Prof. Dr. Stefan M. Kast
Theoretical Physical Chemistry
TU Dortmund University
- Investigations Into Chemically Stabilized Four-Letter DNA for DNA-Encoded Chemistry
Potowski, M. and Kunig, V.B.K. and Eberlein, L. and Škopić, M.K. and Vakalopoulos, A. and Kast, S.M. and Brunschweiger, A.
Frontiers in Chemistry 10 (2022)DNA-encoded libraries are a prime technology for target-based small molecule screening. Native DNA used as genetic compound barcode is chemically vulnerable under many reaction conditions. DNA barcodes that are composed of pyrimidine nucleobases, 7-deazaadenine, and 7-deaza-8-azaguanine have been investigated for their suitability for encoded chemistry both experimentally and computationally. These four-letter barcodes were readily ligated by T4 ligation, amplifiable by Taq polymerase, and the resultant amplicons were correctly sequenced. Chemical stability profiling showed a superior chemical stability compared to native DNA, though higher susceptibility to depurination than a three-letter code based on pyrimidine DNA and 7-deazaadenine. Copyright © 2022 Potowski, Kunig, Eberlein, Škopić, Vakalopoulos, Kast and Brunschweiger.
view abstract 10.3389/fchem.2022.894563
- A Joint Venture of Ab Initio Molecular Dynamics, Coupled Cluster Electronic Structure Methods, and Liquid-State Theory to Compute Accurate Isotropic Hyperfine Constants of Nitroxide Probes in Water
Sharma, B. and Tran, V.A. and Pongratz, T. and Galazzo, L. and Zhurko, I. and Bordignon, E. and Kast, S.M. and Neese, F. and Marx, D.
Journal of Chemical Theory and Computation 17 (2021)The isotropic hyperfine coupling constant (HFCC, Aiso) of a pH-sensitive spin probe in a solution, HMI (2,2,3,4,5,5-hexamethylimidazolidin-1-oxyl, C9H19N2O) in water, is computed using an ensemble of state-of-the-art computational techniques and is gauged against X-band continuous wave electron paramagnetic resonance (EPR) measurement spectra at room temperature. Fundamentally, the investigation aims to delineate the cutting edge of current first-principles-based calculations of EPR parameters in aqueous solutions based on using rigorous statistical mechanics combined with correlated electronic structure techniques. In particular, the impact of solvation is described by exploiting fully atomistic, RISM integral equation, and implicit solvation approaches as offered by ab initio molecular dynamics (AIMD) of the periodic bulk solution (using the spin-polarized revPBE0-D3 hybrid functional), embedded cluster reference interaction site model integral equation theory (EC-RISM), and polarizable continuum embedding (using CPCM) of microsolvated complexes, respectively. HFCCs are obtained from efficient coupled cluster calculations (using open-shell DLPNO-CCSD theory) as well as from hybrid density functional theory (using revPBE0-D3). Re-solvation of "vertically desolvated"spin probe configuration snapshots by EC-RISM embedding is shown to provide significantly improved results compared to CPCM since only the former captures the inherent structural heterogeneity of the solvent close to the spin probe. The average values of the Aiso parameter obtained based on configurational statistics using explicit water within AIMD and from EC-RISM solvation are found to be satisfactorily close. Using either such explicit or RISM solvation in conjunction with DLPNO-CCSD calculations of the HFCCs provides an average Aiso parameter for HMI in aqueous solution at 300 K and 1 bar that is in good agreement with the experimentally determined one. The developed computational strategy is general in the sense that it can be readily applied to other spin probes of similar molecular complexity, to aqueous solutions beyond ambient conditions, as well as to other solvents in the longer run. © 2021 The Authors. Published by American Chemical Society.
view abstract 10.1021/acs.jctc.1c00582
- Asymmetric Interplay Between K+ and Blocker and Atomistic Parameters From Physiological Experiments Quantify K+ Channel Blocker Release
Gabriel, T.S. and Hansen, U.-P. and Urban, M. and Drexler, N. and Winterstein, T. and Rauh, O. and Thiel, G. and Kast, S.M. and Schroeder, I.
Frontiers in Physiology 12 (2021)Modulating the activity of ion channels by blockers yields information on both the mode of drug action and on the biophysics of ion transport. Here we investigate the interplay between ions in the selectivity filter (SF) of K+ channels and the release kinetics of the blocker tetrapropylammonium in the model channel KcvNTS. A quantitative expression calculates blocker release rate constants directly from voltage-dependent ion occupation probabilities in the SF. The latter are obtained by a kinetic model of single-channel currents recorded in the absence of the blocker. The resulting model contains only two adjustable parameters of ion-blocker interaction and holds for both symmetric and asymmetric ionic conditions. This data-derived model is corroborated by 3D reference interaction site model (3D RISM) calculations on several model systems, which show that the K+ occupation probability is unaffected by the blocker, a direct consequence of the strength of the ion-carbonyl attraction in the SF, independent of the specific protein background. Hence, KcvNTS channel blocker release kinetics can be reduced to a small number of system-specific parameters. The pore-independent asymmetric interplay between K+ and blocker ions potentially allows for generalizing these results to similar potassium channels. Copyright © 2021 Gabriel, Hansen, Urban, Drexler, Winterstein, Rauh, Thiel, Kast and Schroeder.
view abstract 10.3389/fphys.2021.737834
- Chemically Stabilized DNA Barcodes for DNA-Encoded Chemistry
Potowski, M. and Kunig, V.B.K. and Eberlein, L. and Vakalopoulos, A. and Kast, S.M. and Brunschweiger, A.
Angewandte Chemie - International Edition 60 (2021)DNA-encoded compound libraries are a widely used small molecule screening technology. One important aim in library design is the coverage of chemical space through structurally diverse molecules. Yet, the chemical reactivity of native DNA barcodes limits the toolbox of reactions for library design. Substituting the chemically vulnerable purines by 7-deazaadenine, which exhibits tautomerization stability similar to natural adenine with respect to the formation of stable Watson–Crick pairs, yielded ligation-competent, amplifiable, and readable DNA barcodes for encoded chemistry with enhanced stability against protic acid- and metal ion-promoted depurination. The barcode stability allowed for straightforward translation of 16 exemplary reactions that included isocyanide multicomponent reactions, acid-promoted Pictet–Spengler and Biginelli reactions, and metal-promoted pyrazole syntheses on controlled pore glass-coupled barcodes for diverse DEL design. The Boc protective group of reaction products offered a convenient handle for encoded compound purification. © 2021 The Authors. Angewandte Chemie International Edition published by Wiley-VCH GmbH
view abstract 10.1002/anie.202104348
- Evaluation of log P, pK a, and log D predictions from the SAMPL7 blind challenge
Bergazin, T.D. and Tielker, N. and Zhang, Y. and Mao, J. and Gunner, M.R. and Francisco, K. and Ballatore, C. and Kast, S.M. and Mobley, D.L.
Journal of Computer-Aided Molecular Design (2021)The Statistical Assessment of Modeling of Proteins and Ligands (SAMPL) challenges focuses the computational modeling community on areas in need of improvement for rational drug design. The SAMPL7 physical property challenge dealt with prediction of octanol-water partition coefficients and pKa for 22 compounds. The dataset was composed of a series of N-acylsulfonamides and related bioisosteres. 17 research groups participated in the log P challenge, submitting 33 blind submissions total. For the pKa challenge, 7 different groups participated, submitting 9 blind submissions in total. Overall, the accuracy of octanol-water log P predictions in the SAMPL7 challenge was lower than octanol-water log P predictions in SAMPL6, likely due to a more diverse dataset. Compared to the SAMPL6 pKa challenge, accuracy remains unchanged in SAMPL7. Interestingly, here, though macroscopic pKa values were often predicted with reasonable accuracy, there was dramatically more disagreement among participants as to which microscopic transitions produced these values (with methods often disagreeing even as to the sign of the free energy change associated with certain transitions), indicating far more work needs to be done on pKa prediction methods. © 2021, The Author(s).
view abstract 10.1007/s10822-021-00397-3
- Perspective on the SAMPL and D3R Blind Prediction Challenges for Physics-Based Free Energy Methods
Tielker, N. and Eberlein, L. and Beckstein, O. and Güssregen, S. and Iorga, B.I. and Kast, S.M. and Liu, S.
ACS Symposium Series 1397 (2021)Solvation and binding thermodynamics of a drug-like molecule is quantified by the respective free energy (FE) change that governs physical properties like log P/log D and binding affinities as well as more complex features such as solubility or permeability. The drug discovery process benefits significantly from reliable predictions of FEs, which are hence a key area for the theoretical and modeling community. Despite the clear physical background rooted in statistical mechanics, the desired accuracy goal is hard to achieve. Current modeling methods still need to be improved in various areas related to the FE problem, such as the quality of force fields and quantum-mechanical approximations, the efficiency of sampling algorithms as well as the robustness of computational workflows. In this context, blind prediction challenges, where participants are tasked with testing their computational methods and workflows on compound property predictions without knowing the experimental data, are excellent testbeds to evaluate and improve the modeling methodology. SAMPL (Statistical Assessment of the Modeling of Proteins and Ligands) and Drug Design Data Resource-Grand Challenges (D3R-GCs) represent widely known initiatives demonstrating how the “blind prediction” concept boosts the development of FE predictions. In this chapter, we summarize the status of recent SAMPL and D3R-GCs from the point of view of long-time participants, with the aim of providing the community with a collection of datasets and references. © 2021 American Chemical Society. All rights reserved.
view abstract 10.1021/bk-2021-1397.ch003
- SAMPL7 physical property prediction from EC-RISM theory
Tielker, N. and Güssregen, S. and Kast, S.M.
Journal of Computer-Aided Molecular Design 35 (2021)Inspired by the successful application of the embedded cluster reference interaction site model (EC-RISM), a combination of quantum–mechanical calculations with three-dimensional RISM theory to predict Gibbs energies of species in solution within the SAMPL6.1 (acidity constants, pKa) and SAMPL6.2 (octanol–water partition coefficients, log P) the methodology was applied to the recent SAMPL7 physical property challenge on aqueous pKa and octanol–water log P values. Not part of the challenge but provided by the organizers, we also computed distribution coefficients log D7.4 from predicted pKa and log P data. While macroscopic pKa predictions compared very favorably with experimental data (root mean square error, RMSE 0.72 pK units), the performance of the log P model (RMSE 1.84) fell behind expectations from the SAMPL6.2 challenge, leading to reasonable log D7.4 predictions (RMSE 1.69) from combining the independent calculations. In the post-submission phase, conformations generated by different methodology yielded results that did not significantly improve the original predictions. While overall satisfactory compared to previous log D challenges, the predicted data suggest that further effort is needed for optimizing the robustness of the partition coefficient model within EC-RISM calculations and for shaping the agreement between experimental conditions and the corresponding model description. © 2021, The Author(s).
view abstract 10.1007/s10822-021-00410-9
- Pressure-dependent electronic structure calculations using integral equation-based solvation models
Pongratz, T. and Kibies, P. and Eberlein, L. and Tielker, N. and Hölzl, C. and Imoto, S. and Beck Erlach, M. and Kurrmann, S. and Schummel, P.H. and Hofmann, M. and Reiser, O. and Winter, R. and Kremer, W. and Kalbitzer, H.R. and Marx, D. and Horinek, D. and Kast, S.M.
Biophysical Chemistry 257 (2020)Recent methodological progress in quantum-chemical calculations using the “embedded cluster reference interaction site model” (EC-RISM) integral equation theory is reviewed in the context of applying it as a solvation model for calculating pressure-dependent thermodynamic and spectroscopic properties of molecules immersed in water. The methodology is based on self-consistent calculations of electronic and solvation structure around dissolved molecules where pressure enters the equations via an appropriately chosen solvent response function and the pure solvent density. Besides specification of a dispersion-repulsion force field for solute-solvent interactions, the EC-RISM approach derives the electrostatic interaction contributions directly from the wave function. We further develop and apply the method to a variety of benchmark cases for which computational or experimental reference data are either available in the literature or are generated specifically for this purpose in this work. Starting with an enhancement to predict hydration free energies at non-ambient pressures, which is the basis for pressure-dependent molecular population estimation, we demonstrate the performance on the calculation of the autoionization constant of water. Spectroscopic problems are addressed by studying the biologically relevant small osmolyte TMAO (trimethylamine N-oxide). Pressure-dependent NMR shifts are predicted and compared to experiments taking into account proper computational referencing methods that extend earlier work. The experimentally observed IR blue-shifts of certain vibrational bands of TMAO as well as of the cyanide anion are reproduced by novel methodology that allows for weighing equilibrium and non-equilibrium solvent relaxation effects. Taken together, the model systems investigated allow for an assessment of the reliability of the EC-RISM approach for studying pressure-dependent biophysical processes. © 2019 Elsevier B.V.
view abstract 10.1016/j.bpc.2019.106258
- Quantum–mechanical property prediction of solvated drug molecules: what have we learned from a decade of SAMPL blind prediction challenges?
Tielker, N. and Eberlein, L. and Hessler, G. and Schmidt, K.F. and Güssregen, S. and Kast, S.M.
Journal of Computer-Aided Molecular Design (2020)Joint academic–industrial projects supporting drug discovery are frequently pursued to deploy and benchmark cutting-edge methodical developments from academia in a real-world industrial environment at different scales. The dimensionality of tasks ranges from small molecule physicochemical property assessment over protein–ligand interaction up to statistical analyses of biological data. This way, method development and usability both benefit from insights gained at both ends, when predictiveness and readiness of novel approaches are confirmed, but the pharmaceutical drug makers get early access to novel tools for the quality of drug products and benefit of patients. Quantum–mechanical and simulation methods particularly fall into this group of methods, as they require skills and expense in their development but also significant resources in their application, thus are comparatively slowly dripping into the realm of industrial use. Nevertheless, these physics-based methods are becoming more and more useful. Starting with a general overview of these and in particular quantum–mechanical methods for drug discovery we review a decade-long and ongoing collaboration between Sanofi and the Kast group focused on the application of the embedded cluster reference interaction site model (EC-RISM), a solvation model for quantum chemistry, to study small molecule chemistry in the context of joint participation in several SAMPL (Statistical Assessment of Modeling of Proteins and Ligands) blind prediction challenges. Starting with early application to tautomer equilibria in water (SAMPL2) the methodology was further developed to allow for challenge contributions related to predictions of distribution coefficients (SAMPL5) and acidity constants (SAMPL6) over the years. Particular emphasis is put on a frequently overlooked aspect of measuring the quality of models, namely the retrospective analysis of earlier datasets and predictions in light of more recent and advanced developments. We therefore demonstrate the performance of the current methodical state of the art as developed and optimized for the SAMPL6 pKa and octanol–water log P challenges when re-applied to the earlier SAMPL5 cyclohexane-water log D and SAMPL2 tautomer equilibria datasets. Systematic improvement is not consistently found throughout despite the similarity of the problem class, i.e. protonation reactions and phase distribution. Hence, it is possible to learn about hidden bias in model assessment, as results derived from more elaborate methods do not necessarily improve quantitative agreement. This indicates the role of chance or coincidence for model development on the one hand which allows for the identification of systematic error and opportunities toward improvement and reveals possible sources of experimental uncertainty on the other. These insights are particularly useful for further academia–industry collaborations, as both partners are then enabled to optimize both the computational and experimental settings for data generation. © 2020, The Author(s).
view abstract 10.1007/s10822-020-00347-5
- Tautomeric Equilibria of Nucleobases in the Hachimoji Expanded Genetic Alphabet
Eberlein, L. and Beierlein, F.R. and Van Eikema Hommes, N.J.R. and Radadiya, A. and Heil, J. and Benner, S.A. and Clark, T. and Kast, S.M. and Richards, N.G.J.
Journal of Chemical Theory and Computation 16 (2020)Evolution has yielded biopolymers that are constructed from exactly four building blocks and are able to support Darwinian evolution. Synthetic biology aims to extend this alphabet, and we recently showed that 8-letter (hachimoji) DNA can support rule-based information encoding. One source of replicative error in non-natural DNA-like systems, however, is the occurrence of alternative tautomeric forms, which pair differently. Unfortunately, little is known about how structural modifications impact free-energy differences between tautomers of the non-natural nucleobases used in the hachimoji expanded genetic alphabet. Determining experimental tautomer ratios is technically difficult, and so, strategies for improving hachimoji DNA replication efficiency will benefit from accurate computational predictions of equilibrium tautomeric ratios. We now report that high-level quantum-chemical calculations in aqueous solution by the embedded cluster reference interaction site model, benchmarked against free-energy molecular simulations for solvation thermodynamics, provide useful quantitative information on the tautomer ratios of both Watson-Crick and hachimoji nucleobases. In agreement with previous computational studies, all four Watson-Crick nucleobases adopt essentially only one tautomer in water. This is not the case, however, for non-natural nucleobases and their analogues. For example, although the enols of isoguanine and a series of related purines are not populated in water, these heterocycles possess N1-H and N3-H keto tautomers that are similar in energy, thereby adversely impacting accurate nucleobase pairing. These robust computational strategies offer a firm basis for improving experimental measurements of tautomeric ratios, which are currently limited to studying molecules that exist only as two tautomers in solution. Copyright © 2020 American Chemical Society.
view abstract 10.1021/acs.jctc.9b01079
- The SAMPL6 challenge on predicting octanol–water partition coefficients from EC-RISM theory
Tielker, N. and Tomazic, D. and Eberlein, L. and Güssregen, S. and Kast, S.M.
Journal of Computer-Aided Molecular Design 34 (2020)Results are reported for octanol–water partition coefficients (log P) of the neutral states of drug-like molecules provided during the SAMPL6 (Statistical Assessment of Modeling of Proteins and Ligands) blind prediction challenge from applying the “embedded cluster reference interaction site model” (EC-RISM) as a solvation model for quantum-chemical calculations. Following the strategy outlined during earlier SAMPL challenges we first train 1- and 2-parameter water-free (“dry”) and water-saturated (“wet”) models for n-octanol solvation Gibbs energies with respect to experimental values from the “Minnesota Solvation Database” (MNSOL), yielding a root mean square error (RMSE) of 1.5 kcal mol−1 for the best-performing 2-parameter wet model, while the optimal water model developed for the pKa part of the SAMPL6 challenge is kept unchanged (RMSE 1.6 kcal mol−1 for neutral compounds from a model trained on both neutral and ionic species). Applying these models to the blind prediction set yields a log P RMSE of less than 0.5 for our best model (2-parameters, wet). Further analysis of our results reveals that a single compound is responsible for most of the error, SM15, without which the RMSE drops to 0.2. Since this is the only compound in the challenge dataset with a hydroxyl group we investigate other alcohols for which Gibbs energy of solvation data for both water and n-octanol are available in the MNSOL database to demonstrate a systematic cause of error and to discuss strategies for improvement. © 2020, The Author(s).
view abstract 10.1007/s10822-020-00283-4
- High pressure response of 1H NMR chemical shifts of purine nucleotides
Munte, C.E. and Karl, M. and Kauter, W. and Eberlein, L. and Pham, T.-V. and Erlach, M.B. and Kast, S.M. and Kremer, W. and Kalbitzer, H.R.
Biophysical Chemistry 254 (2019)The study of the pressure response by NMR spectroscopy provides information on the thermodynamics of conformational equilibria in proteins and nucleic acids. For obtaining a database for expected pressure effects on free nucleotides and nucleotides bound in macromolecular complexes, the pressure response of 1H chemical shifts and J-coupling constants of the purine 5′-ribonucleotides AMP, ADP, ATP, GMP, GDP, and GTP were studied in the absence and presence of Mg2+-ions. Experiments are supported by quantum-chemical calculations of populations and chemical shift differences in order to corroborate structural interpretations and to estimate missing data for AMP. The preference of the ribose S puckering obtained from the analysis of the experimental J-couplings is also confirmed by the calculations. In addition, the pressure response of the non-hydrolysable GTP analogues GppNHp, GppCH2p, and GTPγS was examined within a pressure range up to 200 MPa. As observed earlier for 31P NMR chemical shifts of these nucleotides the pressure dependence of chemical shifts is clearly non-linear in most cases. In di- and tri-phospho nucleosides, the resonances of the two protons bound to the ribose 5′ carbon are non-equivalent and can be observed separately. The gg-rotamer at C4′- C5′ bond is strongly preferred and the downfield shifted resonance can be assigned to the H5″ proton in the nucleotides. In contrast, in adenosine itself the frequencies of the two resonances are interchanged. © 2019 Elsevier B.V.
view abstract 10.1016/j.bpc.2019.106261
- pK a calculations for tautomerizable and conformationally flexible molecules: partition function vs. state transition approach
Tielker, N. and Eberlein, L. and Chodun, C. and Güssregen, S. and Kast, S.M.
Journal of Molecular Modeling 25 (2019)Calculations of acidities of molecules with multiple tautomeric and/or conformational states require adequate treatment of the relative energetics of accessible states accompanied by a statistical-mechanical formulation of their contribution to the macroscopic pK a value. Here, we demonstrate rigorously the formal equivalence of two such approaches: a partition function treatment and statistics over transitions between molecular tautomeric and conformational states in the limit of a theory that does not require adjustment by empirical parameters correcting energetic values. However, for a frequently employed correction scheme, linear scaling of (free) energies and regression with respect to reference data taking an additive constant into account, this equivalence breaks down if more than one acid or base state is involved. The consequences of the resulting inconsistency are discussed on our datasets developed for aqueous pK a predictions during the recent SAMPL6 challenge, where molecular state energetics were computed based on the “embedded cluster reference interaction site model” (EC-RISM). This method couples integral equation theory as a solvation model to quantum-chemical calculations and yielded a test set root mean square error of 1.1 pK units from a partition function ansatz. For all practical purposes, the present results indicate that a state transition approach yields comparable accuracy despite the formal theoretical inconsistency, and that an additive regression intercept, which is strictly constant in the limit of large compound mass only, is a valid approximation. [Figure not available: see fulltext.]. © 2019, Springer-Verlag GmbH Germany, part of Springer Nature.
view abstract 10.1007/s00894-019-4033-4
- Structure and thermodynamics of aqueous urea solutions from ambient to kilobar pressures: From thermodynamic modeling, experiments, and first principles simulations to an accurate force field description
Hölzl, C. and Kibies, P. and Imoto, S. and Noetzel, J. and Knierbein, M. and Salmen, P. and Paulus, M. and Nase, J. and Held, C. and Sadowski, G. and Marx, D. and Kast, S.M. and Horinek, D.
Biophysical Chemistry 254 (2019)Molecular simulations based on classical force fields are a powerful method for shedding light on the complex behavior of biomolecules in solution. When cosolutes are present in addition to water and biomolecules, subtle balances of weak intermolecular forces have to be accounted for. This imposes high demands on the quality of the underlying force fields, and therefore force field development for small cosolutes is still an active field. Here, we present the development of a new urea force field from studies of urea solutions at ambient and elevated hydrostatic pressures based on a combination of experimental and theoretical approaches. Experimental densities and solvation shell properties from ab initio molecular dynamics simulations at ambient conditions served as the target properties for the force field optimization. Since urea is present in many marine life forms, elevated hydrostatic pressure was rigorously addressed: densities at high pressure were measured by vibrating tube densitometry up to 500 bar and by X-ray absorption up to 5 kbar. Densities were determined by the perturbed-chain statistical associating fluid theory equation of state. Solvation properties were determined by embedded cluster integral equation theory and ab initio molecular dynamics. Our new force field is able to capture the properties of urea solutions at high pressures without further high-pressure adaption, unlike trimethylamine-N-oxide, for which a high-pressure adaption is necessary. © 2019
view abstract 10.1016/j.bpc.2019.106260
- Structure of a Therapeutic Full-Length Anti-NPRA IgG4 Antibody: Dissecting Conformational Diversity
Blech, M. and Hörer, S. and Kuhn, A.B. and Kube, S. and Göddeke, H. and Kiefer, H. and Zang, Y. and Alber, Y. and Kast, S.M. and Westermann, M. and Tully, M.D. and Schäfer, L.V. and Garidel, P.
Biophysical Journal 116 (2019)We report the x-ray crystal structure of intact, full-length human immunoglobulin (IgG4) at 1.8 Å resolution. The data for IgG4 (S228P), an antibody targeting the natriuretic peptide receptor A, show a previously unrecognized type of Fab-Fc orientation with a distorted λ-shape in which one Fab-arm is oriented toward the Fc portion. Detailed structural analysis by x-ray crystallography and molecular simulations suggest that this is one of several conformations coexisting in a dynamic equilibrium state. These results were confirmed by small angle x-ray scattering in solution. Furthermore, electron microscopy supported these findings by preserving molecule classes of different conformations. This study fosters our understanding of IgG4 in particular and our appreciation of antibody flexibility in general. Moreover, we give insights into potential biological implications, specifically for the interaction of human anti-natriuretic peptide receptor A IgG4 with the neonatal Fc receptor, Fcγ receptors, and complement-activating C1q by considering conformational flexibility. © 2019 Biophysical Society
view abstract 10.1016/j.bpj.2019.03.036
- Overcoming EGFR G724S-mediated osimertinib resistance through unique binding characteristics of second-generation EGFR inhibitors
Fassunke, J. and Müller, F. and Keul, M. and Michels, S. and Dammert, M.A. and Schmitt, A. and Plenker, D. and Lategahn, J. and Heydt, C. and Brägelmann, J. and Tumbrink, H.L. and Alber, Y. and Klein, S. and Heimsoeth, A. and Dahmen, I. and Fischer, R.N. and Scheffler, M. and Ihle, M.A. and Priesner, V. and Scheel, A.H. and Wagener, S. and Kron, A. and Frank, K. and Garbert, K. and Persigehl, T. and Püsken, M. and Haneder, S. and Schaaf, B. and Rodermann, E. and Engel-Riedel, W. and Felip, E. and Smit, E.F. and Merkelbach-Bruse, S. and Reinhardt, H.C. and Kast, S.M. and Wolf, J. and Rauh, D. and Büttner, R. and Sos, M.L.
Nature Communications 9 (2018)The emergence of acquired resistance against targeted drugs remains a major clinical challenge in lung adenocarcinoma patients. In a subgroup of these patients we identified an association between selection of EGFRT790M-negative but EGFRG724S-positive subclones and osimertinib resistance. We demonstrate that EGFRG724S limits the activity of third-generation EGFR inhibitors both in vitro and in vivo. Structural analyses and computational modeling indicate that EGFRG724S mutations may induce a conformation of the glycine-rich loop, which is incompatible with the binding of third-generation TKIs. Systematic inhibitor screening and in-depth kinetic profiling validate these findings and show that second-generation EGFR inhibitors retain kinase affinity and overcome EGFRG724S-mediated resistance. In the case of afatinib this profile translates into a robust reduction of colony formation and tumor growth of EGFRG724S-driven cells. Our data provide a mechanistic basis for the osimertinib-induced selection of EGFRG724S-mutant clones and a rationale to treat these patients with clinically approved second-generation EGFR inhibitors. © 2018, The Author(s).
view abstract 10.1038/s41467-018-07078-0
- The SAMPL6 challenge on predicting aqueous pK a values from EC-RISM theory
Tielker, N. and Eberlein, L. and Güssregen, S. and Kast, S.M.
Journal of Computer-Aided Molecular Design 32 (2018)The “embedded cluster reference interaction site model” (EC-RISM) integral equation theory is applied to the problem of predicting aqueous pKa values for drug-like molecules based on an ensemble of tautomers. EC-RISM is based on self-consistent calculations of a solute’s electronic structure and the distribution function of surrounding water. Following-up on the workflow developed after the SAMPL5 challenge on cyclohexane-water distribution coefficients we extended and improved the methodology by taking into account exact electrostatic solute–solvent interactions taken from the wave function in solution. As before, the model is calibrated against Gibbs energies of hydration from the “Minnesota Solvation Database” and a public dataset of acidity constants of organic acids and bases by adjusting in total 4 parameters, among which only 3 are relevant for predicting pKa values. While the best-performing training model yields a root-mean-square error (RMSE) of 1 pK unit, the corresponding test set prediction on the full SAMPL6 dataset of macroscopic pKa values using the same level of theory exhibits slightly larger error (1.7 pK units) than the best test set model submitted (1.7 pK units for corresponding training set vs. test set performance of 1.6). Post-submission analysis revealed a number of physical optimization options regarding the numerical treatment of electrostatic interactions and conformational sampling. While the experimental test set data revealed after submission was not used for reparametrizing the methodology, the best physically optimized models consequentially result in RMSEs of 1.5 if only improved electrostatic interactions are considered and of 1.1 if, in addition, conformational sampling accounts for quantum-chemically derived rankings. We conclude that these numbers are probably near the ultimate accuracy achievable with the simple 3-parameter model using a single or the two best-ranking conformations per tautomer or microstate. Finally, relations of the present macrostate approach to microstate pKa results are discussed and some illustrative results for microstate populations are presented. © 2018, Springer Nature Switzerland AG.
view abstract 10.1007/s10822-018-0140-z
- Conversion of an instantaneous activating K+ channel into a slow activating inward rectifier
Baumeister, D. and Hertel, B. and Schroeder, I. and Gazzarrini, S. and Kast, S.M. and Van Etten, J.L. and Moroni, A. and Thiel, G.
FEBS Letters 591 (2017)The miniature channel, Kcv, is a structural equivalent of the pore of all K+ channels. Here, we follow up on a previous observation that a largely voltage-insensitive channel can be converted into a slow activating inward rectifier after extending the outer transmembrane domain by one Ala. This gain of rectification can be rationalized by dynamic salt bridges at the cytosolic entrance to the channel; opening is favored by voltage-sensitive formation of salt bridges and counteracted by their disruption. Such latent voltage sensitivity in the pore could be relevant for the understanding of voltage gating in complex Kv channels. © 2016 Federation of European Biochemical Societies
view abstract 10.1002/1873-3468.12536
- Drugging the catalytically inactive state of RET kinase in RET-rearranged tumors
Plenker, D. and Riedel, M. and Brägelmann, J. and Dammert, M.A. and Chauhan, R. and Knowles, P.P. and Lorenz, C. and Keul, M. and Bührmann, M. and Pagel, O. and Tischler, V. and Scheel, A.H. and Schütte, D. and Song, Y. and Stark, J. and Mrugalla, F. and Alber, Y. and Richters, A. and Engel, J. and Leenders, F. and Heuckmann, J.M. and Wolf, J. and Diebold, J. and Pall, G. and Peifer, M. and Aerts, M. and Gevaert, K. and Zahedi, R.P. and Buettner, R. and Shokat, K.M. and Mcdonald, N.Q. and Kast, S.M. and Gautschi, O. and Thomas, R.K. and Sos, M.L.
Science Translational Medicine 9 (2017)Oncogenic fusion events have been identified in a broad range of tumors. Among them, RET rearrangements represent distinct and potentially druggable targets that are recurrently found in lung adenocarcinomas. We provide further evidence that current anti-RET drugs may not be potent enough to induce durable responses in such tumors. We report that potent inhibitors, such as AD80 or ponatinib, that stably bind in the DFG-out conformation of RET may overcome these limitations and selectively kill RET-rearranged tumors. Using chemical genomics in conjunction with phosphoproteomic analyses in RET-rearranged cells, we identify the CCDC6- RETI788N mutation and drug-induced mitogen-activated protein kinase pathway reactivation as possible mechanisms by which tumors may escape the activity of RET inhibitors. Our data provide mechanistic insight into the druggability of RET kinase fusions that may be of help for the development of effective therapies targeting such tumors.
view abstract 10.1126/scitranslmed.aah6144
- Identification of Intrahelical Bifurcated H-Bonds as a New Type of Gate in K+ Channels
Rauh, O. and Urban, M. and Henkes, L.M. and Winterstein, T. and Greiner, T. and Van Etten, J.L. and Moroni, A. and Kast, S.M. and Thiel, G. and Schroeder, I.
Journal of the American Chemical Society 139 (2017)Gating of ion channels is based on structural transitions between open and closed states. To uncover the chemical basis of individual gates, we performed a comparative experimental and computational analysis between two K+ channels, KcvS and KcvNTS. These small viral encoded K+ channel proteins, with a monomer size of only 82 amino acids, resemble the pore module of all complex K+ channels in terms of structure and function. Even though both proteins share about 90% amino acid sequence identity, they exhibit different open probabilities with ca. 90% in KcvNTS and 40% in KcvS. Single channel analysis, mutational studies and molecular dynamics simulations show that the difference in open probability is caused by one long closed state in KcvS. This state is structurally created in the tetrameric channel by a transient, Ser mediated, intrahelical hydrogen bond. The resulting kink in the inner transmembrane domain swings the aromatic rings from downstream Phes in the cavity of the channel, which blocks ion flux. The frequent occurrence of Ser or Thr based helical kinks in membrane proteins suggests that a similar mechanism could also occur in the gating of other ion channels. © 2017 American Chemical Society.
view abstract 10.1021/jacs.7b01158
- Signatures of Solvation Thermodynamics in Spectra of Intermolecular Vibrations
Persson, R.A.X. and Pattni, V. and Singh, A. and Kast, S.M. and Heyden, M.
Journal of Chemical Theory and Computation 13 (2017)This study explores the thermodynamic and vibrational properties of water in the three-dimensional environment of solvated ions and small molecules using molecular simulations. The spectrum of intermolecular vibrations in liquid solvents provides detailed information on the shape of the local potential energy surface, which in turn determines local thermodynamic properties such as the entropy. Here, we extract this information using a spatially resolved extension of the two-phase thermodynamics method to estimate hydration water entropies based on the local vibrational density of states (3D-2PT). Combined with an analysis of solute-water and water-water interaction energies, this allows us to resolve local contributions to the solvation enthalpy, entropy, and free energy. We use this approach to study effects of ions on their surrounding water hydrogen bond network, its spectrum of intermolecular vibrations, and resulting thermodynamic properties. In the three-dimensional environment of polar and nonpolar functional groups of molecular solutes, we identify distinct hydration water species and classify them by their characteristic vibrational density of states and molecular entropies. In each case, we are able to assign variations in local hydration water entropies to specific changes in the spectrum of intermolecular vibrations. This provides an important link for the thermodynamic interpretation of vibrational spectra that are accessible to far-infrared absorption and Raman spectroscopy experiments. Our analysis provides unique microscopic details regarding the hydration of hydrophobic and hydrophilic functional groups, which enable us to identify interactions and molecular degrees of freedom that determine relevant contributions to the solvation entropy and consequently the free energy. © 2017 American Chemical Society.
view abstract 10.1021/acs.jctc.7b00184
- The hpCADD NDDO Hamiltonian: Parametrization
Thomas, H.B. and Hennemann, M. and Kibies, P. and Hoffgaard, F. and Güssregen, S. and Hessler, G. and Kast, S.M. and Clark, T.
Journal of Chemical Information and Modeling 57 (2017)A neglect of diatomic differential overlap (NDDO) Hamiltonian has been parametrized as an electronic component of a polarizable force field. Coulomb and exchange potentials derived directly from the NDDO Hamiltonian in principle can be used with classical potentials, thus forming the basis for a new generation of efficiently applicable multipolar polarizable force fields. The new hpCADD Hamiltonian uses force-field-like atom types and reproduces the electrostatic properties (dipole moment, molecular electrostatic potential) and Koopmans' theorem ionization potentials closely, as demonstrated for a large training set and an independent test set of small molecules. The Hamiltonian is not intended to reproduce geometries or total energies well, as these will be controlled by the classical force-field potentials. In order to establish the hpCADD Hamiltonian as an electronic component in force-field-based calculations, we tested its performance in combination with the 3D reference interaction site model (3D RISM) for aqueous solutions. Comparison of the resulting solvation free energies for the training and test sets to atomic charges derived from standard procedures, exact solute-solvent electrostatics based on high-level quantum-chemical reference data, and established semiempirical Hamiltonians demonstrates the advantages of the hpCADD parametrization. © 2017 American Chemical Society.
view abstract 10.1021/acs.jcim.7b00080
- Thermodynamic Characterization of Hydration Sites from Integral Equation-Derived Free Energy Densities: Application to Protein Binding Sites and Ligand Series
Güssregen, S. and Matter, H. and Hessler, G. and Lionta, E. and Heil, J. and Kast, S.M.
Journal of Chemical Information and Modeling 57 (2017)Water molecules play an essential role for mediating interactions between ligands and protein binding sites. Displacement of specific water molecules can favorably modulate the free energy of binding of protein-ligand complexes. Here, the nature of water interactions in protein binding sites is investigated by 3D RISM (three-dimensional reference interaction site model) integral equation theory to understand and exploit local thermodynamic features of water molecules by ranking their possible displacement in structure-based design. Unlike molecular dynamics-based approaches, 3D RISM theory allows for fast and noise-free calculations using the same detailed level of solute-solvent interaction description. Here we correlate molecular water entities instead of mere site density maxima with local contributions to the solvation free energy using novel algorithms. Distinct water molecules and hydration sites are investigated in multiple protein-ligand X-ray structures, namely streptavidin, factor Xa, and factor VIIa, based on 3D RISM-derived free energy density fields. Our approach allows the semiquantitative assessment of whether a given structural water molecule can potentially be targeted for replacement in structure-based design. Finally, PLS-based regression models from free energy density fields used within a 3D-QSAR approach (CARMa - comparative analysis of 3D RISM Maps) are shown to be able to extract relevant information for the interpretation of structure-activity relationship (SAR) trends, as demonstrated for a series of serine protease inhibitors. © 2017 American Chemical Society.
view abstract 10.1021/acs.jcim.6b00765
- Design principles for high-pressure force fields: Aqueous TMAO solutions from ambient to kilobar pressures
Hölzl, C. and Kibies, P. and Imoto, S. and Frach, R. and Suladze, S. and Winter, R. and Marx, D. and Horinek, D. and Kast, S.M.
Journal of Chemical Physics 144 (2016)Accurate force fields are one of the major pillars on which successful molecular dynamics simulations of complex biomolecular processes rest. They have been optimized for ambient conditions, whereas high-pressure simulations become increasingly important in pressure perturbation studies, using pressure as an independent thermodynamic variable. Here, we explore the design of non-polarizable force fields tailored to work well in the realm of kilobar pressures - while avoiding complete reparameterization. Our key is to first compute the pressure-induced electronic and structural response of a solute by combining an integral equation approach to include pressure effects on solvent structure with a quantum-chemical treatment of the solute within the embedded cluster reference interaction site model (EC-RISM) framework. Next, the solute's response to compression is taken into account by introducing pressure-dependence into selected parameters of a well-established force field. In our proof-of-principle study, the full machinery is applied to N,N,N-trimethylamine-N-oxide (TMAO) in water being a potent osmolyte that counteracts pressure denaturation. EC-RISM theory is shown to describe well the charge redistribution upon compression of TMAO(aq) to 10 kbar, which is then embodied in force field molecular dynamics by pressure-dependent partial charges. The performance of the high pressure force field is assessed by comparing to experimental and ab initio molecular dynamics data. Beyond its broad usefulness for designing non-polarizable force fields for extreme thermodynamic conditions, a good description of the pressure-response of solutions is highly recommended when constructing and validating polarizable force fields. © 2016 AIP Publishing LLC.
view abstract 10.1063/1.4944991
- Designing molecular complexes using free-energy derivatives from liquid-state integral equation theory
Mrugalla, F. and Kast, S.M.
Journal of Physics Condensed Matter 28 (2016)Complex formation between molecules in solution is the key process by which molecular interactions are translated into functional systems. These processes are governed by the binding or free energy of association which depends on both direct molecular interactions and the solvation contribution. A design goal frequently addressed in pharmaceutical sciences is the optimization of chemical properties of the complex partners in the sense of minimizing their binding free energy with respect to a change in chemical structure. Here, we demonstrate that liquid-state theory in the form of the solute-solute equation of the reference interaction site model provides all necessary information for such a task with high efficiency. In particular, computing derivatives of the potential of mean force (PMF), which defines the free-energy surface of complex formation, with respect to potential parameters can be viewed as a means to define a direction in chemical space toward better binders. We illustrate the methodology in the benchmark case of alkali ion binding to the crown ether 18-crown-6 in aqueous solution. In order to examine the validity of the underlying solute-solute theory, we first compare PMFs computed by different approaches, including explicit free-energy molecular dynamics simulations as a reference. Predictions of an optimally binding ion radius based on free-energy derivatives are then shown to yield consistent results for different ion parameter sets and to compare well with earlier, orders-of-magnitude more costly explicit simulation results. This proof-of-principle study, therefore, demonstrates the potential of liquid-state theory for molecular design problems. © 2016 IOP Publishing Ltd.
view abstract 10.1088/0953-8984/28/34/344004
- Structure and thermodynamics of nondipolar molecular liquids and solutions from integral equation theory
Frach, R. and Heil, J. and Kast, S.M.
Molecular Physics 114 (2016)Solvent-induced solute polarisation of nondipolar solvents originates mainly from specific directional interactions and higher electrostatic multipole moments. Popular continuum solvation models such as the polarisable continuum models ignore such interactions and, therefore, cannot adequately model solvation effects on electronic structure in these environments. Important examples of nondipolar solvents that are indistinguishable by continuum methods are benzene and hexafluorobenzene. Both substances have very similar macroscopic properties, while solutes dissolved in either benzene or hexafluorobenzene behave differently due to their inverted electrostatic quadrupole moments and slightly different size. As a first step towards a proper and computationally feasible description of nondipolar molecular solvents, we present here integral equation theory results based on various forms of the reference interaction site model coupled to quantum-chemical calculations for benzene and hexafluorobenzene solutions of small molecules. We analyse solvation structures, also in comparison with molecular dynamics simulations, and show that predictions of transfer Gibbs energies, which define partition constants, benefit substantially from considering the exact, wave function-derived electrostatic field distribution beyond a simple point charge solute model in comparison with experimental data. Moreover, by constructing artificial uncharged and charge-inverted toy models of the solvents, it is possible to dissect the relative importance of dispersion and quadrupolar electrostatic effects on the partitioning equilibria. Such insight can help to design specifically optimised solvents to control solubility and selectivity for a wide range of applications. © 2016 Informa UK Limited, trading as Taylor & Francis Group
view abstract 10.1080/00268976.2016.1167266
- The Chemical Shift Baseline for High-Pressure NMR Spectra of Proteins
Frach, R. and Kibies, P. and Böttcher, S. and Pongratz, T. and Strohfeldt, S. and Kurrmann, S. and Koehler, J. and Hofmann, M. and Kremer, W. and Kalbitzer, H.R. and Reiser, O. and Horinek, D. and Kast, S.M.
Angewandte Chemie - International Edition 55 (2016)High-pressure (HP) NMR spectroscopy is an important method for detecting rare functional states of proteins by analyzing the pressure response of chemical shifts. However, for the analysis of the shifts it is mandatory to understand the origin of the observed pressure dependence. Here we present experimental HP NMR data on the15N-enriched peptide bond model, N-methylacetamide (NMA), in water, combined with quantum-chemical computations of the magnetic parameters using a pressure-sensitive solvation model. Theoretical analysis of NMA and the experimentally used internal reference standard 4,4-dimethyl-4-silapentane-1-sulfonic (DSS) reveal that a substantial part of observed shifts can be attributed to purely solvent-induced electronic polarization of the backbone. DSS is only marginally responsive to pressure changes and is therefore a reliable sensor for variations in the local magnetic field caused by pressure-induced changes of the magnetic susceptibility of the solvent. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim
view abstract 10.1002/anie.201602054
- The SAMPL5 challenge for embedded-cluster integral equation theory: solvation free energies, aqueous pK a, and cyclohexane–water log D
Tielker, N. and Tomazic, D. and Heil, J. and Kloss, T. and Ehrhart, S. and Güssregen, S. and Schmidt, K.F. and Kast, S.M.
Journal of Computer-Aided Molecular Design 30 (2016)We predict cyclohexane–water distribution coefficients (log D7.4) for drug-like molecules taken from the SAMPL5 blind prediction challenge by the “embedded cluster reference interaction site model” (EC-RISM) integral equation theory. This task involves the coupled problem of predicting both partition coefficients (log P) of neutral species between the solvents and aqueous acidity constants (pKa) in order to account for a change of protonation states. The first issue is addressed by calibrating an EC-RISM-based model for solvation free energies derived from the “Minnesota Solvation Database” (MNSOL) for both water and cyclohexane utilizing a correction based on the partial molar volume, yielding a root mean square error (RMSE) of 2.4 kcal mol−1 for water and 0.8–0.9 kcal mol−1 for cyclohexane depending on the parametrization. The second one is treated by employing on one hand an empirical pKa model (MoKa) and, on the other hand, an EC-RISM-derived regression of published acidity constants (RMSE of 1.5 for a single model covering acids and bases). In total, at most 8 adjustable parameters are necessary (2–3 for each solvent and two for the pKa) for training solvation and acidity models. Applying the final models to the log D7.4 dataset corresponds to evaluating an independent test set comprising other, composite observables, yielding, for different cyclohexane parametrizations, 2.0–2.1 for the RMSE with the first and 2.2–2.8 with the combined first and second SAMPL5 data set batches. Notably, a pure log P model (assuming neutral species only) performs statistically similarly for these particular compounds. The nature of the approximations and possible perspectives for future developments are discussed. © 2016, Springer International Publishing Switzerland.
view abstract 10.1007/s10822-016-9939-7
- Toward Extreme Biophysics: Deciphering the Infrared Response of Biomolecular Solutions at High Pressures
Imoto, S. and Kibies, P. and Rosin, C. and Winter, R. and Kast, S.M. and Marx, D.
Angewandte Chemie - International Edition 55 (2016)Biophysics under extreme conditions is the fundamental platform for scrutinizing life in unusual habitats, such as those in the deep sea or continental subsurfaces, but also for putative extraterrestrial organisms. Therefore, an important thermodynamic variable to explore is pressure. It is shown that the combination of infrared spectroscopy with simulation is an exquisite approach for unraveling the intricate pressure response of the solvation pattern of TMAO in water, which is expected to be transferable to biomolecules in their native solvent. Pressure-enhanced hydrogen bonding was found for TMAO in water. TMAO is a molecule known to stabilize proteins against pressure-induced denaturation in deep-sea organisms. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim
view abstract 10.1002/anie.201602757
- 3D RISM theory with fast reciprocal-space electrostatics
Heil, J. and Kast, S.M.
Journal of Chemical Physics 142 (2015)The calculation of electrostatic solute-solvent interactions in 3D RISM ("three-dimensional reference interaction site model") integral equation theory is recast in a form that allows for a computational treatment analogous to the "particle-mesh Ewald" formalism as used for molecular simulations. In addition, relations that connect 3D RISM correlation functions and interaction potentials with thermodynamic quantities such as the chemical potential and average solute-solvent interaction energy are reformulated in a way that calculations of expensive real-space electrostatic terms on the 3D grid are completely avoided. These methodical enhancements allow for both, a significant speedup particularly for large solute systems and a smoother convergence of predicted thermodynamic quantities with respect to box size, as illustrated for several benchmark systems. © 2015 AIP Publishing LLC.
view abstract 10.1063/1.4914321
- Deuteron magnetic resonance and dielectric studies of guest reorientation and water dynamics in six clathrate hydrates containing ring-type guests
Nelson, H. and Ihrig, A. and Kahlau, R. and Kibies, P. and Kast, S.M. and Böhmer, R.
Journal of Non-Crystalline Solids 407 (2015)Using deuteron nuclear magnetic resonance and high-resolution dielectric spectroscopy the guest dynamics of tetrahydropyran, cyclopentane, trimethylene oxide, 1,3-dioxolane, and 1,4-dioxane clathrate hydrates is studied. By investigating lattice-deuterated as well as guest-deuterated crystals, the anisotropic guest reorientation is scrutinized and compared with previous results for tetrahydrofuran clathrate hydrate. The reorientational energy barriers depend linearly on the size of the guest molecules except for the clathrate hydrate of cyclopentane, a molecule which exhibits a dipole moment of the order of 0.01 D. The ether oxygens of the other guests can induce Bjerrum L defects on the hydrate lattice. Their concentration is examined for ammonia-doped tetrahydrofuran clathrate hydrate. Covering a wide range of NH3 concentrations x, a minimal overall Bjerrum defect concentration is observed that leads to a maximum mobility on the hydrate lattice at x ≈ 0.03%. To examine guest-induced Bjerrum L defects further, the translational motion on the undoped hydrate lattices is studied using stimulated-echo spectroscopy: The proton dynamics of CP clathrate hydrate is virtually identical to that of hexagonal ice and the water motion of THP clathrate hydrate closely matches that of the tetrahydrofuran compound. © 2014 Elsevier B.V.
view abstract 10.1016/j.jnoncrysol.2014.08.059
- Targeting Drug Resistance in EGFR with Covalent Inhibitors: A Structure-Based Design Approach
Engel, J. and Richters, A. and Getlik, M. and Tomassi, S. and Keul, M. and Termathe, M. and Lategahn, J. and Becker, C. and Mayer-Wrangowski, S. and Grütter, C. and Uhlenbrock, N. and Krüll, J. and Schaumann, N. and Eppmann, S. and Kibies, P. and Hoffgaard, F. and Heil, J. and Menninger, S. and Ortiz-Cuaran, S. and Heuckmann, J.M. and Tinnefeld, V. and Zahedi, R.P. and Sos, M.L. and Schultz-Fademrecht, C. and Thomas, R.K. and Kast, S.M. and Rauh, D.
Journal of Medicinal Chemistry 58 (2015)Receptor tyrosine kinases represent one of the prime targets in cancer therapy, as the dysregulation of these elementary transducers of extracellular signals, like the epidermal growth factor receptor (EGFR), contributes to the onset of cancer, such as non-small cell lung cancer (NSCLC). Strong efforts were directed to the development of irreversible inhibitors and led to compound CO-1686, which takes advantage of increased residence time at EGFR by alkylating Cys797 and thereby preventing toxic effects. Here, we present a structure-based approach, rationalized by subsequent computational analysis of conformational ligand ensembles in solution, to design novel and irreversible EGFR inhibitors based on a screening hit that was identified in a phenotype screen of 80 NSCLC cell lines against approximately 1500 compounds. Using protein X-ray crystallography, we deciphered the binding mode in engineered cSrc (T338M/S345C), a validated model system for EGFR-T790M, which constituted the basis for further rational design approaches. Chemical synthesis led to further compound collections that revealed increased biochemical potency and, in part, selectivity toward mutated (L858R and L858R/T790M) vs nonmutated EGFR. Further cell-based and kinetic studies were performed to substantiate our initial findings. Utilizing proteolytic digestion and nano-LC-MS/MS analysis, we confirmed the alkylation of Cys797. © 2015 American Chemical Society.
view abstract 10.1021/acs.jmedchem.5b01082
- Tectonics of a K+ channel: The importance of the N-terminus for channel gating
Hoffgaard, F. and Kast, S.M. and Moroni, A. and Thiel, G. and Hamacher, K.
Biochimica et Biophysica Acta - Biomembranes 1848 (2015)The small K+ channel Kcv represents the pore module of complex potassium channels. It was found that its gating can be modified by sensor domains, which are N-terminally coupled to the pore. This implies that the short N-terminus of the channel can transmit conformational changes from upstream sensors to the channel gates. To understand the functional role of the N-terminus in the context of the entire channel protein, we apply combinatorial screening of the mechanical coupling and long-range interactions in the Kcv potassium channel by reduced molecular models. The dynamics and mechanical connections in the channel complex show that the N-terminus is indeed mechanically connected to the pore domain. This includes a long rang coupling to the pore and the inner and outer transmembrane domains. Since the latter domains host the two gates of the channel, the data support the hypothesis that mechanical perturbation of the N-terminus can be transmitted to the channel gates. This effect is solely determined by the topology of the channel; sequence details only have an implicit effect on the coarse-grained dynamics via the fold and not through biochemical details at a smaller scale. This observation has important implications for engineering of synthetic channels on the basis of a K+ channel pore. © 2015 Elsevier B.V.All rights reserved.
view abstract 10.1016/j.bbamem.2015.09.015
- Acidity in DMSO from the embedded cluster integral equation quantum solvation model
Heil, J. and Tomazic, D. and Egbers, S. and Kast, S.M.
Journal of Molecular Modeling 20 (2014)The embedded cluster reference interaction site model (EC-RISM) is applied to the prediction of acidity constants of organic molecules in dimethyl sulfoxide (DMSO) solution. EC-RISM is based on a self-consistent treatment of the solute's electronic structure and the solvent's structure by coupling quantum-chemical calculations with three-dimensional (3D) RISM integral equation theory. We compare available DMSO force fields with reference calculations obtained using the polarizable continuum model (PCM). The results are evaluated statistically using two different approaches to eliminating the proton contribution: a linear regression model and an analysis of pKa shifts for compound pairs. Suitable levels of theory for the integral equation methodology are benchmarked. The results are further analyzed and illustrated by visualizing solvent site distribution functions and comparing them with an aqueous environment. © Springer-Verlag 2014.
view abstract 10.1007/s00894-014-2161-4
- Bridge function of the repulsive Weeks-Chandler-Andersen (WCA) fluid
Tomazic, D. and Hoffgaard, F. and Kast, S.M.
Chemical Physics Letters 591 (2014)The bridge function of a simple liquid is calculated for the repulsive part of the Weeks-Chandler-Andersen (WCA) separation of the Lennard-Jones potential. We employ explicit molecular dynamics simulations of the potential of mean force between constrained dimers in order to extract bridge data near zero separation and illustrate the difference to full Lennard-Jones results. We compare direct, reciprocal space and iterative, real space inversions of the Ornstein-Zernike equation. Bridge functions for various thermodynamic states are analyzed as to their parametric dependence on the renormalized indirect correlation function, which has consequences for the analytic representation of the free energy functional. © 2013 Elsevier B.V. All rights reserved.
view abstract 10.1016/j.cplett.2013.11.025
- Solvation effects on chemical shifts by embedded cluster integral equation theory
Frach, R. and Kast, S.M.
Journal of Physical Chemistry A 118 (2014)The accurate computational prediction of nuclear magnetic resonance (NMR) parameters like chemical shifts represents a challenge if the species studied is immersed in strongly polarizing environments such as water. Common approaches to treating a solvent in the form of, e.g., the polarizable continuum model (PCM) ignore strong directional interactions such as H-bonds to the solvent which can have substantial impact on magnetic shieldings. We here present a computational methodology that accounts for atomic-level solvent effects on NMR parameters by extending the embedded cluster reference interaction site model (EC-RISM) integral equation theory to the prediction of chemical shifts of N-methylacetamide (NMA) in aqueous solution. We examine the influence of various so-called closure approximations of the underlying three-dimensional RISM theory as well as the impact of basis set size and different treatment of electrostatic solute-solvent interactions. We find considerable and systematic improvement over reference PCM and gas phase calculations. A smaller basis set in combination with a simple point charge model already yields good performance which can be further improved by employing exact electrostatic quantum-mechanical solute-solvent interaction energies. A larger basis set benefits more significantly from exact over point charge electrostatics, which can be related to differences of the solvent's charge distribution. (Figure Presented). © 2014 American Chemical Society.
view abstract 10.1021/jp5084407
- Theoretical chemistry? Overcoming barriers!
Chemie in Unserer Zeit 48 (2014)
view abstract 10.1002/ciuz.201490026
- Viral potassium channels as a robust model system for studies of membrane-protein interaction
Braun, C.J. and Lachnit, C. and Becker, P. and Henkes, L.M. and Arrigoni, C. and Kast, S.M. and Moroni, A. and Thiel, G. and Schroeder, I.
Biochimica et Biophysica Acta - Biomembranes 1838 (2014)The viral channel KcvNTS belongs to the smallest K+ channels known so far. A monomer of a functional homotetramer contains only 82 amino acids. As a consequence of the small size the protein is almost fully submerged into the membrane. This suggests that the channel is presumably sensitive to its lipid environment. Here we perform a comparative analysis for the function of the channel protein embedded in three different membrane environments. 1. Single-channel currents of KcvNTS were recorded with the patch clamp method on the plasma membrane of HEK293 cells. 2. They were also measured after reconstitution of recombinant channel protein into classical planar lipid bilayers and 3. into horizontal bilayers derived from giant unilamellar vesicles (GUVs). The recombinant channel protein was either expressed and purified from Pichia pastoris or from a cell-free expression system; for the latter a new approach with nanolipoprotein particles was used. The data show that single-channel activity can be recorded under all experimental conditions. The main functional features of the channel like a large single-channel conductance (80 pS), high open-probability (> 50%) and the approximate duration of open and closed dwell times are maintained in all experimental systems. An apparent difference between the approaches was only observed with respect to the unitary conductance, which was ca. 35% lower in HEK293 cells than in the other systems. The reason for this might be explained by the fact that the channel is tagged by GFP when expressed in HEK293 cells. Collectively the data demonstrate that the small viral channel exhibits a robust function in different experimental systems. This justifies an extrapolation of functional data from these systems to the potential performance of the channel in the virus/host interaction. This article is part of a Special Issue entitled: Viral Membrane Proteins - Channels for Cellular Networking. © 2013 Elsevier B.V.
view abstract 10.1016/j.bbamem.2013.06.010
- Three-dimensional RISM integral equation theory for polarizable solute models
Hoffgaard, F. and Heil, J. and Kast, S.M.
Journal of Chemical Theory and Computation 9 (2013)Modeling solute polarizability is a key ingredient for improving the description of solvation phenomena. In recent years, polarizable molecular mechanics force fields have emerged that circumvent the limitations of classical fixed charge force fields by the ability to adapt their electrostatic potential distribution to a polarizing environment. Solvation phenomena are characterized by the solute's excess chemical potential, which can be computed by expensive fully atomistic free energy simulations. The alternative is to employ an implicit solvent model, which poses a challenge to the formulation of the solute-solvent interaction term within a polarizable framework. Here, we adapt the three-dimensional reference interaction site model (3D RISM) integral equation theory as a solvent model, which analytically yields the chemical potential, to the polarizable AMOEBA force field using an embedding cluster (EC-RISM) strategy. The methodology is analogous to our earlier approach to the coupling of a quantum-chemical solute description with a classical 3D RISM solvent. We describe the conceptual physical and algorithmic basis as well as the performance for several benchmark cases as a proof of principle. The results consistently show reasonable agreement between AMOEBA and quantum-chemical free energies in solution in general and allow for separate assessment of energetic and solvation-related contributions. We find that, depending on the parametrization, AMOEBA reproduces the chemical potential in better agreement with reference quantum-chemical calculations than the intramolecular energies, which suggests possible routes toward systematic improvement of polarizable force fields. © 2013 American Chemical Society.
view abstract 10.1021/ct400699q
- Communication: An exact bound on the bridge function in integral equation theories
Kast, S.M. and Tomazic, D.
Journal of Chemical Physics 137 (2012)We show that the formal solution of the general closure relation occurring in Ornstein-Zernike-type integral equation theories in terms of the Lambert W function leads to an exact relation between the bridge function and correlation functions, most notably to an inequality that bounds possible bridge values. The analytical results are illustrated on the example of the Lennard-Jones fluid for which the exact bridge function is known from computer simulations under various conditions. The inequality has consequences for the development of bridge function models and rationalizes numerical convergence issues. © 2012 American Institute of Physics.
view abstract 10.1063/1.4766465
- Relevance of lysine snorkeling in the outer transmembrane domain of small viral potassium ion channels
Gebhardt, M. and Henkes, L.M. and Tayefeh, S. and Hertel, B. and Greiner, T. and Van Etten, J.L. and Baumeister, D. and Cosentino, C. and Moroni, A. and Kast, S.M. and Thiel, G.
Biochemistry 51 (2012)Transmembrane domains (TMDs) are often flanked by Lys or Arg because they keep their aliphatic parts in the bilayer and their charged groups in the polar interface. Here we examine the relevance of this so-called " snorkeling" of a cationic amino acid, which is conserved in the outer TMD of small viral K+ channels. Experimentally, snorkeling activity is not mandatory for KcvPBCV-1 because K29 can be replaced by most of the natural amino acids without any corruption of function. Two similar channels, KcvATCV-1 and KcvMT325, lack a cytosolic N-terminus, and neutralization of their equivalent cationic amino acids inhibits their function. To understand the variable importance of the cationic amino acids, we reanalyzed molecular dynamics simulations of KcvPBCV-1 and N-terminally truncated mutants; the truncated mutants mimic KcvATCV-1 and KcvMT325. Structures were analyzed with respect to membrane positioning in relation to the orientation of K29. The results indicate that the architecture of the protein (including the selectivity filter) is only weakly dependent on TMD length and protonation of K29. The penetration depth of Lys in a given protonation state is independent of the TMD architecture, which leads to a distortion of shorter proteins. The data imply that snorkeling can be important for K+ channels; however, its significance depends on the architecture of the entire TMD. The observation that the most severe N-terminal truncation causes the outer TMD to move toward the cytosolic side suggests that snorkeling becomes more relevant if TMDs are not stabilized in the membrane by other domains. © 2012 American Chemical Society.
view abstract 10.1021/bi3006016
- Thermally induced polarizabilities and dipole moments of small tin clusters
Kast, S.M. and Schäfer, S. and Schäfer, R.
Journal of Chemical Physics 136 (2012)We study the influence of thermal excitation on the electric susceptibilities for Sn 6 and Sn 7 clusters by molecular beam electric deflection and Monte-Carlo simulations in conjunction with quantum-chemical calculations. At low temperatures (40 K), no field-induced broadening of the Sn 6 and Sn 7 cluster beams are observed, in agreement with vanishing permanent electric dipole moments due to their centro-symmetrical ground states. The electric polarizabilities of Sn 6 and Sn 7, as inferred from the field-induced molecular beam deflection, are in good agreement with the quantum-chemical predictions. At elevated temperatures of 50-100 K, increased polarizabilities of about 2-3 Å 3 are obtained. Also, we found indications of a field-induced beam broadening which points to the existence of permanent dipole moments of about 0.01-0.02 D per atom at higher temperatures. These results cannot be explained by thermal excitations within a harmonic oscillator model, which would yield a temperature-independent polarizability and fluxional, but not permanent, dipole moments. We analyze this behavior by Monte-Carlo simulations in order to compute average temperature-induced electric dipole moments. For that purpose, we developed a novel technique for predicting observables sampled on the quantum-chemical potential energy surface by an umbrella sampling correction of Monte-Carlo results obtained from simulations utilizing an empirical potential. The calculated, fluxional dipole moments are in tune with the observed beam broadenings. The cluster dynamics underlying the polarizability appear to be intermediate between rigid and floppy molecules which leads to the conclusion that the rotational, not the vibrational temperature seems to be the key parameter that determines the temperature dependence of the polarizability. © 2012 American Institute of Physics.
view abstract 10.1063/1.3699071
- A minimalist model for ion partitioning and competition in a K + channel selectivity filter
Kast, S.M. and Kloss, T. and Tayefeh, S. and Thiel, G.
Journal of General Physiology 138 (2011)
view abstract 10.1085/jgp.201110694
- Membrane anchoring and interaction between transmembrane domains are crucial for K+ channel function
Gebhardt, M. and Hoffgaard, F. and Hamacher, K. and Kast, S.M. and Moroni, A. and Thiel, G.
Journal of Biological Chemistry 286 (2011)The small viral channel Kcv is a Kir-like K+ channel of only 94 amino acids. With this simple structure, the tetramer of Kcv represents the pore module of all complex K+ channels. To examine the structural contribution of the transmembrane domains (TMDs) to channel function, we performed Ala scanning mutagenesis of the two domains and tested the functionality of the mutants in a yeast complementation assay. The data reveal, in combination with computational models, that the upper halves of both TMDs, which face toward the external medium, are rather rigid, whereas the inner parts are more flexible. The rigidity of the outer TMD is conferred by a number of essential aromatic amino acids that face the membrane and probably anchor this domain in the bilayer. The inner TMD is intimately connected with the rigid part of the outer TMD via π⋯πinteractions between a pair of aromatic amino acids. This structural principle is conserved within the viral K + channels and also present in Kir2.2, implying a general importance of this architecture for K+ channel function. © 2011 by The American Society for Biochemistry and Molecular Biology, Inc.
view abstract 10.1074/jbc.M110.211672
- Minimal art: Or why small viral K+ channels are good tools for understanding basic structure and function relations
Thiel, G. and Baumeister, D. and Schroeder, I. and Kast, S.M. and Van Etten, J.L. and Moroni, A.
Biochimica et Biophysica Acta - Biomembranes 1808 (2011)Some algal viruses contain genes that encode proteins with the hallmarks of K+ channels. One feature of these proteins is that they are less than 100 amino acids in size, which make them truly minimal for a K+ channel protein. That is, they consist of only the pore module present in more complex K+ channels. The combination of miniature size and the functional robustness of the viral K+ channels make them ideal model systems for studying how K+ channels work. Here we summarize recent structure/function correlates from these channels, which provide insight into functional properties such as gating, pharmacology and sorting in cells. © 2010 Elsevier B.V. All rights reserved.
view abstract 10.1016/j.bbamem.2010.04.008
- Prediction of tautomer ratios by embedded-cluster integral equation theory
Kast, S.M. and Heil, J. and Güssregen, S. and Schmidt, K.F.
Journal of Computer-Aided Molecular Design 24 (2010)The "embedded cluster reference interaction site model" (EC-RISM) approach combines statistical-mechanical integral equation theory and quantum-chemical calculations for predicting thermodynamic data for chemical reactions in solution. The electronic structure of the solute is determined self-consistently with the structure of the solvent that is described by 3D RISM integral equation theory. The continuous solvent-site distribution is mapped onto a set of discrete background charges ("embedded cluster") that represent an additional contribution to the molecular Hamiltonian. The EC-RISM analysis of the SAMPL2 challenge set of tautomers proceeds in three stages. Firstly, the group of compounds for which quantitative experimental free energy data was provided was taken to determine appropriate levels of quantum-chemical theory for geometry optimization and free energy prediction. Secondly, the resulting workflow was applied to the full set, allowing for chemical interpretations of the results. Thirdly, disclosure of experimental data for parts of the compounds facilitated a detailed analysis of methodical issues and suggestions for future improvements of the model. Without specifically adjusting parameters, the EC-RISM model yields the smallest value of the root mean square error for the first set (0.6 kcal mol-1) as well as for the full set of quantitative reaction data (2.0 kcal mol-1) among the SAMPL2 participants. © 2010 Springer Science+Business Media B.V.
view abstract 10.1007/s10822-010-9340-x
- Proapoptotic influenza A virus protein PB1-F2 forms a nonselective ion channel
Henkel, M. and Mitzner, D. and Henklein, P. and Meyer-Almes, F.-J. and Moroni, A. and DiFrancesco, M.L. and Henkes, L.M. and Kreim, M. and Kast, S.M. and Schubert, U. and Thiel, G.
PLoS ONE 5 (2010)Background: PB1-F2 is a proapoptotic influenza A virus protein of approximately 90 amino acids in length that is located in the nucleus, cytosol and in the mitochondria membrane of infected cells. Previous studies indicated that the molecule destabilizes planar lipid bilayers and has a strong inherent tendency for multimerization. This may be correlate with its capacity to induce mitochondrial membrane depolarization. Methodology/Principal Findings: Here, we investigated whether PB1-F2 is able to form ion channels within planar lipid bilayers and microsomes. For that purpose, a set of biologically active synthetic versions of PB1-F2 (sPB1-F2) derived from the IAV isolates A/Puerto Rico/8/34(H1N1) (IAVPR8), from A/Brevig Mission/1/1918(H1N1) (IAVSF2) or the H5N1 consensus sequence (IAVBF2) were used. Electrical and fluorimetric measurements show that all three peptides generate in planar lipid bilayers or in liposomes, respectively, a barely selective conductance that is associated with stochastic channel type fluctuations between a closed state and at least two defined open states. Unitary channel fluctuations were also generated when a truncated protein comprising only the 37 c-terminal amino acids of sPB1-F2 was reconstituted in bilayers. Experiments were complemented by extensive molecular dynamics simulations of the truncated fragment in a lipid bilayer. The results indicate that the c-terminal region exhibits a slightly bent helical fold, which is stable and remains embedded in the bilayer for over 180 ns. Conclusion/Significance: The data support the idea that PB1-F2 is able to form protein channel pores with no appreciable selectivity in membranes and that the c-terminus is important for this function. This information could be important for drug development. © 2010 Henkel et al.
view abstract 10.1371/journal.pone.0011112
- Salt bridges in the miniature viral channel Kcv are important for function
Hertel, B. and Tayefeh, S. and Kloss, T. and Hewing, J. and Gebhardt, M. and Baumeister, D. and Moroni, A. and Thiel, G. and Kast, S.M.
European Biophysics Journal 39 (2010)The viral potassium channel Kcv comprises only 94 amino acids, which represent the pore module of more complex K+channels. As for Kir-type channels, Kcv also has a short N-terminal helix exposed to the cytoplasm, upstream of the Wrst transmembrane domain. Here we show that this helix is relevant for Kcv function. The presence of charged amino acids, which form dynamic inter- and intrasubunit salt bridges is crucial. Electrophysiological measurements, yeast rescue experiments and molecular dynamics simulations show that mutants in which the critical salt bridge formation is impaired have no or reduced channel activity. We conclude that these salt bridges destabilise the complexation of K+ions by negative charges on the inner transmembrane domain at the entrance into the cavity. This feature facilitates a continuous and coordinated transfer of ions between the cavity and the cytoplasm for channels without the canonical bundle crossing. © European Biophysical Societies' Association 2009.
view abstract 10.1007/s00249-009-0451-z