Target-ligand binding affinity from single point enthalpy calculation and elemental composition.

Reliable target-ligand binding thermodynamics data are essential for successful drug design and molecular engineering projects. Besides experimental methods, a number of theoretical approaches have been introduced for the generation of binding thermodynamics data. However, available approaches often neglect electronic effects or explicit water molecules influencing target-ligand interactions. To handle electronic effects within a reasonable time frame, we introduce a fast calculator QMH-L using a single target-ligand complex structure pre-optimized at the molecular mechanics level. QMH-L is composed of the semi-empirical quantum mechanics calculation of binding enthalpy with predicted explicit water molecules at the complex interface, and a simple descriptor based on the elemental composition of the ligand. QMH-L estimates the target-ligand binding free energy with a root mean square error (RMSE) of 0.94 kcal mol-1. The calculations also provide binding enthalpy values and they were compared with experimental binding thermodynamics data collected from the most reliable isothermal titration calorimetry studies of systems including various protein targets and challenging, large peptide ligands with a molecular weight of up to 2-3 thousand. The single point enthalpy calculations of QMH-L require modest computational resources and are based on short runs with open source and/or free software like Gromacs, Mopac, MobyWat, and Fragmenter. QMH-L can be applied for fast, automated scoring of drug candidates during a virtual screen, enthalpic engineering of new ligands or thermodynamic explanation of complex interactions.

A Fragmenting Protocol with Explicit Hydration for Calculation of Binding Enthalpies of Target-Ligand Complexes at a Quantum Mechanical Level.

Optimization of the enthalpy component of binding thermodynamics of drug candidates is a successful pathway of rational molecular design. However, the large size and missing hydration structure of target-ligand complexes often hinder such optimizations with quantum mechanical (QM) methods. At the same time, QM calculations are often necessitated for proper handling of electronic effects. To overcome the above problems, and help the QM design of new drugs, a protocol is introduced for atomic level determination of hydration structure and extraction of structures of target-ligand complex interfaces. The protocol is a combination of a previously published program MobyWat, an engine for assigning explicit water positions, and Fragmenter, a new tool for optimal fragmentation of protein targets. The protocol fostered a series of fast calculations of ligand binding enthalpies at the semi-empirical QM level. Ligands of diverse chemistry ranging from small aromatic compounds up to a large peptide helix of a molecular weight of 3000 targeting a leukemia protein were selected for systematic investigations. Comparison of various combinations of implicit and explicit water models demonstrated that the presence of accurately predicted explicit water molecules in the complex interface considerably improved the agreement with experimental results. A single scaling factor was derived for conversion of QM reaction heats into binding enthalpy values. The factor links molecular structure with binding thermodynamics via QM calculations. The new protocol and scaling factor will help automated optimization of binding enthalpy in future molecular design projects.

Analysis of the influence of simulation parameters on biomolecule-linked water networks.

Advancement of computational molecular dynamics allows rapid calculation of large biomolecular systems in their water surroundings. New approaches of prediction of hydration networks of biomolecular surfaces and complex interfaces are also based on molecular dynamics (MD). Calculations with explicit solvent models can trace thousands of water molecules individually on a real time scale, yielding information on their mobility, and predicting their networking with biomolecular solutes and other water partners. Here, we investigate the effect of key parameters of molecular dynamics simulations on the quality of such predictions. Accordingly, systematic scans on temperature, pressure, force field, explicit water model and thermodynamic ensemble are performed. Explanations of optimal parameter values are provided using structural examples and analyses of the corresponding hydration networks.

Systematic exploration of multiple drug binding sites.

BACKGROUND: Targets with multiple (prerequisite or allosteric) binding sites have an increasing importance in drug design. Experimental determination of atomic resolution structures of ligands weakly bound to multiple binding sites is often challenging. Blind docking has been widely used for fast mapping of the entire target surface for multiple binding sites. Reliability of blind docking is limited by approximations of hydration models, simplified handling of molecular flexibility, and imperfect search algorithms. RESULTS: To overcome such limitations, the present study introduces Wrap 'n' Shake (WnS), an atomic resolution method that systematically "wraps" the entire target into a monolayer of ligand molecules. Functional binding sites are extracted by a rapid molecular dynamics shaker. WnS is tested on biologically important systems such as mitogen-activated protein, tyrosine-protein kinases, key players of cellular signaling, and farnesyl pyrophosphate synthase, a target of antitumor agents.

Dynamic changes in binding interaction networks of sex steroids establish their non-classical effects.

Non-classical signaling in the intracellular second messenger system plays a pivotal role in the cytoprotective effect of estradiol. Estrogen receptor is a common target of sex steroids and important in mediating estradiol-induced neuroprotection. Whereas the mechanism of genomic effects of sex steroids is fairly understood, their non-classical effects have not been elucidated completely. We use real time molecular dynamics calculations to uncover the interaction network of estradiol and activator estren. Besides steroid interactions, we also investigate the co-activation of the receptor. We show how steroid binding to the alternative binding site of the non-classical action is facilitated by the presence of a steroid in the classical binding site and the absence of the co-activator peptide. Uncovering such dynamic mechanisms behind steroid action will help the structure-based design of new drugs with non-classical responses and cytoprotective potential.

Regulation of the Equilibrium between Closed and Open Conformations of Annexin A2 by N-Terminal Phosphorylation and S100A4-Binding.

Annexin A2 (ANXA2) has a versatile role in membrane-associated functions including membrane aggregation, endo- and exocytosis, and it is regulated by post-translational modifications and protein-protein interactions through the unstructured N-terminal domain (NTD). Our sequence analysis revealed a short motif responsible for clamping the NTD to the C-terminal core domain (CTD). Structural studies indicated that the flexibility of the NTD and CTD are interrelated and oppositely regulated by Tyr24 phosphorylation and Ser26Glu phosphomimicking mutation. The crystal structure of the ANXA2-S100A4 complex showed that asymmetric binding of S100A4 induces dislocation of the NTD from the CTD and, similar to the Ser26Glu mutation, unmasks the concave side of ANXA2. In contrast, pTyr24 anchors the NTD to the CTD and hampers the membrane-bridging function. This inhibition can be restored by S100A4 and S100A10 binding. Based on our results we provide a structural model for regulation of ANXA2-mediated membrane aggregation by NTD phosphorylation and S100 binding.

[Attitudes, knowledge and use of complementary and alternative medicine among perioperative healthcare professionals]. / Komplementer terápiás gyógymódok megítélése a perioperatív ellátásban dolgozó egészségügyi szakdolgozók között.

INTRODUCTION: Perioperative healthcare professionals' attitudes towards non-conventional treatments have not been explored in Hungary yet. AIM: Our goal was to survey healthcare professionals' attitude and knowledge towards naturopathy in six clinics of the Semmelweis University that provide perioperative care. METHOD: An anonymous, paper-based questionnaire was used. With an 82% response rate, the data was gained from 119 questionnaires and was processed using statistical analysis and chi-squared test. RESULTS: Only 25.2% of those surveyed considered themselves to be well-informed in this field. 68.1% of the participants had an interest in naturopathy and 60.5% would have liked to learn about naturopathy. 70.6% would be willing to use non-conventional treatments in their daily work, predominantly those who have used these methods in the case of their own illness, p = 0.0027. The most popular treatment methods included homeopathy, alternative massage and movement therapy, acupuncture and manual therapy. CONCLUSION: As anticipated based on international literature in this field, those Hungarian healthcare professionals who took part in our survey showed openness and interest towards naturopathy. Orv. Hetil., 2017, 158(10), 368-375.

Complementary and alternative medicine: attitudes, knowledge and use among surgeons and anaesthesiologists in Hungary.

BACKGROUND: Despite their worldwide popularity the question of using non-conventional treatments is a source of controversy among medical professionals. Although these methods may have potential benefits it presents a problem when patients use non-conventional treatments in the perioperative period without informing their attending physician about it and this may cause adverse events and complications. To prevent this, physicians need to have a profound knowledge about non-conventional treatments. METHODS: An anonymous questionnaire was distributed among surgeons and anaesthesiologists working in Hungarian university clinics and in selected city or county hospitals. Questionnaires were distributed by post, online or in person. Altogether 258 questionnaires were received from 22 clinical and hospital departments. RESULTS: Anaesthesiologists and surgeons use reflexology, Traditional Chinese Medicine, herbal medicine and manual therapy most frequently in their clinical practice. Traditional Chinese Medicine was considered to be the most scientifically sound method, while homeopathy was perceived as the least well-grounded method. Neural therapy was the least well-known method among our subjects. Among the subjects of our survey only 3.1 % of perioperative care physicians had some qualifications in non-conventional medicine, 12.4 % considered themselves to be well-informed in this topic and 48.4 % would like to study some complementary method. Women were significantly more interested in alternative treatments than men, p = 0.001427; OR: 2.2765. Anaesthesiologists would be significantly more willing to learn non-conventional methods than surgeons. 86.4 % of the participants thought that non-conventional treatments should be evaluated from the point of view of evidence. Both surgeons and anaesthesiologists accept the application of integrative medicine and they also approve of the idea of teaching these methods at universities. CONCLUSIONS: According to perioperative care physicians, non-conventional methods should be evaluated based on evidence. They also expressed a willingness to learn about those treatments that meet the criteria of evidence and apply these in their clinical practice.

[Complementary and alternative medicine use in surgical patients]. / Nem konvencionális gyógymódok használata sebészeti betegek között.

INTRODUCTION: Due to the rise in use of non-conventional therapies, we may consider the application of those in perioperative setting. AIM: The aims of the authors were to measure the attitude of patients waiting for elective surgery towards naturopathic methods, to determine their use and factors influencing their usage. METHOD: A questionnaire was applied that patients filled in individually and anonymously at the First Department of Surgery of Semmelweis University, between July 1, 2014 and April 30, 2016. RESULTS: 63.6% of the 519 participants (response rate = 21%) were interested in non-conventional therapies, and 26.8% of them applied naturopathy. In this group there were significantly more females (p = 0.022; OR: 1.066-2.3635), patients with university degree (p = 0.000315; OR: 1.3915-3.1132), aged 40-49 (p = 0.012419; OR: 1.1451-3.2405), and patients with hormonal disease (p = 0.039482; OR: 1.0186-5.7242). In terms of lifetime prevalence the most popular methods were traditional Chinese medicine (8.9%), alternative movement and massage therapy (7.5%) and homeopathy (7.3%). Only 12.9% of the patients reported the application of these methods to the physician. CONCLUSION: Surgical patients are interested in naturopathic methods, and one-fourth of them actually use them even in the perioperative period. Orv. Hetil., 2016, 157(37), 1483-1488.

Exploration of Interfacial Hydration Networks of Target-Ligand Complexes.

Interfacial hydration strongly influences interactions between biomolecules. For example, drug-target complexes are often stabilized by hydration networks formed between hydrophilic residues and water molecules at the interface. Exhaustive exploration of hydration networks is challenging for experimental as well as theoretical methods due to high mobility of participating water molecules. In the present study, we introduced a tool for determination of the complete, void-free hydration structures of molecular interfaces. The tool was applied to 31 complexes including histone proteins, a HIV-1 protease, a G-protein-signaling modulator, and peptide ligands of various lengths. The complexes contained 344 experimentally determined water positions used for validation, and excellent agreement with these was obtained. High-level cooperation between interfacial water molecules was detected by a new approach based on the decomposition of hydration networks into static and dynamic network regions (subnets). Besides providing hydration structures at the atomic level, our results uncovered hitherto hidden networking fundaments of integrity and stability of complex biomolecular interfaces filling an important gap in the toolkit of drug design and structural biochemistry. The presence of continuous, static regions of the interfacial hydration network was found necessary also for stable complexes of histone proteins participating in chromatin assembly and epigenetic regulation.

Herbal medicine use by surgery patients in Hungary: a descriptive study.

BACKGROUND: The popularity of non-conventional treatments, especially the consumption of herbs is showing an increasing tendency all over the world. The consumption of herbal medicines might cause several complications during perioperative care. METHODS: The survey was conducted at the First Department of Surgery of Semmelweis University and focused on the demographics of patients consuming herbal medicines who had undergone elective surgery between July 1(st) 2014 and February 28(th) 2015. A one-page questionnaire, that the patients filled in individually and anonymously, was used. The response rate was 17.3 %. RESULTS: Out of the 390 patients who filled in the questionnaire, 7.2 % (28 patients) used herbal medicines, 3.6 % (14 patients) of them two weeks prior to their hospitalization. The other 3.6 % (14 patients) took herbal medicines sometime in the past. The majority of those who have ever consumed herbs are women (18/28), have completed secondary or tertiary education (23/28), more than half of them suffer from tumorous diseases and only a quarter of them (7/28) informed their physician about their use of herbal medication of their own accord. CONCLUSIONS: Attention must be paid to the exploration of herb consumption habits of surgery patients during the preoperative examinations in order to avoid potential side effects, complications or drug interactions.

Structural assembly of the signaling competent ERK2-RSK1 heterodimeric protein kinase complex.

Mitogen-activated protein kinases (MAPKs) bind and activate their downstream kinase substrates, MAPK-activated protein kinases (MAPKAPKs). Notably, extracellular signal regulated kinase 2 (ERK2) phosphorylates ribosomal S6 kinase 1 (RSK1), which promotes cellular growth. Here, we determined the crystal structure of an RSK1 construct in complex with its activator kinase. The structure captures the kinase-kinase complex in a precatalytic state where the activation loop of the downstream kinase (RSK1) faces the enzyme's (ERK2) catalytic site. Molecular dynamics simulation was used to show how this heterodimer could shift into a signaling-competent state. This structural analysis combined with biochemical and cellular studies on MAPK→MAPKAPK signaling showed that the interaction between the MAPK binding linear motif (residing in a disordered kinase domain extension) and the ERK2 "docking" groove plays the major role in making an encounter complex. This interaction holds kinase domains proximal as they "readjust," whereas generic kinase domain surface contacts bring them into a catalytically competent state.

Mobility-based prediction of hydration structures of protein surfaces.

MOTIVATION: Hydration largely determines solubility, aggregation of proteins and influences interactions between proteins and drug molecules. Despite the importance of hydration, structural determination of hydration structure of protein surfaces is still challenging from both experimental and theoretical viewpoints. The precision of experimental measurements is often affected by fluctuations and mobility of water molecules resulting in uncertain assignment of water positions. RESULTS: Our method can utilize mobility as an information source for the prediction of hydration structure. The necessary information can be produced by molecular dynamics simulations accounting for all atomic interactions including water-water contacts. The predictions were validated and tested by comparison to more than 1500 crystallographic water positions in 20 hydrated protein molecules including enzymes of biomedical importance such as cyclin-dependent kinase 2. The agreement with experimental water positions was larger than 80% on average. The predictions can be particularly useful in situations where no or limited experimental knowledge is available on hydration structures of molecular surfaces. AVAILABILITY AND IMPLEMENTATION: The method is implemented in a standalone C program MobyWat released under the GNU General Public License, freely accessible with full documentation at http://www.mobywat.com.