is bound, backmapping is a possibility to obtain higher resolution information for further ligand optimisation or design. All figures were rendered using VMD (Humphrey et al., Reference Humphrey, Dalke and Schulten1996).

Several approaches have been proposed for the identification of cryptic sites. While some of them are entirely based on the analysis of protein crystallographic structures (Le Guilloux et al., Reference Le Guilloux, Schmidtke and Tuffery2009), the majority use MD for the identification of cryptic sites (Le Guilloux et al., Reference Le Guilloux, Schmidtke and Tuffery2009; Kokh et al., Reference Kokh, Richter, Henrich, Czodrowski, Rippmann and Wade2013; Laurent et al., Reference Laurent, Chavent, Cragnolini, Dahl, Pasquali, Derreumaux, Sansom and Baaden2015; Cimermancic et al., Reference Cimermancic, Weinkam, Rettenmaier, Bichmann, Keedy, Woldeyes, Schneidman-Duhovny, Demerdash, Mitchell, Wells, Fraser and Sali2016; Kuzmanic et al., Reference Kuzmanic, Bowman, Juarez-Jimenez, Michel and Gervasio2020; Zheng, Reference Zheng2021; Shan et al., Reference Shan, Mysore, Leffler, Kim, Sagawa and Shaw2022).

Cryptic sites are not usually captured in the 180,000+ tridimensional structures obtained by state-of-the-art experimental methods (Bank, 2021); their opening generally occurs on the microsecond-to-millisecond time timescale (Kuzmanic et al., Reference Kuzmanic, Bowman, Juarez-Jimenez, Michel and Gervasio2020). These timescales are only accessible to all-atom (AA) MD simulations relying on specialised hardware, like the Anton3 (Dror et al., Reference Dror, Young, Shaw and Padua2011; Shaw et al., Reference Shaw, Adams, Azaria, Bank, Batson, Bell, Bergdorf, Bhatt, Butts, Correia, Dirks, Dror, Eastwood, Edwards, Even, Feldmann, Fenn, Fenton, Forte, Gagliardo, Gill, Gorlatova, Greskamp, Grossman, Gullingsrud, Harper, Hasenplaugh, Heily, Heshmat, Hunt, Ierardi, Iserovich, Jackson, Johnson, Kirk, Klepeis, Kuskin, Mackenzie, Mader, McGowen, McLaughlin, Moraes, Nasr, Nociolo, O’Donnell, Parker, Peticolas, Pocina, Predescu, Quan, Salmon, Schwink, Shim, Siddique, Spengler, Szalay, Tabladillo, Tartler, Taube, Theobald, Towles, Vick, Wang, Wazlowski, Weingarten, Williams and Yuh2021), or massive distributed computing, as in the Folding@home project (Zimmerman et al., Reference Zimmerman, Porter, Ward, Singh, Vithani, Meller, Mallimadugula, Kuhn, Borowsky, Wiewiora, Hurley, Harbison, Fogarty, Coffland, Fadda, Voelz, Chodera and Bowman2021), but not yet for standard GPU-accelerated hardware (Schlick and Portillo-Ledesma, Reference Schlick and Portillo-Ledesma2021). As a workaround, AA MD-based approaches involve the addition of hydrophilic (e.g. acetic acid, isopropanol) or hydrophobic (e.g. benzene) molecules in the simulation, the so-called mixed-solvent MD (Ghanakota and Carlson, Reference Ghanakota and Carlson2016), the addition of the drug in high concentration, the so-called ‘flooding’ MD approach (Amaro and Li, Reference Amaro and Li2010; Gray et al., Reference Gray, Ma, Wagner and van der Vaart2017), or fragment-based screening (MacKerell et al., Reference MacKerell, Jo, Lakkaraju, Lind and Yu2020). However, also in this case the opening of cryptic pockets may still require several microseconds (Kuzmanic et al., Reference Kuzmanic, Bowman, Juarez-Jimenez, Michel and Gervasio2020). Enhanced sampling approaches have also been used (Bono et al., Reference Bono, De Smet, Herbert, De Bock, Georgiadou, Fons, Tjwa, Alcouffe, Ny, Bianciotto, Jonckx, Murakami, Lanahan, Michielsen, Sibrac, Dol-Gleizes, Mazzone, Zacchigna, Herault, Fischer, Rigon, Ruiz de Almodovar, Claes, Blanc, Poesen, Zhang, Segura, Gueguen, Bordes, Lambrechts, Broussy, van de Wouwer, Michaux, Shimada, Jean, Blacher, Noel, Motte, Rom, Rakic, Katsuma, Schaeffer, Yayon, Van Schepdael, Schwalbe, Gervasio, Carmeliet, Rozensky, Dewerchin, Simons, Christopoulos, Herbert and Carmeliet2013; Herbert et al., Reference Herbert, Schieborr, Saxena, Juraszek, De Smet, Alcouffe, Bianciotto, Saladino, Sibrac, Kudlinzki, Sreeramulu, Brown, Rigon, Herault, Lassalle, Blundell, Rousseau, Gils, Schymkowitz, Tompa, Herbert, Carmeliet, Gervasio, Schwalbe and Bono2013; Oleinikovas et al., Reference Oleinikovas, Saladino, Cossins and Gervasio2016). For the collective variable (CV)-based approaches, the central challenge is choosing a suitable CV (Kuzmanic et al., Reference Kuzmanic, Bowman, Juarez-Jimenez, Michel and Gervasio2020). For the CV-independent methods, running many simulations still entails high computational costs (Earl and Deem, Reference Earl and Deem2005; Kokh et al., Reference Kokh, Czodrowski, Rippmann and Wade2016), which constitutes the main limiting step.

The Martini 3 CG FF, with its increased accuracy and expanded coverage of the chemical space (Souza et al., Reference Souza, Alessandri, Barnoud, Thallmair, Faustino, Grünewald, Patmanidis, Abdizadeh, Bruininks, Wassenaar, Kroon, Melcr, Nieto, Corradi, Khan, Domański, Javanainen, Martinez-Seara, Reuter, Best, Vattulainen, Monticelli, Periole, Tieleman, de Vries and Marrink2021a; Alessandri et al., Reference Alessandri, Barnoud, Gertsen, Patmanidis, de Vries, Souza and Marrink2022), represents a competitive alternative for extracting and targeting druggable structures on such timescales and/or predicting ligand–target interactions (Souza et al., Reference Souza, Thallmair, Conflitti, Ramírez-Palacios, Alessandri, Raniolo, Limongelli and Marrink2020, Reference Souza, Limongelli, Wu, Marrink and Monticelli2021b). So far, one of the limitations of the Martini models is the description of proteins’ conformational flexibility (Poma et al., Reference Poma, Cieplak and Theodorakis2017; Souza et al., Reference Souza, Thallmair, Marrink and Mera-Adasme2019), which is fundamentally linked to biological function (Henzler-Wildman and Kern, Reference Henzler-Wildman and Kern2007; Luo, Reference Luo2012; Veesler and Johnson, Reference Veesler and Johnson2012; Campaner et al., Reference Campaner, Rustighi, Zannini, Cristiani, Piazza, Ciani, Kalid, Golan, Baloglu, Shacham, Valsasina, Cucchi, Pippione, Lolli, Giabbai, Storici, Carloni, Rossetti, Benvenuti, Bello, D’Incalci, Cappuzzello, Rosato and Del Sal2017; Hadden et al., Reference Hadden, Perilla, Schlicksup, Venkatakrishnan, Zlotnick and Schulten2018; Matthes et al., Reference Matthes, Massari, Bochicchio, Schorpp, Schilling, Weber, Offermann, Desantis, Wanker, Carloni, Hadian, Tabarrini, Rossetti and Krauss2018; Maggi et al., Reference Maggi, Carloni and Rossetti2020; Bolnykh et al., Reference Bolnykh, Rossetti, Rothlisberger and Carloni2021; Noreng et al., Reference Noreng, Li and Payandeh2021; Jackson et al., Reference Jackson, Farzan, Chen and Choe2022) and pivotal to design new therapeutics (Hammes, Reference Hammes2002; Campaner et al., Reference Campaner, Rustighi, Zannini, Cristiani, Piazza, Ciani, Kalid, Golan, Baloglu, Shacham, Valsasina, Cucchi, Pippione, Lolli, Giabbai, Storici, Carloni, Rossetti, Benvenuti, Bello, D’Incalci, Cappuzzello, Rosato and Del Sal2017; Sengupta and Udgaonkar, Reference Sengupta and Udgaonkar2019; Schulz-Schaeffer et al., Reference Schulz-Schaeffer, Wemheuer, Wrede and Ennaji2020; Gossen et al., Reference Gossen, Albani, Hanke, Joseph, Bergh, Kuzikov, Costanzi, Manelfi, Storici, Gribbon, Beccari, Talarico, Spyrakis, Lindahl, Zaliani, Carloni, Wade, Musiani, Kokh and Rossetti2021; Xiao et al., Reference Xiao, Bondarenko and Wang2021; Zhao et al., Reference Zhao, Capelli, Carloni, Lüscher, Li and Rossetti2021; Margreiter et al., Reference Margreiter, Witzenberger, Wasser, Davydova, Janowski, Metz, Habib, Sahnoun, Sobisch, Poma, Palomino-Hernandez, Wagner, Carell, Jon Shah, Schulz, Niessing, Voigt and Rossetti2022).

Commonly, Martini-based approaches implement an elastic network (EN), that is addition of a network of harmonic restraints to stabilise protein tertiary structure (Periole et al., Reference Periole, Cavalli, Marrink and Ceruso2009). The restraints are usually added based on a distance criterion, introducing a strong bias towards the starting conformation (Periole et al., Reference Periole, Cavalli, Marrink and Ceruso2009). Different strategies were devised to address this issue (Deplazes et al., Reference Deplazes, Louhivuori, Jayatilaka, Marrink and Corry2012; Lelimousin et al., Reference Lelimousin, Limongelli and Sansom2016; Poma et al., Reference Poma, Cieplak and Theodorakis2017): (i) localised distance-restraints on selected secondary structure elements, often driven by experimental information. For example, this approach was used to study the activation of the epidermal growth factor receptor, coupling Martini 2 CG simulations with enhanced sampling techniques, such as well-tempered metadynamics (Barducci et al., Reference Barducci, Bussi and Parrinello2008) and distance-based restraints on transmembrane helices (Lelimousin et al., Reference Lelimousin, Limongelli and Sansom2016). (ii) implementation of Gō-like models (GōMartini) by establishing a Lennard–Jones (LJ) potential based on the contact map of the native protein structure instead of the harmonic based potential (Poma et al., Reference Poma, Cieplak and Theodorakis2017; Souza et al., Reference Souza, Thallmair, Marrink and Mera-Adasme2019; Mahmood et al., Reference Mahmood, Poma and Okazaki2021). Different contact map definitions for GōMartini were tested on three protein systems (cohesin, titin and ubiquitin) and reproduced protein flexibility as observed in AA simulations. Two different contact map definitions were tested and compared against ENs. The first variant only considers van der Waals spheres (OV) overlaps, while the second builds on top of the OV approach and includes chemical information from the atoms in question. Here a contact between residues requires that the number of attractive contacts between atoms be larger than the number of repulsive ones (Wołek et al., Reference Wołek, Gómez-Sicilia and Cieplak2015; Poma et al., Reference Poma, Cieplak and Theodorakis2017).

Other approaches also exist to characterise conformational transitions between two or more conformational states in the presence of ENs (Kim et al., Reference Kim, Jernigan and Chirikjian2002; Miyashita et al., Reference Miyashita, Onuchic and Wolynes2003; Feng et al., Reference Feng, Yang, Kloczkowski and Jernigan2009; Das et al., Reference Das, Gur, Cheng, Jo, Bahar and Roux2014), like gradually switching between two different types of EN connectivity through a switching parameter or the so-called ‘generalised elastic network’ (Poma et al., Reference Poma, Li and Theodorakis2018) which, within a given cut-off, implements a canonical EN with harmonic potentials and above the chosen cutoff instead implements Gō-like contacts to the system. Recently, adaptive ENs have been developed as well (Kanada et al., Reference Kanada, Terayama, Tokuhisa, Matsumoto and Okuno2022). These strategies represent a potential powerful development strategy for Martini models.

The Martini model can be coupled with strategies to introduce proteins’ dynamics, as discussed above, and combined with enhanced sampling approaches to ideally push the system towards the exploration of ‘rare’ events, like cryptic pocket opening. The use of artificial intelligence algorithms to identify and speed-up the slower modes, as done in Bonati et al. (Reference Bonati, Rizzi and Parrinello2020 and Reference Bonati, Piccini and Parrinello2021) could also be exploited to steer cryptic pockets’ opening. This represents a valid and computationally cheaper solution to identify and target cryptic pockets. Once possible pockets are identified at the CG level, the protein structure could be converted into atomistic resolution (Wassenaar et al., Reference Wassenaar, Pluhackova, Böckmann, Marrink and Tieleman2014; Vickery and Stansfeld, Reference Vickery and Stansfeld2021) for further investigation and ligand design within a virtual screening (VS) workflow.

Protein binding pockets in membrane environments

A fast-growing area for Martini simulations is the analysis of protein–ligand interactions in membrane environments, which is experimentally and computationally rather challenging. Here, the ligand may be an endogenous lipid, that is, natively part of the physiological environment, or an exogenous compound targeting an allosteric pocket of a transmembrane protein or at the protein–lipid interface (Fig. 1). In this context, the structural characterisation of the ligand-binding sites in the transmembrane region and ranking based on binding energetics extracted by CG MD simulations is particularly attractive. This is even more so because standard computational approaches for protein–ligand binding like molecular docking, that do not account for the specificity of the membrane environment, that is, the strong hydrophobic character and the competition with native lipids, are prone to fail. Recently, several CG MD investigations of protein–ligand interactions in the transmembrane region of pharmacologically relevant targets have been reported. In general, the common computational strategy involves: (i) binding-site identification and structural characterisation of the protein–ligand complex using, among other methods, unbiased CG MD simulations and ligand-density maps (Ferraro et al., Reference Ferraro, Masetti, Recanatini, Cavalli and Bottegoni2016; Dämgen and Biggin, Reference Dämgen and Biggin2021); (ii) ranking of binding modes by binding affinity calculations based on equilibrium MD (Souza et al., Reference Souza, Thallmair, Conflitti, Ramírez-Palacios, Alessandri, Raniolo, Limongelli and Marrink2020), potential of mean force (PMF), alchemical transformations, metadynamics (Corey et al., Reference Corey, Vickery, Sansom and Stansfeld2019) or binding saturation curves (Ansell et al., Reference Ansell, Curran, Horrell, Pipatpolkai, Letham, Song, Siebold, Stansfeld, Sansom and Corey2021); and (iii) structural refinement of the protein ligand complex via backmapping to atomistic models (Wassenaar et al., Reference Wassenaar, Pluhackova, Böckmann, Marrink and Tieleman2014). Overall, the main advantage of CG modelling is the ability to converge on sampling the protein–ligand conformational space, currently out-of-reach by typical unbiased atomistic simulations. As a result, within the limits of the accuracy of the model, trends in dissociation constants (K_d) and rates (K_off) can potentially be accessed from unbiased MD (Souza et al., Reference Souza, Thallmair, Conflitti, Ramírez-Palacios, Alessandri, Raniolo, Limongelli and Marrink2020, Reference Souza, Limongelli, Wu, Marrink and Monticelli2021b).

The vast majority of CG MD analyses of protein–ligand interactions in membrane environments involve protein–lipid binding based on Martini 2.2 simulations (De Jong et al., Reference De Jong, Singh, Bennett, Arnarez, Wassenaar, Schäfer, Periole, Tieleman and Marrink2013). The use of the Martini 2.2 FF has allowed not only to discern specific versus nonspecific interactions but also to characterise the energetics involved in the binding reaction. Earlier efforts focused on the prediction of the binding site(s) for cholesterol, which is the most abundant endogenous steroid in mammalian cell membranes and was shown to modulate several membrane proteins including ion channels. Using multi-microsecond CG MD simulations of a homology model of the serotonin transporter embedded in a raft-like membrane, Ferraro et al (Reference Ferraro, Masetti, Recanatini, Cavalli and Bottegoni2016) provided evidence of the existence of specific binding sites for cholesterol, identifying a hotspot that largely overlaps with the cholesterol-binding site illuminated by X-ray crystallography of the closely related dopamine transporter (Ferraro et al., Reference Ferraro, Masetti, Recanatini, Cavalli and Bottegoni2016). By combining CG MD simulations and PMF calculations, Ansell et al (Reference Ansell, Curran, Horrell, Pipatpolkai, Letham, Song, Siebold, Stansfeld, Sansom and Corey2021) characterised the interaction between cholesterol and several membrane proteins including an ATP-dependent pump, a sterol receptor/transporter protein and a member of the TRP ion-channel family. A similar analysis of the chemokine receptor 3, a GPCR responsible for trafficking white blood cells, allowed for the identification of six cholesterol-binding sites, suggesting that recognition of cholesterol at these sites may modulate the affinity for agonists/antagonists allosterically via a rigidification of the protein structure (van Aalst et al., Reference van Aalst, Koneri and Wylie2021). Using CG MD simulations and lipid-density maps, Damgen and Biggin (Reference Dämgen and Biggin2021) explored the affinity of cholesterol and different lipid types for the glycine receptor channel in its active and resting states and found that lipids may act as allosteric modulators because their strength of binding strongly depend(s) on the physiological state of the receptor. In a similar study, protein–lipid interactions on the homologous nicotinic acetylcholine receptor were investigated using a complex quasi-neuronal membrane composed of 36 species of lipids, including cholesterol, in a binding competition assay (Sharp and Brannigan, Reference Sharp and Brannigan2021). Interestingly, the CG MD simulations suggested that cholesterol binds to concave inter-subunit sites and polyunsaturated fatty acids prefer convex sites at the outer transmembrane helix M4, while monounsaturated and saturated lipids are enriched at the protein–lipid interface (Sharp and Brannigan, Reference Sharp and Brannigan2021). Recently, the interaction of the anionic lipids cardiolipins with 42 inner membrane proteins from Escherichia. coli has been investigated by CG MD simulations. Overall, >700 independent cardiolipin binding sites were identified and structurally characterised, thus providing a molecular basis for protein–cardiolipin interactions (Corey et al., Reference Corey, Song, Duncan, Ansell, Sansom and Stansfeld2021). In the context of systematic comparative analyses, the method by Ansell et al. (Reference Ansell, Curran, Horrell, Pipatpolkai, Letham, Song, Siebold, Stansfeld, Sansom and Corey2021) for protein–ligand binding affinities based on binding saturation curves appears particularly appealing as a high-throughput approach for binding-site comparison and ranking.

In addition to protein–lipid interactions, a potential area of development for CG simulations involves the exploration of modulatory ligand binding, such as agonists, antagonists and allosteric modulators, to the transmembrane region of proteins. In this case, and unlike for most lipid molecules, a serious difficulty is introduced by the lack of off-the-shelf CG parameters to model the ligand(s). As a result, examples of studies focusing on the allosteric modulation of transmembrane proteins via protein–ligand interactions are still rare in the literature. One of them focused on the investigation of the binding pathway of two orthosteric agonists of the μ-opioid receptor, that is, fentanyl and morphine (Sutcliffe et al., Reference Sutcliffe, Corey, Charlton, Sessions, Henderson and Kelly2021). Using CG MD simulations and free energy calculations, Sutcliffe et al. (Reference Sutcliffe, Corey, Charlton, Sessions, Henderson and Kelly2021) compared the aqueous and lipophilic binding pathways to the orthosteric site and found that the synthetic opioid fentanyl prefers the lipophilic route, which might explain its lower susceptibility to overdose reversal. Since more and more high-resolution structures of relevant pharmacological targets highlight the existence of multiple allosteric sites in the transmembrane region of these proteins (Cerdan et al., Reference Cerdan, Sisquellas, Pereira, Barreto Gomes, Changeux and Cecchini2020), the development of automatic parameterisation tools to facilitate the setup of CG MD simulations, similar to what is currently available for AA MD, is expected to leverage more exploratory analyses of protein–ligand interactions in the membrane environment and open to high-throughput screening powered by CG MD simulations. Additionally, the new Martini 3 FF offers an extended chemical space (Souza et al., Reference Souza, Thallmair, Conflitti, Ramírez-Palacios, Alessandri, Raniolo, Limongelli and Marrink2020, Reference Souza, Alessandri, Barnoud, Thallmair, Faustino, Grünewald, Patmanidis, Abdizadeh, Bruininks, Wassenaar, Kroon, Melcr, Nieto, Corradi, Khan, Domański, Javanainen, Martinez-Seara, Reuter, Best, Vattulainen, Monticelli, Periole, Tieleman, de Vries and Marrink2021a, Reference Souza, Limongelli, Wu, Marrink and Monticelli2021b), providing an excellent platform for developing automatic parameterisation tools for ligands.

Drugs targeting protein–protein interactions

PPIs have been considered as promising drug targets since the early 2000s, with the hope to overcome the decline in the efficiency of conventional drug development. Three major types of PPI modulators currently described in the literature are small molecules, antibodies and peptides (Mabonga and Kappo, Reference Mabonga and Kappo2019; Lu et al., Reference Lu, Zhou, He, Jiang, Peng, Tong and Shi2020; Martino et al., Reference Martino, Chiarugi, Margheriti and Garau2021). Small molecules typically require a prototypical binding site. The PPI interface is usually flat, shallow and hydrophobic, without an actual pocket where small-molecule ligands may bind (Lu et al., Reference Lu, Zhou, He, Jiang, Peng, Tong and Shi2020). The natural alternative would be to increase the size of the modulator to maximise PPI interface coverage and establish many hydrophobic contacts (Lu et al., Reference Lu, Zhou, He, Jiang, Peng, Tong and Shi2020). However, increasing small-molecule-based PPI modulator size may lead to undesirable pharmacokinetic profiles (An and Fu, Reference An and Fu2018; Lu et al., Reference Lu, Zhou, He, Jiang, Peng, Tong and Shi2020; Martino et al., Reference Martino, Chiarugi, Margheriti and Garau2021). Antibodies present an alternative therapeutic avenue, since these can fully cover the PPI interface due to their size (Bojadzic and Buchwald, Reference Bojadzic and Buchwald2018; Martino et al., Reference Martino, Chiarugi, Margheriti and Garau2021) and there is potential for the general application of antibody-based therapies when combined with novel drug delivery systems (Slastnikova et al., Reference Slastnikova, Ulasov, Rosenkranz and Sobolev2018). Peptides can also be used to modulate PPIs as they bind the PPI interface with high affinity (Cabri et al., Reference Cabri, Cantelmi, Corbisiero, Fantoni, Ferrazzano, Martelli, Mattellone and Tolomelli2021), but they may exhibit short half-lives and toxicity risks (Gupta et al., Reference Gupta, Kapoor, Chaudhary, Gautam, Kumar, Consortium and Raghava2013; Nevola and Giralt, Reference Nevola and Giralt2015; Mabonga and Kappo, Reference Mabonga and Kappo2019). Examples of small-molecule PPI modulators are venetoclax, to treat chronic lymphoblastic leukaemia (Lu et al., Reference Lu, Zhou, He, Jiang, Peng, Tong and Shi2020), and pomalidomide to treat myeloma (Dimopoulos et al., Reference Dimopoulos, Leleu, Palumbo, Moreau, Delforge, Cavo, Ludwig, Morgan, Davies, Sonneveld, Schey, Zweegman, Hansson, Weisel, Mateos, Facon and Miguel2014). ALRN-6924 is an α-helical peptide aimed at leukaemia therapy (Carvajal et al., Reference Carvajal, Neriah, Senecal, Benard, Thiruthuvanathan, Yatsenko, Narayanagari, Wheat, Todorova, Mitchell, Kenworthy, Guerlavais, Annis, Bartholdy, Will, Anampa, Mantzaris, Aivado, Singer, Coleman, Verma and Steidl2018) while Bavencio is an antibody-based drug targeting Merkel cell carcinoma (Boyerinas et al., Reference Boyerinas, Jochems, Fantini, Heery, Gulley, Tsang and Schlom2015).

Recently, a new type of PPI modulator technology gained momentum: the Proteolysis Targeting Chimeras (PROTACs) (Sakamoto et al., Reference Sakamoto, Kim, Kumagai, Mercurio, Crews and Deshaies2001). These bivalent molecules consist of a linker connecting a small molecule binding the target (i.e. ‘warhead’) and a second small molecule binding an E3 ligase (the ‘recruiter’), acting as a PPI enhancer like molecular glues (Wang et al., Reference Wang, Jiang, Feng, Liu and Sun2020; Alabi and Crews, Reference Alabi and Crews2021; Bond and Crews, Reference Bond and Crews2021; Békés et al., Reference Békés, Langley and Crews2022). Simultaneous binding of both proteins by the PROTAC brings them into proximity, provoking target ubiquitination and posterior degradation by proteasome machinery (Wang et al., Reference Wang, Jiang, Feng, Liu and Sun2020; Alabi and Crews, Reference Alabi and Crews2021; Bond and Crews, Reference Bond and Crews2021; Békés et al., Reference Békés, Langley and Crews2022). Compared to small-molecule inhibitors, PROTACs work catalytically, requiring less compound concentration, having fewer off-target effects and exhibiting improved target selectivity (Troup et al., Reference Troup, Fallan and Baud2020; Alabi and Crews, Reference Alabi and Crews2021; Békés et al., Reference Békés, Langley and Crews2022). In the last years, PROTACs attracted the interest of academic and pharmaceutical companies and currently two molecules developed by Arvinas were forwarded to Phase II clinical trials (Petrylak et al., Reference Petrylak, Gao, Vogelzang, Garfield, Taylor, Dougan Moore, Peck and Burris2020; Békés et al., Reference Békés, Langley and Crews2022). Key steps in PROTAC development include the selection of the E3 ligase to pair with the target of interest (Cecchini et al., Reference Cecchini, Pannilunghi, Tardy and Scapozza2021), the accurate prediction of the ternary complex structure (Zaidman et al., Reference Zaidman, Prilusky and London2020) and linker design (Troup et al., Reference Troup, Fallan and Baud2020; Bemis et al., Reference Bemis, La Clair and Burkart2021).

Computational modelling and simulations can help the rational design of PROTACs (Fig. 2). In the absence of ternary complex crystal structures, which must contain the target, the PROTAC and the ligase, one of the first steps of in silico design is sampling the conformational landscape of the complex, which is achievable by protein–protein docking (Hayashi et al., Reference Hayashi, Matsuzaki, Yanagisawa, Ohue and Akiyama2018; Drummond and Williams, Reference Drummond and Williams2019; Drummond et al., Reference Drummond, Henry, Li and Williams2020; Rosell and Fernández-Recio, Reference Rosell and Fernández-Recio2020; Zaidman et al., Reference Zaidman, Prilusky and London2020; Bluntzer et al., Reference Bluntzer, O’Connell, Baker, Michel and Hulme2021; Bai et al., Reference Bai, Miller, Andrianov, Yates, Kirubakaran and Karanicolas2021, Reference Bai, Riching, Makaju, Wu, Acker, Ou, Zhang, Shen, Bulloch, Rui, Gibson, Daniels, Urh, Rock and Humphreys2022; Weng et al., Reference Weng, Li, Kang and Hou2021) and/or MD simulations at various levels of detail (Rakers et al., Reference Rakers, Bermudez, Keller, Mortier and Wolber2015; Yu et al., Reference Yu, Jo, Lakkaraju, Weber and MacKerell2019; Perez et al., Reference Perez, Perez and Perez2021). For very large systems however, AA MD can become prohibitively expensive (Durrant and McCammon, Reference Durrant and McCammon2011; Amaro et al., Reference Amaro, Baudry, Chodera, Demir, McCammon, Miao and Smith2018; Jung et al., Reference Jung, Kobayashi, Kasahara, Tan, Kuroda, Minami, Ishiduki, Nishiki, Inoue, Ishikawa, Feig and Sugita2021). This is particularly true when considering a VS campaign applied to ternary complexes in explicit solvent, due to system size and complexity. As an alternative, docking and MD simulations based on the Martini 2 and 3 CG framework (Roel-Touris et al., Reference Roel-Touris, Don, Honorato, Rodrigues and Bonvin2019; Roel-Touris and Bonvin, Reference Roel-Touris and Bonvin2020; Souza et al., Reference Souza, Limongelli, Wu, Marrink and Monticelli2021b) may be used to facilitate the study of these large macromolecular systems. In a first stage, CG protein–protein docking can be used to capture the most important features of the interaction complex, providing many potential binding modes. It can then be combined with long and affordable CG MD simulations to probe complex stability, which is critical for PPI drug discovery. One example of CG-docking methods is HADDOCK (Roel-Touris et al., Reference Roel-Touris, Don, Honorato, Rodrigues and Bonvin2019; Roel-Touris and Bonvin, Reference Roel-Touris and Bonvin2020). A limitation of some docking approaches is the treatment of proteins as rigid bodies (Vakser, Reference Vakser2020; Harmalkar and Gray, Reference Harmalkar and Gray2021). Recently, docking approaches including protein flexibility have been developed, including ‘divide-and-conquer’ (Karaca and Bonvin, Reference Karaca and Bonvin2011) and normal mode analysis-based strategies (May and Zacharias, Reference May and Zacharias2008; Moal and Bates, Reference Moal and Bates2010; Jiménez-García et al., Reference Jiménez-García, Roel-Touris, Romero-Durana, Vidal, Jiménez-González and Fernández-Recio2018; Diaz et al., Reference Diaz, Frezza and Martin2021). Alternatively, GōMartini simulations (Poma et al., Reference Poma, Cieplak and Theodorakis2017) could be used to cheaply produce protein–protein conformations which, after a back-mapping procedure, could be used in ensemble docking (Amaro et al., Reference Amaro, Baudry, Chodera, Demir, McCammon, Miao and Smith2018).

Fig. 2.

Important steps in PROTAC design for drug discovery campaigns. (a) Protein–protein docking either at the atomistic (ribbons) or coarse-grained level (red and cyan spheres). The E3 ligase is represented in red and the target protein in blue. (b) Coarse-graining of a small -molecule using the Martini 3 force field. (c) Dynamical motions of the ligase and the target (blue and red arrows, respectively) are important to query ternary complex stability in the presence of the PROTAC (represented as van der Waals spheres). All figures were rendered using VMD (Humphrey et al., Reference Humphrey, Dalke and Schulten1996). The ternary complex structure is from Nowak et al. (Reference Nowak, DeAngelo, Buckley, He, Donovan, An, Safaee, Jedrychowski, Ponthier, Ishoey, Zhang, Mancias, Gray, Bradner and Fischer2018) with the PDB ID code 6BN7.

Massive protein–protein docking for target identification (Zhang et al., Reference Zhang, Tang, Wang and Lai2014) of other PPI modulators can also greatly benefit from the use of CG approaches. In the case of PROTACS, not only the target but also the choice of E3 Ligase is fundamental for the stability of the ternary complex and cell-specific target degradation (Békés et al., Reference Békés, Langley and Crews2022). Only a limited number of E3 ligases have been explored towards PROTAC development (Burslem and Crews, Reference Burslem and Crews2020; Troup et al., Reference Troup, Fallan and Baud2020; Alabi and Crews, Reference Alabi and Crews2021). Examples are the von Hippel-Landau or Cereblon E3 ligases (He et al., Reference He, Khan, Huo, Lv, Zhang, Liu, Yuan, Hromas, Xu, Zheng and Zhou2020; Bricelj et al., Reference Bricelj, Steinebach, Kuchta, Gütschow and Sosič2021). However, some ligases, for which there is currently no crystal PROTAC ternary complex available, are known to be enriched in specific cell types (Békés et al., Reference Békés, Langley and Crews2022). Combining CG docking between a PROTAC-containing target and several candidate ligases separately with subsequent CG MD simulations could help to identify the most suitable target-ligase pair, enabling cell-type-based therapeutic PROTAC approaches.

Another PROTAC-specific challenge is the design of the linker portion (Alabi and Crews, Reference Alabi and Crews2021) as there exist no common practices or guidelines, and linker size and flexibility affect the degradation efficiency of PROTACs (Cyrus et al., Reference Cyrus, Wehenkel, Choi, Han, Lee, Swanson and Kim2011; Crew et al., Reference Crew, Raina, Dong, Qian, Wang, Vigil, Serebrenik, Hamman, Morgan, Ferraro, Siu, Neklesa, Winkler, Coleman and Crews2018; Troup et al., Reference Troup, Fallan and Baud2020). Optimal linkers should be long and flexible enough to promote a ternary complex orientation that allow ubiquitin transfer to the lysines on the target surface. However, overly flexible linkers may hamper target degradation efficiency (Cecchini et al., Reference Cecchini, Pannilunghi, Tardy and Scapozza2021). CG-based approaches can help linker optimisation. For example, PROTAC CG docking simulations could be used to evaluate the possibility of other PROTAC molecules fitting into the available volume at the binding interface of a ligase/target complex. One route would be by harnessing structural data like the warhead-recruiter distances, extracted from ternary complexes from the Protein Data Bank (Burley et al., Reference Burley, Bhikadiya, Bi, Bittrich, Chen, Crichlow, Christie, Dalenberg, Di Costanzo, Duarte, Dutta, Feng, Ganesan, Goodsell, Ghosh, Green, Guranović, Guzenko, Hudson, Lawson, Liang, Lowe, Namkoong, Peisach, Persikova, Randle, Rose, Rose, Sali, Segura, Sekharan, Shao, Tao, Voigt, Westbrook, Young, Zardecki and Zhuravleva2021) or from protein–protein docking experiments, as constraints. Filtering the predicted complexes using this information in combination with the docking score and other observables would allow retrieval of the best binding poses per system (Zaidman et al., Reference Zaidman, Prilusky and London2020). From the most stable complexes, probed by CG MD, a linker template could then be designed and subsequently used in VS campaigns targeting chemically diverse linker libraries. Further, chemical modifications around the linker template would enable fine tuning of PROTAC properties like solubility, lipophilicity or toxicity effects (Troup et al., Reference Troup, Fallan and Baud2020). Recently, the group of Kihlberg illustrated that PROTACs cell permeability is deeply related to the linkers’ conformational flexibility. Although these compounds do not conform to oral bioavailability defined by the Lipinski rule-of-5 (Lipinski et al., Reference Lipinski, Lombardo, Dominy and Feeney2001), by acting as ‘molecular chameleons’ they are able to fold-in on themselves in aqueous solution and reduce their solvent-accessible polar surface area to increase cell permeability and then unfurl after crossing the membrane (Atilaw et al., Reference Atilaw, Poongavanam, Svensson Nilsson, Nguyen, Giese, Meibom, Erdelyi and Kihlberg2021). Thus, some of the key factors playing a role in PROTAC cell permeability are linker size (Klein et al., Reference Klein, Townsend, Testa, Zengerle, Maniaci, Hughes, Chan, Ciulli and Lokey2020), polarity and rigidity (Atilaw et al., Reference Atilaw, Poongavanam, Svensson Nilsson, Nguyen, Giese, Meibom, Erdelyi and Kihlberg2021), further highlighting the importance of a rational linker design strategy. Similar concerns related to polarity and membrane permeability are also prevalent in PPI-targeting peptide design (Sugita et al., Reference Sugita, Sugiyama, Fujie, Yoshikawa, Yanagisawa, Ohue and Akiyama2021). As such, transfer free energy calculations carried out at the CG level could enable the direct investigation of the ability of different PPI modulators to cross biological membranes in an efficient and affordable manner while still achieving a high degree of accuracy.

Tuning soft nanoparticles with Martini

Drug efficacy correlates with the ability of the drug to reach the target site in sufficient quantities. A high percentage of approved drugs display low aqueous solubility and are fast degraded. To tackle these problems, delivery systems have been developed (Malmsten, Reference Malmsten2006; Wang et al., Reference Wang, Ye, Gao and Ouyang2021b). Different physicochemical properties of the delivery system, such as morphology, composition and stiffness, can contribute to the drug solubility, targeting efficiency and stability (Zhang et al., Reference Zhang, Gao and Bao2015; Yu et al., Reference Yu, Xu, Tian, Su, Zheng, Yang, Wang, Wang, Zhu, Guo, Zhang, Gan, Shi and Gao2018). As drug carrier rigidity affects physiological membrane crossing, developing soft nanoparticle (SN) systems that can easily deform appears attractive.

SNs include carriers consisting of lipids, polymers or surfactants. Lipid-based carriers are generally biocompatible and highly permeable; however, they exhibit low mechanical stability (Sercombe et al., Reference Sercombe, Veerati, Moheimani, Wu, Sood and Hua2015). Polymer-based carriers, on the other hand, have higher mechanical stability but lower biocompatibility and permeability (Jana et al., Reference Jana, Shyam, Singh, Jayaprakash and Dev2021). It is also possible to combine lipids and polymers and to harness the advantages of each component (Reimhult and Virk, Reference Reimhult and Virk2021). Studies have shown that the mechanism of delivery for SNs depends on their morphology and composition, which is in turn correlated with the distribution of the drug within the carrier (El Maghraby et al., Reference El Maghraby, Barry and Williams2008). However, little is known about the morphology and mechanism of delivery for these hybrid systems (Reimhult and Virk, Reference Reimhult and Virk2021).

CG modelling is a valuable tool for investigating the formation of SNs, their morphology, drug distribution within the carrier and the mechanism of delivery, including the interaction with different biological membranes (Yang et al., Reference Yang, Guo, Tian and Chen2021; Parchekani et al., Reference Parchekani, Allahverdi, Taghdir and Naderi-Manesh2022). The first obstacle for using CG models is constructing the system. Fortunately, an increasing number of tools have been developed for building such CG models, examples being TS2CG, Charmm-GUI and Nano Disc builder, allowing the construction of vesicles and other SNs for drug delivery (Qi et al., Reference Qi, Ingólfsson, Cheng, Lee, Marrink and Im2015; Hsu et al., Reference Hsu, Bruininks, Jefferies, Souza, Lee, Patel, Marrink, Qi, Khalid and Im2017; Kjølbye et al., Reference Kjølbye, De Maria, Wassenaar, Abdizadeh, Marrink, Ferkingoff-Borg and Schiøtt2020; Pezeshkian et al., Reference Pezeshkian, König, Wassenaar and Marrink2020), the Polyply package for constructing polymer-based systems (Grünewald et al., Reference Grünewald, Alessandri, Kroon, Monticelli, Souza and Marrink2022) or the Insane.py script for bilayers (Wassenaar et al., Reference Wassenaar, Ingólfsson, Böckmann, Tieleman and Marrink2015). In combination, protocols for simulating soft delivery systems have also started to appear in the literature (Bruininks et al., Reference Bruininks, Souza and Marrink2019). Several CG studies have been performed using the Martini 2 model, investigating the morphology, size and internal organisation of the different components in lipid and polymer-based carriers (Hashemzadeh et al., Reference Hashemzadeh, Javadi and Darvishi2020; Bono et al., Reference Bono, Coloma Smith, Moreschi, Redaelli, Gautieri and Candiani2021; Gao et al., Reference Gao, Nicolas and Ha-Duong2021). Among the first described SNs are liposomes, consisting of a lipid bilayer surrounding a hydrophilic core, capable of trapping both hydrophobic and hydrophilic drugs. Liposomes were the first delivery system to reach clinical application (Doxil) (James et al., Reference James, Coker, Tomlinson, Harris, Gompels, Pinching and Stewart1994) and have been widely used and characterised for many different therapeutics (Allen and Cullis, Reference Allen and Cullis2013). Further development of liposomes resulted in cationic lipids and subsequently cationic polymers for delivery of NAs, which proved invaluable at the outbreak of the COVID-19 pandemic (Polack et al., Reference Polack, Thomas, Kitchin, Absalon, Gurtman, Lockhart, Perez, Pérez Marc, Moreira, Zerbini, Bailey, Swanson, Roychoudhury, Koury, Li, Kalina, Cooper, Frenck, Hammitt, Türeci, Nell, Schaefer, Ünal, Tresnan, Mather, Dormitzer, Şahin, Jansen and Gruber2020; Baden et al., Reference Baden, El Sahly, Essink, Kotloff, Frey, Novak, Diemert, Spector, Rouphael, Creech, McGettigan, Khetan, Segall, Solis, Brosz, Fierro, Schwartz, Neuzil, Corey, Gilbert, Janes, Follmann, Marovich, Mascola, Polakowski, Ledgerwood, Graham, Bennett, Pajon, Knightly, Leav, Deng, Zhou, Han, Ivarsson, Miller and Zaks2021). Cationic lipids or polymers can condense NA efficiently, thanks to the electrostatic interaction with the negatively charged NA to form lipoplexes and polyplexes, respectively (Li and Szoka, Reference Li and Szoka2007; Schlich et al., Reference Schlich, Palomba, Costabile, Mizrahy, Pannuzzo, Peer and Decuzzi2021). Accurate description of the electrostatic interactions is a major challenge in the case of highly charged lipo- or polyplexes. The challenge could be tackled by developing polarisable Martini models, so far only available for water, ions and proteins with the Martini 2 FF (Yesylevskyy et al., Reference Yesylevskyy, Schäfer, Sengupta and Marrink2010; De Jong et al., Reference De Jong, Singh, Bennett, Arnarez, Wassenaar, Schäfer, Periole, Tieleman and Marrink2013; Michalowsky et al., Reference Michalowsky, Schäfer, Holm and Smiatek2017, Reference Michalowsky, Zeman, Holm and Smiatek2018; Sahoo et al., Reference Sahoo, Lee and Matysiak2022).

The main drawback of permanently charged cationic components is their toxicity and rapid elimination from circulation (Li and Szoka, Reference Li and Szoka2007; Schlich et al., Reference Schlich, Palomba, Costabile, Mizrahy, Pannuzzo, Peer and Decuzzi2021). To avoid the toxicity and increase the circulation time and stability, particles can be covered by a PEGylated lipid shield (Li and Szoka, Reference Li and Szoka2007), although PEGylation has shown to diminish particle uptake in target cells (PEG dilemma) (Gjetting et al., Reference Gjetting, Arildsen, Christensen, Poulsen, Roth, Handlos and Poulsen2010). The Martini model has eased the way to study polymer coating in membranes (Grünewald et al., Reference Grünewald, Rossi, de Vries, Marrink and Monticelli2018; Lemaalem et al., Reference Lemaalem, Hadrioui, Derouiche and Ridouane2020) and NPs (Pannuzzo et al., Reference Pannuzzo, Esposito, Wu, Key, Aryal, Celia, di Marzio, Moghimi and Decuzzi2020).

A step further in the optimisation led to ionisable components, resulting in the formulation of lipid nanoparticles (LNPs) (Schlich et al., Reference Schlich, Palomba, Costabile, Mizrahy, Pannuzzo, Peer and Decuzzi2021) and dendrimers (Palmerston Mendes et al., Reference Palmerston Mendes, Pan and Torchilin2017), branched polymers with well-defined molecular weights. The ionisable components are positively charged at low pH to encapsulate NA, and neutral at higher pH, for example, in the blood, thereby avoiding the drawbacks of lipo- and polyplexes. However, it has been shown that only 2–3% of the nucleotide drug load reaches the cytosol using LNPs (Gilleron et al., Reference Gilleron, Querbes, Zeigerer, Borodovsky, Marsico, Schubert, Manygoats, Seifert, Andree, Stöter, Epstein-Barash, Zhang, Koteliansky, Fitzgerald, Fava, Bickle, Kalaidzidis, Akinc, Maier and Zerial2013). Once the LNP or dendrimer is endocytosed, endosomes eventually fuse with lysosomes and their cargo is degraded. For optimised release, the cargo needs to escape the endosome before fusion with the lysosome (Schlich et al., Reference Schlich, Palomba, Costabile, Mizrahy, Pannuzzo, Peer and Decuzzi2021). A general understanding of the delivery mechanism and its pH dependence is lacking. For investigating pH dependent release routes or interactions with NA, constant pH CG approaches are available (Grünewald et al., Reference Grünewald, Souza, Abdizadeh, Barnoud, de Vries and Marrink2020; Aho et al., Reference Aho, Buslaev, Jansen, Bauer, Groenhof and Hess2022). As a proof of concept, collective interactions between titratable sites in a G5 dendrimer poly(propylene imine) were simulated at different pH values, revealing how the particle expands in radius and increases in degree of protonation with decreasing pH, consistent with previous atomistic studies (Grünewald et al., Reference Grünewald, Souza, Abdizadeh, Barnoud, de Vries and Marrink2020).

The delivery depends on the structural properties of the carrier. For LNPs, two different internal organisations have been proposed based on CG modelling with Martini 2 and cryo-transmission electron microscopy (Leung et al., Reference Leung, Hafez, Baoukina, Belliveau, Zhigaltsev, Afshinmanesh, Tieleman, Hansen, Hope and Cullis2012; Kulkarni et al., Reference Kulkarni, Darjuan, Mercer, Chen, van der Meel, Thewalt, Tam and Cullis2018). Understanding the structure–activity relationship is of paramount importance for the rational design of optimised LNPs and for cell-specific targeting. Cell specific LNPs can be built by changing one or more of the lipid components (Liu et al., Reference Liu, Cheng, Wei, Yu, Johnson, Farbiak and Siegwart2021; Żak and Zangi, Reference Żak and Zangi2021), but models of synthetic lipids are not always available. The combination of the Martini 3 FF, with its extended chemical space, and building tools enables the prediction of properties of both empty structures of SNs, such as LNPs, and complexes with cargo of various sizes, from small interfering RNA (siRNAs) to large messenger RNA (mRNA) molecules, enabling studies of the internal organisation and interactions.

Cell specificity and drug efficacy can, in principle, be optimised in terms of interaction and fusion with the endosomal membrane. To this end, Martini 2 models of complex membranes have previously been constructed (Ingólfsson et al., Reference Ingólfsson, Melo, van Eerden, Arnarez, Lopez, Wassenaar, Periole, de Vries, Tieleman and Marrink2014, Reference Ingólfsson, Bhatia, Zeppelin, Bennett, Carpenter, Hsu, Dharuman, Bremer, Schiøtt, Lightstone and Carpenter2020), which demonstrates the possibility of studying the interaction between various SNs formulations (Lee et al., Reference Lee, Cheng, Yu, Liu, Johnson and Siegwart2021) and cell-specific plasma and endosomal membranes. However, this field remains to be explored.

In perspective, there is a general need to implement alternative design strategies to further optimise SNs. Tuning the chemical groups of the lipids or polymer, along with ratios of components, is key for altering the properties of SNs. However, synthesising and testing combinations of lipid or polymer variables are costly and time consuming. In silico screening of promising formulations is a viable alternative to study the role that each component plays in the SN morphology and delivery process (Fig. 3). One drawback when studying lipid-based systems using CG approaches is the loss of resolution compared to AA representations. For instance, changes in tail composition are not always well captured. Nevertheless, in the new version of Martini different tail chemistries can be easier to represent in the future as a result of the use of small and tiny beads.

Fig. 3.

CG modelling enables predictions of organisation, size and stability of SNs containing various building blocks and cargo. Moreover, it can be used to study the interaction between various SN formulations and biological barriers, such as plasma and endosomal membranes. All figures were rendered using VMD (Humphrey et al., Reference Humphrey, Dalke and Schulten1996).

Summary and future directions

For in silico studies of large complex systems, aiming at identifying possible druggable sites, predicting and optimising protein ligand binding for drug design or studying drug delivery systems, the Martini model provides an efficient approach relative to AA MD. Due to the timescales reachable by CG Martini simulations, it is possible to probe systems with respect to pockets formed transiently, interesting for drug discovery campaigns. However, further benchmarking is required to assess the accuracy of the FF. Furthermore, maintaining proteins’ tertiary structure in Martini models requires inclusion of EN or GōMartini potentials. Thus, a reasonable definition of the contact map, from which to draw the network of potentials, is critical. Improvements to the definition of contact maps may consider an ensemble of conformations and use knowledge of hydrogen bonds and residue protonation. Additionally, the use of LJ potentials in GōMartini enables the development of multi-basin models, as previously shown for AA MD (Okazaki et al., Reference Okazaki, Koga, Takada, Onuchic and Wolynes2006), combining Gō-models of different protein conformations to promote conformational transitions.

Currently, a major challenge towards the use of the Martini CG model in drug design and drug delivery is the automatic parameterisation of ligands and components of delivery vectors, including AA-to-CG mapping, construction of the bonded parameters and bead-type assignment. To address this issue, tools like Swarm-CG (Empereur-Mot et al., Reference Empereur-Mot, Pesce, Doni, Bochicchio, Capelli, Perego and Pavan2020) or PyCGTOOL (Graham et al., Reference Graham, Essex and Khalid2017) have been developed. However, these approaches focus solely on optimising the bonded parameters. Automated parameterisation workflows for Martini 2 models of small molecules are available (Bereau and Kremer, Reference Bereau and Kremer2015; Potter et al., Reference Potter, Barrett and Miller2021), including mapping, bonded-parameter definition and bead type selection based on optimisation of oil–water partitioning free energies. However, since the covered chemical space is larger in Martini 3, adapting these codes to Martini 3 is not straightforward. Equally important will be the generation of curated and extended libraries of Martini models, such as MAD (the MArtini Database server – https://mad.ibcp.fr), which can be used as reference to access the accuracy of such automatic approaches (Hilpert et al., Reference Hilpert, Beranger, Souza, Vainikka, Nieto, Marrink, Monticelli and Launay2022). However, the current library of Martini 3 small-molecule models (Alessandri et al., Reference Alessandri, Barnoud, Gertsen, Patmanidis, de Vries, Souza and Marrink2022) may already allow initial benchmarks based on fragment-based strategies. Another challenge is the backmapping procedure from CG to AA resolution (Wassenaar et al., Reference Wassenaar, Pluhackova, Böckmann, Marrink and Tieleman2014; Vickery and Stansfeld, Reference Vickery and Stansfeld2021), as protein side-chain directionality is kept, but the binding mode may not be accurate. A standard solution is to perform cycles of energy minimisation and equilibration on the backmapped structure to improve side-chain packing. Another option in this direction would involve the use of machine learning methods to optimise side-chain orientation (Misiura et al., Reference Misiura, Shroff, Thyer and Kolomeisky2022).

Backmapping and small-molecule automatic parameterisation are fundamental goals towards VS of molecules targeting PPI systems, like PROTACS. Additionally, available tools for CG protein–protein docking with the Martini 3 FF could efficiently provide researchers with reasonable starting structures for these large complexes, whose dynamics can be probed by MD. This is the premise of the currently in-development CG version of LightDock (Roel-Touris et al., Reference Roel-Touris, Bonvin and Jiménez-García2020a, Reference Roel-Touris, Jiménez-García and Bonvin2020b), implementing the Martini 3 FF. Coupling these tools with CG docking and MD simulations would allow to derive rules for PROTAC linker design and screening and/or to evaluate ternary complex stability when varying the Ligase protein. Within the field of drug delivery, the Martini 3 model combined with the implementation of tools and protocols available for constructing and simulating soft delivery systems, such as LNPs, will enable in silico screening of various formulations, permitting more efficient optimisation or rational design of delivery methods. However, for NA-containing drug delivery systems, the parameters for RNA/DNA are still under development in Martini 3 and the lack of experimentally resolved structures complicates FF parameter optimisation. While previous Martini 2 NA models were rather rigid (Uusitalo et al., Reference Uusitalo, Ingólfsson, Akhshi, Tieleman and Marrink2015, Reference Uusitalo, Ingólfsson, Marrink and Faustino2017), improving the dynamics of the future NA Martini 3 models is of utmost importance for the simulations of NA delivery systems.

Overcoming these challenges is fundamental for broader applications of the Martini 3 model in biologically relevant systems like SNs, protein–protein interactions, membrane systems and efficient discovery of druggable cryptic pockets, enabling an even larger impact of CG models in fields of drug discovery and delivery. For validation of the CG modelling within drug discovery, one example is the technique of co-crystallisation or soaking macromolecular crystals, essentially replacing solvent with a ligand within the crystal, enabling the comparison to for example, flooding CG-MD simulations for pocket identification (Wienen-Schmidt et al., Reference Wienen-Schmidt, Oebbeke, Ngo, Heine and Klebe2021). Within the drug delivery field, one could imagine correlating predicted structures and organisation of SNs based on CG-MD simulation with fusion and transfection efficacy (Miao et al., Reference Miao, Lin, Huang, Li, Delcassian, Ge, Shi and Anderson2020) measured experimentally, combined with fluorescence studies (Chen et al., Reference Chen, Zhang, Su, Bao, Xie, Zuo, Yang, Wang, Jiang, Lin and Fang2019) enhancing the understanding and development of such delivery methods.