Quantification of Solvent Contribution to the Stability of Noncovalent Complexes

We introduce an indirect approach to estimate the solvation contributions to the thermodynamics of noncovalent complex formation through molecular dynamics simulation. This estimation is demonstrated by potential of mean force and entropy calculations on the binding process between β-cyclodextrin (host) and four drug molecules puerarin, daidzin, daidzein, and nabumetone (guest) in explicit water, followed by a stepwise extraction of individual enthalpy (ΔH) and entropy (ΔS) terms from the total free energy. Detailed analysis on the energetics of the host−guest complexation demonstrates that flexibility of the binding partners and solvation-related ΔH and ΔS need to be included explicitly for accurate estimation of the binding thermodynamics. From this, and our previous work on the solvent dependency of binding energies (Zhang et al. J. Phys. Chem. B 2012, 116, 12684−12693), it follows that calculations neglecting host or guest flexibility, or those employing implicit solvent, will not be able to systematically predict binding free energies. The approach presented here can be readily adopted for obtaining a deeper understanding of the mechanisms governing noncovalent associations in solution

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

Mechanism of blebbistatin inhibition of myosin II

Blebbistatin is a recently discovered small molecule inhibitor showing high affinity and selectivity toward myosin II. Here we report a detailed investigation of its mechanism of inhibition. Blebbistatin does not compete with nucleotide binding to the skeletal muscle myosin subfragment-1. The inhibitor preferentially binds to the ATPase intermediate with ADP and phosphate bound at the active site, and it slows down phosphate release. Blebbistatin interferes neither with binding of myosin to actin nor with ATP-induced actomyosin dissociation. Instead, it blocks the myosin heads in a products complex with low actin affinity. Blind docking molecular simulations indicate that the productive blebbistatin-binding site of the myosin head is within the aqueous cavity between the nucleotide pocket and the cleft of the actin-binding interface. The property that blebbistatin blocks myosin II in an actin-detached state makes the compound useful both in muscle physiology and in exploring the cellular function of cytoplasmic myosin II isoforms, whereas the stabilization of a specific myosin intermediate confers a great potential in structural studies

A perm és a triász időszak határán lezajlott környezeti változások, magyarországi szelvények vizsgálata alapján = Environmental changes at the Permian-Triassic boundary, based on studies of boundary sections in Hungary

Kutatási programunk célja az volt, hogy képet nyerjünk a paleozoikum és a mezozoikum határán lejátszódó, a fanerozoikum legnagyobb kihalásához vezető környezeti változások pontos menetéről és ennek alapján megkíséreljük az okok feltárását is. A bükki szelvények vizsgálata során biosztratigráfiai módszerekkel tisztáztuk a határ pontos helyzetét, részletes mikrofácies-elemzést végeztünk. Kimutattuk, hogy a legfelső perm rétegekben a karbonátkiválasztó szervezetek maradványai rövid szakaszon belül, de fokozatosan tünnek el. A maradványok eltűnésével együtt kezdődik el a delta 13C értékek fokozatos eltolódása negatív irányba. Az ezt követő szakaszt elszegényedett fosszilia-együttes és litológiai változás ("határ márga") is jellemzi. A "túlélő" permi szervezetek eltűnése egybeesik a delta 13C értékek negatív csúcsával, amit a P-T határ kemosztratigráfiai jelzőjének tekintenek. Negatív eltolódás az erős vízmozgású sekélytengerben képződött dunánúli-középhegységi rétegsorok ooidos határszakaszán is egyértelműen kimutatható. A triász kezdetén mikrobás karbonátok, illetve a sekély, erős vizmozgású szubtidális övezetekben oolit rétegek képződése jellemző. Az eredmények bebizonyították, hogy a Bálvány-észak elnevezésű alapszelvény a perm és a triász határán lezajlott események megismerése szempontjából az egyik legteljesebb és a legjobban tanulmányozható szelvény Európában és világviszonylatban is kiemelkedő jelentőségű. | The aim of the research project was to contribute for better understanding of environmental changes, which resulted in the largest extension of the Phanerozoic at the boundary between the Paleozoic and Mesozoic. Applying biostratigraphic methods, the exact position of the boundary was determined in the sections of the Bükk Mountains and detailed microfacies analyses were carried out. It was proved that in the uppermost Permian layers, remnants of carbonate secreting organisms gradually disappear in a short interval. A negative shift of delta 13C values starts at the level of onset of gradual decrease in the amount of bioclasts. The next interval is characterised by an impoverished fossil assemblage and also a change in the lithology ('boundary shale'). Disappearance of the 'survivor' Permian biota coincides with a negative delta 13C peak that is considered as the chemostratigraphic marker of the Permian-Triassic boundary. The negative shift was also encountered in the oolitic boundary interval of the Transdanubian Range, which was deposited in a high-energy shallow marine environment. In the earliest Triassic formation of microbial carbonates on the low-energy sea-bottom and oolites in the high-energy environments was typical. Results of the project evidenced that the Bálvány-North section is one of the most complete and best-exposed Permian-Triassic boundary sections in Europe and it has an outstanding importance world-wide

Prerequisite Binding Modes Determine the Dynamics of Action of Covalent Agonists of Ion Channel TRPA1

Transient receptor potential ankyrin 1 (TRPA1) is a transmembrane protein channeling the influx of calcium ions. As a polymodal nocisensor, TRPA1 can be activated by thermal, mechanical stimuli and a wide range of chemically damaging molecules including small volatile environmental toxicants and endogenous algogenic lipids. After activation by such compounds, the ion channel opens up, its central pore widens allowing calcium influx into the cytosol inducing signal transduction pathways. Afterwards, the calcium influx desensitizes irritant evoked responses and results in an inactive state of the ion channel. Recent experimental determination of structures of apo and holo forms of TRPA1 opened the way towards the design of new agonists, which can activate the ion channel. The present study is aimed at the elucidation of binding dynamics of agonists using experimental structures of TRPA1-agonist complexes at the atomic level applying molecular docking and dynamics methods accounting for covalent and non-covalent interactions. Following a test of docking methods focused on the final, holo structures, prerequisite binding modes were detected involving the apo forms. It was shown how reversible interactions with prerequisite binding sites contribute to structural changes of TRPA1 leading to covalent bonding of agonists. The proposed dynamics of action allowed a mechanism-based forecast of new, druggable binding sites of potent agonists