Conformational Energy Research Articles

Controlling achiral and chiral conformations of benzyl alcohol by ortho-halogenation, collisional relaxation and dimerisation.

Ortho-Halogenated benzyl alcohol can exist in two different low energy chiral conformations, only one of them with an OH-X contact (X = Cl, Br, I). A third, achiral conformation is enabled by the halogen substitution. We show by IR spectroscopy in supersonic jets that the achiral monomer is less stable than the chiral conformation with OH-X contact, but both can be produced in similar amounts using helium as a carrier gas. The robust OH transition observed for the achiral monomer is a sensitive benchmark for the conformational energy sequence, since the chiral conformation without OH-X contact is at least an order of magnitude less abundant, although it is often predicted by DFT to be slightly more stable and separated from the achiral conformation by a low barrier. This competing chiral conformation must be energetically higher by at least a few tenths of a kJ mol-1 to be consistent with experimental observations. That is indeed predicted by high-level energy calculations at the DFT-optimised structures. The most stable dimers of ortho-halogenated benzyl alcohols involve torsionally homo- and heterochiral pairings of the two OH groups, where the hydrogen bond-accepting OH group forms a cooperative intramolecular OH-X contact. The achiral monomer conformation is suppressed in these dimers. A homochiral dimer is formed almost exclusively for Cl, whereas its heterochiral variant is progressively co-stabilised with increasing halogen size. The stretching wavenumber of the donor OH in the dimers depends on the relative chirality of the donor and acceptor conformations. The consistent picture that emerges for Cl, Br and I substitution in ortho-position of benzyl alcohol is discussed in the context of interconversion barriers, heavy atom tunneling, π-π stacking, suppression of OH-π bonding, chirality synchronisation, and shortcomings of DFT approaches in reproducing the observations. The homochiral aggregation preference observed for simple benzyl alcohol is conserved and even enhanced upon ortho-halogenation, albeit partly by different interactions.

Sequence-dependent and -independent information in a combined random energy model for protein folding and coding.

Random energy models (REMs) provide a simple description of the energy landscapes that guide protein folding and evolution. The requirement of a large energy gap between the native structure and unfolded conformations, considered necessary for cooperative, protein-like, folding behavior, indicates that proteins differ markedly from random heteropolymers. It has been suggested, therefore, that natural selection might have acted to choose nonrandom amino acid sequences satisfying this particular condition, implying that a large fraction of possible, unselected random sequences, would not fold to any structure. From an informational perspective, however, this scenario could indicate that protein structures, regarded as messages to be transmitted through a communication channel, would not be efficiently encoded in amino acid sequences, regarded as the communication channel for this transmission, since a large fraction of possible channel states would not be used. Here, we use a combined REM for conformations and sequences, with previously estimated parameters for natural proteins, to explore an alternative possibility in which the appropriate shape of the landscape results mainly from the deviation from randomness of possible native structures instead of sequences. We observe that this situation emerges naturally if the distribution of conformational energies happens to arise from two independent contributions corresponding to sequence-dependent and -independent terms. This construction is consistent with the hypothesis of a protein burial folding code, with native structures being determined by a modest amount of sequence-dependent atomic burial information with sequence-independent constraints imposed by unspecific hydrogen bond formation. More generally, an appropriate combination of sequence-dependent and -independent information accommodates the possibility of an efficient structural encoding with the main physical requirement for folding, providing possible insight not only on the folding process but also on several aspects sequence evolution such as neutral networks, conformational coverage, and de novo gene emergence.

Ancestral Reconstruction and the Evolution of Protein Energy Landscapes.

A protein's sequence determines its conformational energy landscape. This, in turn, determines the protein's function. Understanding the evolution of new protein functions therefore requires understanding how mutations alter the protein energy landscape. Ancestral sequence reconstruction (ASR) has proven a valuable tool for tackling this problem. In ASR, one phylogenetically infers the sequences of ancient proteins, allowing characterization of their properties. When coupled to biophysical, biochemical, and functional characterization, ASR can reveal how historical mutations altered the energy landscape of ancient proteins, allowing the evolution of enzyme activity, altered conformations, binding specificity, oligomerization, and many other protein features. In this article, we review how ASR studies have been used to dissect the evolution of energy landscapes. We also discuss ASR studies that reveal how energy landscapes have shaped protein evolution. Finally, we propose that thinking about evolution from the perspective of an energy landscape can improve how we approach and interpret ASR studies.

Ruxolitinib'in COVID-19 majör proteaz enzimine ve SARS CoV-2 spike glikoproteinine karşı inhibitör aktivitesi: Bir moleküler kenetlenme çalışması.

Ruxolitinib (C17H18N6) is a Janus kinase (JAK) inhibitor that inhibits JAK1, JAK2, and JAK3 and with its tyrosine kinase inhibitor function It is the first drug approved for use in the treatment of myelofibrosis. The possible conformations of the ruxolitinib molecule were searched using PM3 technique and the Spartan06 software. The estimated molecular energies of the Ruxolitinib conformers, obtained by the variations in dihedral angles, were compared, and the most stable conformer was determined. To enlighten the inhibitory activity of Ruxolitinib agaist the apo (PDB ID: 6M03) and holo (PDB ID: 6LU7) forms of the main protease enzyme (Mpro) of COVID-19 and the SARSCoV-2 spike glycoprotein (PDB ID: 6VXX), molecular docking simulations were performed. The binding affinities and binding modes were determined. The binding free energies of ruxolitinib and 6M03, 6LU7, 6VXX targets calculated by the combination of Molecular Mechanics/Generalized Born Surface Area (MMGBSA) and Molecular Mechanics/Poisson-Boltzmann Surface Area (MM-PBSA) methods {MM/PB(GB)SA approach}, were found to be -22.24, -19.96 and -22.44 kcal/mol, respectively.

In silico and in vitro evaluation of newly synthesized pyrazolo-pyridine fused tetrazolo-pyrimidines derivatives as potential anticancer and antimicrobial agents

Diversely functionalized pyrazolo-pyridine fused tetrazolo-pyrimidines 10aa-am and 10ba-bn were successfully synthesized via a catalyst-free synthetic protocol with moderate to very good yields. The compounds were evaluated for cytotoxicity against MCF-7 and HEK-293 cells using MTT assay. Among the tested compounds, 10ab (IC50- 23.83 µM) and 10ah (IC50- 23.30 µM) demonstrated the highest potency against MCF-7 cells, while 10bc (IC50- 14.46 µM) and 10bh (IC50- 2.53 µM) exhibited excellent cytotoxicity against HEK-293 cells. Additionally, antibacterial screening was performed against three Gram-negative bacteria (E. coli, P. aeruginosa, and S. enterica) and three Gram-positive bacteria (S. aureus, B. megaterium, and B. subtilis) using broth dilution method, while antifungal activity was assessed against three fungal strains (A. niger, Penicillium, and S. cerevisiae) using agar well diffusion method. In antimicrobial screening, the majority of the compounds demonstrated significant antibacterial efficacy compared to antifungal activity. We also conducted comprehensive computational studies, including DFT calculations, molecular docking and dynamics, and drug-likeness assessments. In the DFT study, compounds 10ac and 10bc displayed stable conformations, indicating their potential for higher therapeutic activity. Molecular docking analyses revealed compelling interactions, with compound 10ah demonstrating docking score −7.42 kcal/mol against catalytical domain PARP1 (PDB ID: 7KK4) and 10bh exhibiting a best docking score −10.77 kcal/mol against human corticotropin-releasing factor receptor 1 (PDB ID: 4Z9G). A 100 ns molecular dynamics (MD) simulation study of compounds 10ah and 10bh revealed the stable conformation and binding energy in a stimulating environment. In drug-likeness assessments, both the compounds 10ah and 10bh adhere all the established guidelines. Communicated by Ramaswamy H. Sarma

Excited state dynamics of a double ESIPT unit comprising fluorophore

A comprehensive experimental and computational analysis on the photophysical characteristics of a double ESIPT unit based fluorescent molecule, 2,2′-(1,4-phenylenebis(1H-benzo[d]imidazole-1,2-diyl))diphenol (PBIDP), was carried out. Photoluminescence spectra and lifetime decays have been measured in various polar and nonpolar solvents to explore the fluorescence properties. Furthermore, time-resolved area normalized emission spectra are exploited to identify the different conformers to the unsymmetrical keto emission band correlating with their lifetime values. To corroborate the experimental observations, computations have been enacted by calculating the relative energy, excitation and emission energies of different conformers. Especially, the simulation facilitates to trace the reason behind the triple emissions, uncovering the proton transfer dynamics in the double ESIPT based PBIDP system. Additionally, to understand the ESIPT mechanism in the fluorophore, the potential energy curve and transition state in the ground, and excited state were calculated.

Using Metadynamics to Reveal Extractant Conformational Free Energy Landscapes.

Understanding the impact of extractant functionalization on metal-binding energetics in liquid-liquid extraction is essential to guide the development of better separation processes. Traditionally, computational extractant design uses electronic structure calculations on metal-ligand clusters to determine the metal-binding energy of the lowest energy state. Although highly accurate, this approach does not account for all of the relevant physics encountered under experimental conditions. Such methodologies often neglect entropic contributions such as temperature effects and ligand flexibility, in addition to approximating solvent-extractant interactions with implicit solvent models. In this study, we use classical molecular dynamics simulations with an advanced sampling method, metadynamics, to map out extractant molecule conformational free energies in the condensed phase. We generate the complete conformational landscape in solution for a family of bidentate malonamide-based extractants with different functionalizations of the headgroup and the side chains. In particular, we show how such alkyl functionalization reshapes the free energy landscape, affecting the free energy penalty of organizing the extractant into the cis-like metal-binding conformation from the trans-like conformation of the free extractant in solution. Specifically, functionalizing alkyl tails to the center of the headgroup has a greater influence on increasing molecular rigidity and disfavoring the binding conformation than functionalizing side chains. These findings are consistent with trends in metal-binding energetics based on experimentally reported distribution ratios. We also consider a different bidentate extractant molecule, carbamoylmethylphosphine oxide, and show how the choice of solvent can further reshape the conformational energetic landscape. This study demonstrates the feasibility of using molecular dynamics simulations with advanced sampling techniques to investigate extractant conformational energetics in solution, which, more broadly, will enable extractant design that accounts for entropic effects and explicit solvation.

Identification of a buried β-strand as a novel disease-related motif in the human polysialyltransferases

The polysialyltransferases ST8SIA2 and ST8SIA4 and their product, polysialic acid (polySia), are known to be related to cancers and mental disorders. ST8SIA2 and ST8SIA4 have conserved amino acid (AA) sequence motifs essential for the synthesis of the polySia structures on the neural cell adhesion molecule. To search for a new motif in the polysialyltransferases, we adopted the in silico Individual Meta Random Forest program that can predict disease-related AA substitutions. The Individual Meta Random Forest program predicted a new eight-amino-acids sequence motif consisting of highly pathogenic AA residues, thus designated as the pathogenic (P) motif. A series of alanine point mutation experiments in the pathogenic motif (P motif) showed that most P motif mutants lost the polysialylation activity without changing the proper enzyme expression levels or localization in the Golgi. In addition, we evaluated the enzyme stability of the P motif mutants using newly established calculations of mutation energy, demonstrating that the subtle change of the conformational energy regulates the activity. In the AlphaFold2 model, we found that the P motif was a buried β-strand underneath the known surface motifs unique to ST8SIA2 and ST8SIA4. Taken together, the P motif is a novel buried β-strand that regulates the full activity of polysialyltransferases from the inside of the molecule.

Distinct activation mechanisms of β-arrestin-1 revealed by 19F NMR spectroscopy

β-Arrestins (βarrs) are functionally versatile proteins that play critical roles in the G-protein-coupled receptor (GPCR) signaling pathways. While it is well established that the phosphorylated receptor tail plays a central role in βarr activation, emerging evidence highlights the contribution from membrane lipids. However, detailed molecular mechanisms of βarr activation by different binding partners remain elusive. In this work, we present a comprehensive study of the structural changes in critical regions of βarr1 during activation using 19F NMR spectroscopy. We show that phosphopeptides derived from different classes of GPCRs display different βarr1 activation abilities, whereas binding of the membrane phosphoinositide PIP2 stabilizes a distinct partially activated conformational state. Our results further unveil a sparsely-populated activation intermediate as well as complex cross-talks between different binding partners, implying a highly multifaceted conformational energy landscape of βarr1 that can be intricately modulated during signaling.

Exploration of the Conformational Scenario for α-, β-, and γ-Cyclodextrins in Dry and Wet Conditions, from Monomers to Crystal Structures: A Quantum-Mechanical Study

Cyclodextrins (CDs) constitute a class of cyclic oligosaccharides that are well recognized and largely applied in the drug delivery field, thanks to their biocompatibility, low cost, and the possibility to be derivatized in order to tune and optimize the complexation/release of the specific drug. The conformational flexibility of these systems is one of their key properties and requires a cost-effective methodology to be studied by combining the accuracy of results with the possibility of exploring a large set of conformations. In the present paper, we have explored the conformational potential energy surface of the monomers and dimers of α-, β-, and γ-cyclodextrins (i.e., 6, 7, and 8 monomeric units, respectively) by means of fast but accurate semiempirical methods, which are then refined by state-of-the-art DFT functionals. Moreover, the crystal structure is considered for a more suitable comparison with the IR spectrum experimentally recorded. Calculations are carried out in the gas phase and in water environments, applying both implicit and explicit treatments. We show that the conformation of the studied molecules changes from the gas phase to the water, even if treated implicitly, thus modifying their complexation capability.

Potential and kinetic interaction of two internal tops in molecules belonging to C2v(M) molecular symmetry group

Fourier analysis of the kinetic and potential interactions of non-coaxial internal tops in the molecules C6H4(OH)2, HO(CH2)OH, HOOOH, HOSOH, HSSSH, and HSOSH was carried out. It was found that for the all six molecules, in which both tops are characterized by a period 2 π, the harmonics with a period of π are dominate, with its contribution to the Fourier representation of potential surfaces increasing in the sequence mentioned above. Contributions of internal tops interactions to the kinetic and potential energies were determined for analyzed molecules. The influence of potential and kinetic interactions of internal tops on 1) the features of tunneling splitting of the ground and excited torsional states of molecules, 2) the landscape of 2D potential energy surfaces, 3) frequencies of fundamental torsional vibrations of hydroxyl and thiol groups, 4) the ratio of trans - and cis - conformer energies is also analyzed.

Conformational energies of biomolecules in solution: Extending the MPCONF196 benchmark with explicit water molecules.

A prerequisite for the computational prediction of molecular properties like conformational energies of biomolecules is a reliable, robust, and computationally affordable method usually selected according to its performance for relevant benchmark sets. However, most of these sets comprise molecules in the gas phase and do not cover interactions with a solvent, even though biomolecules typically occur in aqueous solution. To address this issue, we introduce a with explicit water molecules solvated version of a gas-phase benchmark set containing 196 conformers of 13 peptides and other relevant macrocycles, namely MPCONF196 [J. Řezáč et al., JCTC 2018, 14, 1254-1266], and provide very accurate PNO-LCCSD(T)-F12b/AVQZ' reference values. The novel solvMPCONF196 benchmark set features two additional challenges beyond the description of conformers in the gas phase: conformer-water and water-water interactions. The overall best performing method for this set is the double hybrid revDSDPBEP86-D4/def2-QZVPP yielding conformational energies of almost coupled cluster quality. Furthermore, some (meta-)GGAs and hybrid functionals like B97M-V and B97M-D with a large basis set reproduce the coupled cluster reference with an MAD below 1kcal mol . If more efficient methods are required, the composite DFT-method r SCAN-3c (MAD of 1.2kcal mol ) is a good alternative, and when conformational energies of polypeptides or macrocycles with more than 500-1000 atoms are in the focus, the semi-empirical GFN2-xTB or the MMFF94 force field (for very large systems) are recommended.

Improved Description of Intra- and Intermolecular Interactions through Dispersion-Corrected Second-Order Møller-Plesset Perturbation Theory.

ConspectusThe quantum chemical modeling of organic crystals and other molecular condensed-phase problems requires computationally affordable electronic structure methods which can simultaneously describe intramolecular conformational energies and intermolecular interactions accurately. To achieve this, we have developed a spin-component-scaled, dispersion-corrected second-order Møller-Plesset perturbation theory (SCS-MP2D) model. SCS-MP2D augments canonical MP2 with a dispersion correction which removes the uncoupled Hartree-Fock dispersion energy present in canonical MP2 and replaces it with a more reliable coupled Kohn-Sham treatment, all evaluated within the framework of Grimme's D3 dispersion model. The spin-component scaling is then used to improve the description of the residual (nondispersion) portion of the correlation energy.The SCS-MP2D model improves upon earlier corrected MP2 models in a few ways. Compared to the highly successful dispersion-corrected MP2C model, which is based solely on intermolecular perturbation theory, the SCS-MP2D dispersion correction improves the description of both inter- and intramolecular interactions. The dispersion correction can also be evaluated with trivial computational cost, and nuclear analytic gradients are computed readily to enable geometry optimizations. In contrast to earlier spin-component scaling MP2 models, the optimal spin-component scaling coefficients are only mildly sensitive to the choice of training data, and a single global parametrization of the model can describe both thermochemistry and noncovalent interactions.The resulting dispersion-corrected, spin-component-scaled MP2 (SCS-MP2D) model predicts conformational energies and intermolecular interactions with accuracy comparable to or better than those of many range-separated and double-hybrid density functionals, as is demonstrated on a variety of benchmark tests. Among the functionals considered here, only the revDSD-PBEP86-D3(BJ) functional gives consistently smaller errors in benchmark tests. The results presented also hint that further improvements of SCS-MP2D may be possible through a more robust fitting procedure for the seven empirical parameters.To demonstrate the performance of SCS-MP2D further, several applications to molecular crystal problems are presented. The three chosen examples all represent cases where density-driven delocalization error causes GGA or hybrid density functionals to artificially stabilize crystals exhibiting more extended π-conjugation. Our pragmatic strategy addresses the delocalization error by combining a periodic density functional theory (DFT) treatment of the infinite lattice with intramolecular/conformational energy corrections computed with SCS-MP2D. For the anticancer drug axitinib, applying the SCS-MP2D conformational energy correction produces crystal polymorph stabilities that are consistent with experiment, in contrast to earlier studies. For the crystal structure prediction of the ROY molecule, so named for its colorful red, orange, and yellow crystals, this approach leads to the first plausible crystal energy landscape, and it reveals that the lowest-energy polymorphs have already been found experimentally. Finally, in the context of photomechanical crystals, which transform light into mechanical work, these techniques are used to predict the structural transformations and extract design principles for maximizing the work performed.

Effect of Main and Side Chains on the Folding Mechanism of the Trp-Cage Miniprotein.

Proteins that do not fold into their functional native state have been linked to diseases. In this study, the influence of the main and side chains of individual amino acids on the folding of the tryptophan cage (Trp-cage), a designed 20-residue miniprotein, was analyzed. For this purpose, we calculated the solvation free energy (SFE) contributions of individual atoms by using the 3D-reference interaction site model with the atomic decomposition method. The mechanism by which the Trp-cage is stabilized during the folding process was examined by calculating the total energy, which is the sum of the conformational energy and SFE. The folding process of the Trp-cage resulted in a stable native state, with a total energy that was 62.4 kcal/mol lower than that of the unfolded state. The solvation entropy, which is considered to be responsible for the hydrophobic effect, contributed 31.3 kcal/mol to structural stabilization. In other words, the contribution of the solvation entropy accounted for approximately half of the total contribution to Trp-cage folding. The hydrophobic core centered on Trp6 contributed 15.6 kcal/mol to the total energy, whereas the solvation entropy contribution was 6.3 kcal/mol. The salt bridge formed by the hydrophilic side chains of Asp9 and Arg16 contributed 10.9 and 5.0 kcal/mol, respectively. This indicates that not only the hydrophobic core but also the salt bridge of the hydrophilic side chains gain solvation entropy and contribute to stabilizing the native structure of the Trp-cage.

Optimizing the regularization in size-consistent second-order Brillouin-Wigner perturbation theory.

Despite its simplicity and relatively low computational cost, second-order Møller-Plesset perturbation theory (MP2) is well-known to overbind noncovalent interactions between polarizable monomers and some organometallic bonds. In such situations, the pairwise-additive correlation energy expression in MP2 is inadequate. Although energy-gap dependent amplitude regularization can substantially improve the accuracy of conventional MP2 in these regimes, the same regularization parameter worsens the accuracy for small molecule thermochemistry and density-dependent properties. Recently, we proposed a repartitioning of Brillouin-Wigner perturbation theory that is size-consistent to second order (BW-s2), and a free parameter (α) was set to recover the exact dissociation limit of H2 in a minimal basis set. Alternatively α can be viewed as a regularization parameter, where each value of α represents a valid variant of BW-s2, which we denote as BW-s2(α). In this work, we semi-empirically optimize α for noncovalent interactions, thermochemistry, alkane conformational energies, electronic response properties, and transition metal datasets, leading to improvements in accuracy relative to the abinitio parameterization of BW-s2 and MP2. We demonstrate that the optimal α parameter (α = 4) is more transferable across chemical problems than energy-gap-dependent regularization parameters. This is attributable to the fact that the BW-s2(α) regularization strength depends on all of the information encoded in the t amplitudes rather than just orbital energy differences. While the computational scaling of BW-s2(α) is iterative O(N5), this effective and transferable approach to amplitude regularization is a promising route to incorporate higher-order correlation effects at second-order cost.

QUANTUM CHEMICAL CALCULATION OF STRUCTURAL AND THERMODYNAMIC PROPERTIES OF ETHYL METHYL SULFONE IN THE GAS PHASE

A detailed conformational analysis of ethyl methyl sulfone has been carried out using quantum chemical approaches, by revealing all stable conformers, their energy, structural parameters, relative population, and IR spectra at different levels of theory. Thermochemical parameters, such as energy, entropy and heat capacity of ethyl methyl sulfone stable conformers in the gas phase were calculated directly using the wB97XD/6-311++G(2df, 2pd) density functional theory method. Some correlation has been established between the structural characteristics of various conformers and their thermodynamic properties.

Modulation of Delayed Fluorescence Guided by Conformational Effect-Mediated Thermally Enhanced Phosphorescence in Phenothiazines-Quinoline-Cl Conjugates.

Triplet energy harvesting via thermally activated delayed fluorescence (TADF) from pure organic systems has attracted great attention in organic light-emitting diodes, sensing, and photocatalysis. However, the realization of thermally enhanced phosphorescence (TEP)-guided efficient TADF with a high rate of reverse intersystem crossing (kRISC) still needs to be discovered. Herein, we report two phenothiazine-quinoline conjugates (P2QC, P2QMC) comprising two phenothiazine donors covalently attached to the chlorine-substituted quinolinyl acceptor. Spectroscopic analysis in conjunction with quantum chemistry calculations reveals that TEP in P2QC originated due to slow internal conversion from higher-lying triplet to lowest triplet (T2' → T1') of the quasi-axial (QA) conformer and TADF (kRISC = 1.44 × 108 s-1) originated from the quasi-equatorial (QE) conformer caused by a low singlet-triplet gap (ΔES1-T1 = 0.11 eV) and triplet energy transfer from QA to QE owing to the degenerate ground state of the conformers. In contrast, TADF (kRISC = 0.74 × 108 s-1) and dual phosphorescence under ambient conditions are observed in P2QMC. This study provides a sustainable guideline for developing efficient TADF emitters via conformation effects and energy transfer mechanisms.

Distribution of Bound Conformations in Conformational Ensembles for X-ray Ligands Predicted by the ANI-2X Machine Learning Potential.

In this study, we systematically studied the energy distribution of bioactive conformations of small molecular ligands in their conformational ensembles using ANI-2X, a machine learning potential, in conjunction with one of our recently developed geometry optimization algorithms, known as a conjugate gradient with backtracking line search (CG-BS). We first evaluated the combination of these methods (ANI-2X/CG-BS) using two molecule sets. For the 231-molecule set, ab initio calculations were performed at both the ωB97X/6-31G(d) and B3LYP-D3BJ/DZVP levels for accuracy comparison, while for the 8,992-molecule set, ab initio calculations were carried out at the B3LYP-D3BJ/DZVP level. For each molecule in the two molecular sets, up to 10 conformations were generated, which diminish the influence of individual outliers on the performance evaluation. Encouraged by the performance of ANI-2x/CG-BS in these evaluations, we calculated the energy distributions using ANI-2x/CG-BS for more than 27,000 ligands in the protein data bank (PDB). Each ligand has at least one conformation bound to a biological molecule, and this ligand conformation is labeled as a bound conformation. Besides the bound conformations, up to 200 conformations were generated using OpenEye's Omega2 software (https://docs.eyesopen.com/applications/ omega/) for each conformation. We performed a statistical analysis of how the bound conformation energies are distributed in the ensembles for 17,197 PDB ligands that have their bound conformation energies within the energy ranges of the Omega2-generated conformation ensembles. We found that half of the ligands have their relative conformation energy lower than 2.91 kcal/mol for the bound conformations in comparison with the global conformations, and about 90% of the bound conformations are within 10 kcal/mol above the global conformation energies. This information is useful to guide the construction of libraries for shape-based virtual screening and to improve the docking algorithm to efficiently sample bound conformations.

Structural titration reveals Ca2+-dependent conformational landscape of the IP3 receptor

Inositol 1,4,5-trisphosphate receptors (IP3Rs) are endoplasmic reticulum Ca2+ channels whose biphasic dependence on cytosolic Ca2+ gives rise to Ca2+ oscillations that regulate fertilization, cell division and cell death. Despite the critical roles of IP3R-mediated Ca2+ responses, the structural underpinnings of the biphasic Ca2+ dependence that underlies Ca2+ oscillations are incompletely understood. Here, we collect cryo-EM images of an IP3R with Ca2+ concentrations spanning five orders of magnitude. Unbiased image analysis reveals that Ca2+ binding does not explicitly induce conformational changes but rather biases a complex conformational landscape consisting of resting, preactivated, activated, and inhibited states. Using particle counts as a proxy for relative conformational free energy, we demonstrate that Ca2+ binding at a high-affinity site allows IP3Rs to activate by escaping a low-energy resting state through an ensemble of preactivated states. At high Ca2+ concentrations, IP3Rs preferentially enter an inhibited state stabilized by a second, low-affinity Ca2+ binding site. Together, these studies provide a mechanistic basis for the biphasic Ca2+-dependence of IP3R channel activity.

Molecular interaction studies of antituberculosis drug Isoniazid in aq. β-cyclodextrin solution: A volumetric, spectroscopic and molecular docking approach

Volumetric and compressibility investigations are crucial to understanding the molecular interactions prevailing between various components of solutions. At distinct temperatures and ambient pressure (P = 0.1 MPa), the effect of β-cyclodextrin on the antituberculosis drug Isoniazid (INH) was studied at concentrations ranging from 0.0304-0.2698 mol.kg−1. Some thermodynamic properties of the drug Isoniazid, viz., limiting apparent molar volume and limiting compressibility (V°ϕ and K°S,ϕ) are derived from the appropriate density (ρ) and ultrasonic velocity (u) data, with experimental slopes Sv and Sk describing solute–solute interactional parameters at infinite dilution. Furthermore, transfer properties of drug, such as limiting transfer volume (ΔtrV°ϕ) and limiting transfer compressibility (Δtr K°S,ϕ) of drug, reveal key information regarding the interaction of drug with a solvent or a cosolute. The hydration number (nH) was computed to figure out the hydration behaviour of the studied drug in both the mediums. The encapsulation of isoniazid drug in the hydrophobic region of cosolute (β-cyclodextrin) in the solution phase was evaluated using 1H NMR titration. Additionally, theoretical molecular docking was employed to determine the possible conformation and binding energy of the non-covalent inclusion complex.