Broadening access to small-molecule parameterization with the force field toolkit.

Access to accurate force-field parameters for small molecules is crucial for computational studies of their interactions with proteins. Although a number of general force fields for small molecules exist, e.g., CGenFF, GAFF, and OPLS, they do not cover all common chemical groups and their combinations. The Force Field Toolkit (ffTK) provides a comprehensive graphical interface that streamlines the development of classical parameters for small molecules directly from quantum mechanical (QM) calculations, allowing for force-field generation for almost any chemical group and validation of the fit relative to the target data. ffTK relies on supported external software for the QM calculations, but it can generate the necessary QM input files and parse and analyze the QM output. In previous ffTK versions, support for Gaussian and ORCA QM packages was implemented. Here, we add support for Psi4, an open-source QM package free for all users, thereby broadening user access to ffTK. We also compare the parameter sets obtained with the new ffTK version using Gaussian, ORCA, and Psi4 for three molecules: pyrrolidine, n-propylammonium cation, and chlorobenzene. Despite minor differences between the resulting parameter sets for each compound, most prominently in the dihedral and improper terms, we show that conformational distributions sampled in molecular dynamics simulations using these parameter sets are quite comparable.

Embedding Dynamics in Intrinsic Physicochemical Profiles of Market-Stage Antibody-Based Biotherapeutics.

Adequate stability, manufacturability, and safety are crucial to bringing an antibody-based biotherapeutic to the market. Following the concept of holistic in silico developability, we introduce a physicochemical description of 91 market-stage antibody-based biotherapeutics based on orthogonal molecular properties of variable regions (Fvs) embedded in different simulation environments, mimicking conditions experienced by antibodies during manufacturing, formulation, and in vivo. In this work, the evaluation of molecular properties includes conformational flexibility of the Fvs using molecular dynamics (MD) simulations. The comparison between static homology models and simulations shows that MD significantly affects certain molecular descriptors like surface molecular patches. Moreover, the structural stability of a subset of Fv regions is linked to changes in their specific molecular interactions with ions in different experimental conditions. This is supported by the observation of differences in protein melting temperatures upon addition of NaCl. A DEvelopability Navigator In Silico (DENIS) is proposed to compare mAb candidates for their similarity with market-stage biotherapeutics in terms of physicochemical properties and conformational stability. Expanding on our previous developability guidelines (Ahmed et al. Proc. Natl. Acad. Sci. 2021, 118 (37), e2020577118), the hydrodynamic radius and the protein strand ratio are introduced as two additional descriptors that enable a more comprehensive in silico characterization of biotherapeutic drug candidates. Test cases show how this approach can facilitate identification and optimization of intrinsically developable lead candidates. DENIS represents an advanced computational tool to progress biotherapeutic drug candidates from discovery into early development by predicting drug properties in different aqueous environments.

Membrane Mixer: A Toolkit for Efficient Shuffling of Lipids in Heterogeneous Biological Membranes.

Molecular dynamics (MD) simulations of biological membranes have achieved such levels of sophistication that are commonly used to predict unresolved structures and various properties of lipids and to substantiate experimental data. While achieving sufficient sampling of lipid dynamics remains a major challenge, a commonly used method to improve lipid sampling, e.g., in terms of specific interactions with membrane-associated proteins, is to randomize the initial arrangement of lipid constituents in multiple replicas of simulations, without changing the overall lipid composition of the membrane of interest. Here, we introduce a method that can rapidly generate multiple replicas of lipid bilayers with different spatial and conformational configurations for any given lipid composition. The underlying algorithm, which allows one to shuffle lipids at any desired level, relies on the application of an external potential, here referred to as the "carving potential", that removes clashes/entanglements before lipid positions are exchanged (shuffled), thereby minimizing the energy penalty due to abrupt lipid repositioning. The method is implemented as "Membrane Mixer Plugin (MMP) 1.0" in VMD, with a convenient graphical user interface that guides the user in setting various options and parameters. The plugin is fully automated and generates new membrane replicas more rapidly and conveniently than other analogous tools. The plugin and its capabilities introduced here can be extended to include additional features in future versions.

Flipper Probes for the Community.

This article describes four fluorescent membrane tension probes that have been designed, synthesized, evaluated, commercialized and applied to current biology challenges in the context of the NCCR Chemical Biology. Their names are Flipper-TR®, ER Flipper-TR®, Lyso Flipper-TR®, and Mito Flipper-TR®. They are available from Spirochrome.

A Chalcogen-Bonding Cascade Switch for Planarizable Push-Pull Probes.

Planarizable push-pull probes have been introduced to demonstrate physical forces in biology. However, the donors and acceptors needed to polarize mechanically planarized probes are incompatible with their twisted resting state. The objective of this study was to overcome this "flipper dilemma" with chalcogen-bonding cascade switches that turn on donors and acceptors only in response to mechanical planarization of the probe. This concept is explored by molecular dynamics simulations as well as chemical double-mutant cycle analysis. Cascade switched flipper probes turn out to excel with chemical stability, red shifts adding up to high significance, and focused mechanosensitivity. Most important, however, is the introduction of a new, general and fundamental concept that operates with non-trivial supramolecular chemistry, solves an important practical problem and opens a wide chemical space.

Detecting order and lateral pressure at biomimetic interfaces using a mechanosensitive second-harmonic-generation probe.

A planarizable push-pull molecular probe with mechanosensitive properties was investigated at several biomimetic interfaces, consisting of different phospholipid monolayers located between dodecane and an aqueous buffer solution, using the interface-specific surface-second-harmonic-generation (SSHG) technique. Whereas the SSHG spectra recorded at liquid-disordered interfaces were similar to the absorption spectra in bulk solutions, those measured at liquid-ordered phases exhibited a remarkable shift towards lower energies to an extent depending on the surface pressure of the phospholipid monolayer. On the basis of quantum-chemical calculations, this effect was accounted for by the planarization of the mechanosensitive probe. Polarization-resolved SSHG measurements revealed that the average orientation of the probe at the interface is an even more sensitive reporter of lateral pressure and order than the spectral shape. Additionally, time-resolved SSHG measurements pointed to slower dynamics upon intercalation inside the phospholipid monolayer, most likely due to the more constrained environment. This study demonstrates that the concept of mechanosensitive optical probes can be further exploited when combined with a surface-selective nonlinear optical technique.

Influence of the hydrogen-bond interactions on the excited-state dynamics of a push-pull azobenzene dye: the case of Methyl Orange.

The excited-state dynamics of the push-pull azobenzene Methyl Orange (MO) were investigated in several solvents and water/glycerol mixtures using a combination of ultrafast time-resolved fluorescence and transient absorption in both the UV-visible and the IR regions, as well as quantum chemical calculations. Optical excitation of MO in its trans form results in the population of the S2 ππ* state and is followed by internal conversion to the S1 nπ* state in ∼50 fs. The population of this state decays on the sub-picosecond timescale by both internal conversion to the trans ground state and isomerisation to the cis ground state. Finally, the cis form converts thermally to the trans form on a timescale ranging from less than 50 ms to several minutes. Significant differences depending on the hydrogen-bond donor strength of the solvents, quantified by the Kamlet Taft parameter α, were observed: compared to the other solvents, in highly protic solvents (α > 1), (i) the viscosity dependence of the S1 state lifetime is less pronounced, (ii) the S1 state lifetime is shorter by a factor of ≈1.5 for the same viscosity, (iii) the trans-to-cis photoisomerisation efficiency is smaller, and (iv) the thermal cis-to-trans isomerisation is faster by a factor of ≥103. These differences are explained in terms of hydrogen-bond interactions between the solvent and the azo nitrogen atoms of MO, which not only change the nature of the S1 state but also have an impact on the shape of ground- and excited-state potentials, and, thus, affect the deactivation pathways from the excited state.

White-Fluorescent Dual-Emission Mechanosensitive Membrane Probes that Function by Bending Rather than Twisting.

Bent N,N'-diphenyl-dihydrodibenzo[a,c]phenazine amphiphiles are introduced as mechanosensitive membrane probes that operate by an unprecedented mechanism, namely, unbending in the excited state as opposed to the previously reported untwisting in the ground and twisting in the excited state. Their dual emission from bent or "closed" and planarized or "open" excited states is shown to discriminate between micelles in water and monomers in solid-ordered (So ), liquid-disordered (Ld ) and bulk membranes. The dual-emission spectra cover enough of the visible range to produce vesicles that emit white light with ratiometrically encoded information. Strategies to improve the bent mechanophores with expanded π systems and auxochromes are reported, and compatibility with imaging of membrane domains in giant unilamellar vesicles by two-photon excitation fluorescence (TPEF) microscopy is demonstrated.

Exploring Fluorescent Dyes at Biomimetic Interfaces with Second Harmonic Generation and Molecular Dynamics.

The adsorption of a DNA fluorescent probe belonging to the thiazole orange family at the dodecane/water and dodecane/phospholipid/water interfaces has been investigated using a combination of surface second harmonic generation (SSHG) and all-atomistic molecular dynamics (MD) simulations. Both approaches point to a high affinity of the cationic dye for the dodecane/water interface with a Gibbs free energy of adsorption on the order of -45 kJ/mol. Similar affinity was observed with a monolayer of negatively charged DPPG (1,2-dipalmitoyl-sn-glycero-3-phospho-rac-(1-glycerol)) lipids. On the other hand, no significant adsorption could be found with the zwitterionic DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine) lipids. This was rationalized in terms of Coulombic interactions between the monolayer surface and the cationic dye. The similar affinity for the interface with and without DPPG, despite the favorable Coulombic attraction in the latter case, could be explained after investigating the interfacial orientation of the dye. In the absence of a monolayer, the dye adsorbs with its molecular plane almost flat at the interface, whereas in the presence of DPPG it has to intercalate into the monolayer and adopt a significantly different orientation to benefit from the electrostatic stabilization.

Fluorescent DNA probes at liquid/liquid interfaces studied by surface second harmonic generation.

The properties of a series of oxazole yellow dyes, including the dicationic YOPRO-1 and its homodimeric parent YOYO-1 and two monocationic dyes (YOSAC-1 and YOSAC-3), have been investigated at the dodecane/water interface using stationary and time-resolved surface second harmonic generation (SSHG) combined with quantum chemical calculations. Whereas YOYO-1 exists predominantly as a H-dimer in aqueous solution, the stationary SSHG spectra reveal that such dimers are not formed at the interface. No significant H-aggregation was observed with YOPRO-1, neither in solution nor at the interface. In the case of the monocationic YOSAC dyes, a distinct SSHG band due to H-aggregates was measured at the interface, whereas only weak aggregation was found in solution. These distinct aggregation behaviors can be explained by the different orientations of the dyes at the interface, as revealed from the analysis of polarization-resolved experiments, the doubly-charged dyes lying more flat on the interface than the singly charged ones. Although YOYO-1 and YOPRO-1 do not form H-dimer/aggregates at the interface, time-resolved SSHG measurements point to the occurrence of intra- and intermolecular interactions, respectively, which inhibit the ultrafast non-radiative decay of the excited dyes via large amplitude motion, and lead to a nanosecond excited-state lifetime. The distinct behavior evidenced here for YOYO-1 and YOSAC dyes points to their potential use as fluorescent or SHG interfacial probes.

Effective in silico prediction of new oxazolidinone antibiotics: force field simulations of the antibiotic-ribosome complex supervised by experiment and electronic structure methods.

We propose several new and promising antibacterial agents for the treatment of serious Gram-positive infections. Our predictions rely on force field simulations, supervised by first principle calculations and available experimental data. Different force fields were tested in order to reproduce linezolid's conformational space in terms of a) the isolated and b) the ribosomal bound state. In a first step, an all-atom model of the bacterial ribosome consisting of nearly 1600 atoms was constructed and evaluated. The conformational space of 30 different ribosomal/oxazolidinone complexes was scanned by stochastic methods, followed by an evaluation of their enthalpic penalties or rewards and the mechanical strengths of the relevant hydrogen bonds (relaxed force constants; compliance constants). The protocol was able to reproduce the experimentally known enantioselectivity favoring the S-enantiomer. In a second step, the experimentally known MIC values of eight linezolid analogues were used in order to crosscheck the robustness of our model. In a final step, this benchmarking led to the prediction of several new and promising lead compounds. Synthesis and biological evaluation of the new compounds are on the way.

Correction: Effective in silico prediction of new oxazolidinone antibiotics: force field simulations of the antibiotic-ribosome complex supervised by experiment and electronic structure methods.

[This corrects the article DOI: 10.3762/bjoc.12.45.].

Predicting deamidation and isomerization sites in therapeutic antibodies using structure-based in silico approaches.

Asparagine (Asn) deamidation and aspartic acid (Asp) isomerization are common degradation pathways that affect the stability of therapeutic antibodies. These modifications can pose a significant challenge in the development of biopharmaceuticals. As such, the early engineering and selection of chemically stable monoclonal antibodies (mAbs) can substantially mitigate the risk of subsequent failure. In this study, we introduce a novel in silico approach for predicting deamidation and isomerization sites in therapeutic antibodies by analyzing the structural environment surrounding asparagine and aspartate residues. The resulting quantitative structure-activity relationship (QSAR) model was trained using previously published forced degradation data from 57 clinical-stage mAbs. The predictive accuracy of the model was evaluated for four different states of the protein structure: (1) static homology models, (2) enhancing low-frequency vibrational modes during short molecular dynamics (MD) runs, (3) a combination of (2) with a protonation state reassignment, and (4) conventional full-atomistic MD simulations. The most effective QSAR model considered the accessible surface area (ASA) of the residue, the pKa value of the backbone amide, and the root mean square deviations of both the alpha carbon and the side chain. The accuracy was further enhanced by incorporating the QSAR model into a decision tree, which also includes empirical information about the sequential successor and the position in the protein. The resulting model has been implemented as a plugin named "Forecasting Reactivity of Isomerization and Deamidation in Antibodies" in MOE software, completed with a user-friendly graphical interface to facilitate its use.

Stress-dependent Flexibility of a Full-length Human Monoclonal Antibody: Insights from Molecular Dynamics to Support Biopharmaceutical Development.

After several decades of advancements in drug discovery, product development of biopharmaceuticals remains a time- and resource-consuming endeavor. One of the main reasons is associated to the lack of fundamental understanding of conformational dynamics of such biologic entities, and how they respond to various stresses encountered during manufacturing, storage, and shipping. In this work, we have studied the conformational dynamics of human IgG1κ b12 monoclonal antibody (mAb) using molecular dynamics simulations. The hundreds of nanoseconds long trajectories reveal that b12 mAb is highly flexible. Its variable domains show greater conformational fluctuations than the constant domains. Additionally, it collapses towards a more globular shape in response to thermal stress, leading to decrease in the total solvent exposed surface area and radius of gyration. This behavior is more pronounced for the deglycosylated b12 mAb, and it appears to correlate with increase in inter-domain contacts between specific regions of the antibody. Conformational fluctuations also cause transient formation and disruption of hydrophobic and charged patches on the antibody surface, which is particularly important for the prediction of CMC properties during development phases of antibody-based biotherapeutics. The insights gained through these simulations may help the development of biologic drugs.

Beyond the Threshold: A Study of Chalcogenophene-Based Two-Photon Initiators.

A series of nine soluble, symmetric chalcogenophenes bearing hexyl-substituted triphenylamines, indolocarbazoles, or phenylcarbazoles was designed and synthesized as potential two-photon absorption (2PA) initiators. A detailed photophysical analysis of these molecules revealed good 2PA properties of the series and, in particular, a strong influence of selenium on the 2PA cross sections, rendering these materials especially promising new 2PA photoinitiators. Structuring and threshold tests proved the efficiency and broad spectral versatility of two selenium-containing lead compounds as well as their applicability in an acrylate resin formulation. A comparison with commercial photoinitiators Irg369 and BAPO as well as sensitizer ITX showed that the newly designed selenium-based materials TPA-S and TPA-BBS outperform these traditional initiators by far both in terms of reactivity and dose. Moreover, by increasing the ultralow concentration of TPA-BBS, a further reduction of the polymerization threshold can be achieved, revealing the great potential of this series for application in two-photon polymerization (2PP) systems where only low laser power is available.

Twisting and tilting of a mechanosensitive molecular probe detects order in membranes.

Lateral forces in biological membranes affect a variety of dynamic cellular processes. Recent synthetic efforts have introduced fluorescent "flippers" as environment-sensitive planarizable push-pull probes that can detect lipid packing and membrane tension, and respond to lipid-induced mechanical forces by a shift in their spectroscopic properties. Herein, we investigate the molecular origin of the mechanosensitivity of the best known flipper, Flipper-TR, by an extended set of molecular dynamics (MD) simulations in membranes of increasing complexity and under different physicochemical conditions, revealing unprecedented details of the sensing process. Simulations enabled by accurate refinement of Flipper-TR force field using quantum mechanical calculations allowed us to unambiguously correlate the planarization of the two fluorescent flippers to spectroscopic response. In particular, Flipper-TR conformation exhibits bimodal distribution in disordered membranes and a unimodal distribution in highly ordered membranes. Such dramatic change was associated with a shift in Flipper-TR excitation spectra, as supported both by our simulated and experimentally-measured spectra. Flipper-TR sensitivity to phase-transition is confirmed by a temperature-jump protocol that alters the lipid phase of an ordered membrane, triggering an instantaneous mechanical twisting of the probe. Simulations show that the probe is also sensitive to surface tension, since even in a naturally disordered membrane, the unimodal distribution of coplanar flippers can be achieved if a sufficiently negative surface tension is applied to the membrane. MD simulations in ternary mixtures containing raft-like nanodomains show that the probe can discriminate lipid domains in phase-separated complex bilayers. A histogram-based approach, called DOB-phase classification, is introduced that can differentiate regions of disordered and ordered lipid phases by comparing dihedral distributions of Flipper-TR. Moreover, a new sensing mechanism involving the orientation of Flipper-TR is elucidated, corroborating experimental evidence that the probe tilt angle is strongly dependent on lipid ordering. The obtained atomic-resolution description of Flipper-TR mechanosensitivity is key to the interpretation of experimental data and to the design of novel mechanosensors with improved spectroscopic properties.

Molecular Dynamics Simulations of Bimolecular Electron Transfer: Testing the Coulomb Term in the Weller Equation.

Reliable estimation of the driving force for photoinduced electron transfer between neutral reactants is of utmost importance for most practical applications of these reactions. The driving force is usually calculated from the Weller equation, which contains a Coulomb term, C, whose magnitude in polar solvents is debated. We have performed umbrella sampling molecular dynamics simulations to determine C from the potentials of mean force between neutral and ionic donor/acceptor pairs of different sizes in solvents of varying polarity. According to the simulations, C in polar solvents is a factor of 2 more negative than typically calculated according to the Weller equation. Use of the π-stack contact distance in the Weller equation instead of the van der Waals radius recovers the correct value of C, but this is mostly fortuitous due to the compensating effects of overestimating the dielectric screening at contact and neglecting both charge dilution and desolvation.

Polymer-Peptide Conjugates Convert Amyloid into Protein Nanobundles through Fragmentation and Lateral Association.

The assembly of proteins into amyloid fibrils has become linked not only with the progression of myriad human diseases, but also important biological functions. Understanding and controlling the formation, structure, and stability of amyloid fibrils is therefore a major scientific goal. Here we utilize electron microscopy-based approaches combined with quantitative statistical analysis to show how recently developed kind of amyloid modulators-multivalent polymer-peptide conjugates (mPPCs)-can be applied to control the structure and stability of amyloid fibrils. In doing so, we demonstrate that mPPCs are able to convert 40-residue amyloid beta fibrils into ordered nanostructures through a combination of fragmentation and bundling. Fragmentation is shown to be consistent with a model where the rate constant of fibril breakage is independent of the fibril length, suggesting a local and specific interaction between fibrils and mPPCs. Subsequent bundling, which was previously not observed, leads to the formation of sheet-like nanostructures which are surprisingly much more uniform than the starting fibrils. These nanostructures have dimensions independent of the molecular weight of the mPPC and retain the molecular-level ordering of the starting amyloid fibrils. Collectively, we reveal quantitative and nanoscopic understanding of how mPPCs can be applied to control amyloid structure and stability, and demonstrate approaches to elucidate nanoscale amyloid phase behavior in the presence of functional macromolecules and other modulators.

Tuning symmetry breaking charge separation in perylene bichromophores by conformational control.

Understanding structure-property relationships in multichromophoric molecular architectures is a crucial step in establishing new design principles in organic electronics as well as to fully understand how nature exploits solar energy. Here, we study the excited state dynamics of three bichromophores consisting of two perylene chromophores linked to three different crown-ether backbones, using stationary and ultrafast electronic spectroscopy combined with molecular dynamics simulations. The conformational space available to the bichromophores depends on the structure and geometry of the crown-ether and can be significantly changed upon cation binding, strongly affecting the excited-state dynamics. We show that, depending on the conformational restrictions and the local environment, the nature of the excited state varies greatly, going from an excimer to a symmetry-broken charge separated state. These results can be rationalised in terms of a structure-property relationship that includes the effect of the local environment.

Multivalent Polymer-Peptide Conjugates-A General Platform for Inhibiting Amyloid Beta Peptide Aggregation.

Protein aggregation is implicated in multiple deposition diseases including Alzheimer's Disease, which features the formation of toxic aggregates of amyloid beta (Aß) peptides. Many inhibitors have been developed to impede or reverse Aß aggregation. Multivalent inhibitors, however, have been largely overlooked despite the promise of high inhibition efficiency endowed by the multivalent nature of Aß aggregates. In this work, we report the success of multivalent polymer-peptide conjugates (mPPCs) as a general class of inhibitors of the aggregation of Aß40. Significantly delayed onset of fibril formation was realized using mPPCs prepared from three peptide/peptoid ligands covering a range of polymer molecular weights (MWs) and ligand loadings. Dose dependence studies showed that the nature of the ligands is a key factor in mPPC inhibition potency. The negatively charged ligand LPFFD (LD) leads to more efficient mPPCs compared to the neutral ligands, and is most effective at 7% ligand loading across different MWs. Molecular dynamics simulations along with dynamic light scattering experiments suggest that mPPCs form globular structures in solution due to ligand-ligand interactions. Such interactions are key to the spatial proximity of ligands and thus to the multivalency effect of mPPC inhibition. Excess ligand-ligand interactions, however, reduce the accessibility of mPPC ligands to Aß peptides, and impair the overall inhibition potency.