Fragment‐Based Discovery of a Dual pan‐RET/VEGFR2 Kinase Inhibitor Optimized for Single‐Agent Polypharmacology

Oncogenic conversion of the RET (rearranged during transfection) tyrosine kinase is associated with several cancers. A fragment‐based chemical screen led to the identification of a novel RET inhibitor, Pz‐1. Modeling and kinetic analysis identified Pz‐1 as a type II tyrosine kinase inhibitor that is able to bind the “DFG‐out” conformation of the kinase. Importantly, from a single‐agent polypharmacology standpoint, Pz‐1 was shown to be active on VEGFR2, which can block the blood supply required for RET‐stimulated growth. In cell‐based assays, 1.0 nM of Pz‐1 strongly inhibited phosphorylation of all tested RET oncoproteins. At 1.0 mg kg^?1 day^?1 per os, Pz‐1 abrogated the formation of tumors induced by RET‐mutant fibroblasts and blocked the phosphorylation of both RET and VEGFR2 in tumor tissue. Pz‐1 featured no detectable toxicity at concentrations of up to 100.0 mg kg^?1, which indicates a large therapeutic window. This study validates the effectiveness and usefulness of a medicinal chemistry/polypharmacology approach to obtain an inhibitor capable of targeting multiple oncogenic pathways.     

Construction and validation of a RET TK catalytic domain by homology modeling

RET tyrosine kinase (TK) oncoproteins are potential targets for anticancer therapy. However, the search for novel RET inhibitors has been hampered by the lack of a 3D structure of the receptor. In this study, the "open" and the "closed" structure of the RET TK catalytic domain have been built by homology modeling techniques. The structures were validated by extensive docking studies with practically all the inhibitors reported in the literature and through molecular dynamics simulations of the resulting complexes. All the expected major interactions between the active domain amino acids and the inhibitors have been reproduced in their details. Furthermore, the proposed 3D models are in agreement with the results of available mutation studies. Therefore, these models could be profitably used to filter off from large libraries new potential hit compounds able to target this enzyme.     

Applications of fluorescence and bioluminescence resonance energy transfer to drug discovery at G protein coupled receptors

The role of G protein coupled receptors (GPCRs) in numerous physiological processes that may be disrupted or modified in disease makes them key targets for the development of new therapeutic medicines. A wide variety of resonance energy transfer (RET) techniques such as fluorescence RET and bioluminescence RET have been developed in recent years to detect protein–protein interactions in living cells. Furthermore, these techniques are now being exploited to screen for novel compounds that activate or block GPCRs and to search for new, previously undiscovered signaling pathways activated by well-known pharmacologically classified drugs. The high resolution that can be achieved with these RET methods means that they are well suited to study both intramolecular conformational changes in response to ligand binding at the receptor level and intermolecular interactions involving protein translocation in subcellular compartments resulting from external stimuli. In this review we highlight the latest advances in these technologies to illustrate general principles.     

Beyond the Förster formulation for resonance energy transfer: the role of dark states

Resonance Energy Transfer (RET) is investigated in pairs of charge-transfer (CT) chromophores. CT chromophores are an interesting class of π conjugated chromophores decorated with one or more electron-donor and acceptor groups in polar (D-π-A), quadrupolar (D-π-A-π-D or A-π-D-π-A) or octupolar (D(-π-A)(3) or A(-π-D)(3)) structures. Essential-state models accurately describe low-energy linear and nonlinear spectra of CT-chromophores and proved very useful to describe spectroscopic effects of electrostatic interchromophore interactions in multichromophoric assemblies. Here we apply the same approach to describe RET between CT-chromophores. The results are quantitatively validated by an extensive comparison with time-dependent density functional theory (TDDFT) calculations, confirming that essential-state models offer a simple and reliable approach for the calculation of electrostatic interchromophore interactions. This is an important result since it sets the basis for more refined treatments of RET: essential-state models are in fact easily extended to account for molecular vibrations in truly non-adiabatic approaches and to account for inhomogeneous broadening effects due to polar solvation. Optically forbidden (dark) states of quadrupolar and octupolar chromophores offer an interesting opportunity to verify the reliability of the dipolar approximation. In striking contrast with the dipolar approximation that strictly forbids RET towards or from dark states, our results demonstrate that dark states can take an active role in RET with interaction energies that, depending on the relative orientation of the chromophores, can be even larger than those relevant to allowed states. Essential-state models, whose predictions are quantitatively confirmed by TDDFT results, allow us to relate RET interaction energies towards allowed and dark states to the supramolecular symmetry of the RET-pair, offering reliable design strategies to optimize RET-interactions.     

Photocatalytic activity enhanced by plasmonic resonant energy transfer from metal to semiconductor

Plasmonic metal nanostructures have been incorporated into semiconductors to enhance the solar-light harvesting and the energy-conversion efficiency. So far the mechanism of energy transfer from the plasmonic metal to semiconductors remains unclear. Herein the underlying plasmonic energy-transfer mechanism is unambiguously determined in Au@SiO(2)@Cu(2)O sandwich nanostructures by transient-absorption and photocatalysis action spectrum measurement. The gold core converts the energy of incident photons into localized surface plasmon resonance oscillations and transfers the plasmonic energy to the Cu(2)O semiconductor shell via resonant energy transfer (RET). RET generates electron-hole pairs in the semiconductor by the dipole-dipole interaction between the plasmonic metal (donor) and semiconductor (acceptor), which greatly enhances the visible-light photocatalytic activity as compared to the semiconductor alone. RET from a plasmonic metal to a semiconductor is a viable and efficient mechanism that can be used to guide the design of photocatalysts, photovoltaics, and other optoelectronic devices.     

Inelastic scattering of OH(X2Pi) with Ar and He: a combined polarization spectroscopy and quantum scattering study

One-colour polarization spectroscopy (PS) on the OH A (2)Sigma(+)- X (2)Pi(0,0) band has been used to measure the removal of bulk rotational angular momentum alignment of ground-state OH(X (2)Pi) in collisions with He and Ar. Pseudo-first-order PS signal decays at different collider partial pressures were used to determine second-order decay rate constants for the X (2)Pi(3/2), J = 1.5-6.5, e states. The PS signal decay rate constant, k(PS), is sensitive to all processes that remove population and destroy polarization. The contribution to k(PS) from pure (elastic) alignment depolarization within the initial level, k(DEP), can be extracted by subtracting the independently measured or predicted sum of the rate constants for total rotational energy transfer (RET), k(RET), and for Lambda-doublet changing, k(Lambda), collisions from k(PS). Literature values of k(RET) and k(Lambda) are available from experiments with He and Ar, and from quantum scattering calculations for Ar only. We therefore also present the results of new, exact, fully quantum mechanical calculations of k(RET) and k(Lambda) on the most recent ab initio OH(X)-He potential energy surface of Lee et al. [J. Chem. Phys. 2000, 113, 5736]. The results for k(DEP) from this subtraction for He are found to be modest, around 0.4 x 10(-10) cm(3) s(-1), whereas for Ar k(DEP) is found to range between 0.6 +/- 0.2 x 10(-10) cm(3) s(-1) and 1.7 +/- 0.3 x 10(-10) cm(3) s(-1), comparable to total population removal rate constants. The differences between k(DEP) for the two colliders are most likely explained by the presence of a substantially deeper attractive well for Ar than for He. The measurement of k(DEP) may provide a useful new tool that is more sensitive to the form of the long-range part of the intermolecular potential than rotational state-changing collisions.     

In vivo synthesized proteins with monoexponential fluorescence decay kinetics

Tryptophan, when in a protein, typically shows multiexponential fluorescence decay kinetics. Complex kinetics prevents a straightforward interpretation of time-resolved fluorescence protein data, particularly in anisotropy studies or if the effect of a dynamic quencher or a resonance energy transfer (RET) acceptor is investigated. Here, time-resolved fluorescence data are presented of an isosteric tryptophan analogue, 5-fluorotryptophan, which when biosynthetically incorporated in proteins shows monoexponential decay kinetics. Data are presented indicating that the presence of a fluoro atom at the 5-position suppresses the electron transfer rate from the excited indole moiety to the peptide bond. This process has been related to the multiexponential fluorescence decay of tryptophan in proteins. The monoexponential decay of 5-fluorotryptophan makes it possible to measure simultaneously multiple distances between 5-fluorotryptophan and a RET acceptor. We demonstrate that for an oligomeric protein, consisting of two single-tryptophan-containing subunits, the individual distances between 5-fluorotryptophan and the single substrate binding site can be resolved using a substrate harboring a RET acceptor.     

Resonance energy transfer (RET)-Induced intermolecular pairing force: a tunable weak interaction and its application in SWNT separation

This paper explores evidence of an optically mediated interaction that is active in the separation mechanism of certain selective agents through consideration of the contrasting selective behaviors of two conjugated polymers with distinct optical properties. The involvement of a RET-induced intermolecular pairing force is implied by the different illumination response behaviors. The magnitude of this interaction scales with the external stimulus parameter, the illumination irradiance (I), and thus is tunable. This suggests a facile technique to modify the selectivity of polymers toward specific SWNT species by altering the polymer structure to adjust the corresponding intermolecular interaction. This is the first experimental verification and application of a RET-induced intermolecular pairing force to SWNT separation. With this kind of interaction taken into account, reasonable interpretation of some conflicting data, especially PLE maps, can be easily made. The above conclusion can be applied to other substances as long as they are electrically neutral and there is photon-induced RET between them. The significant magnitude of this interaction makes direct manipulation of molecules/particles possible and is expected to have applications in molecular engineering.     

Negative ions of nitroethane and its clusters

Valence and dipole-bound negative ions of the nitroethane (NE) molecule and its clusters are studied using photoelectron spectroscopy (PES), Rydberg electron transfer (RET) techniques, and ab initio methods. Valence adiabatic electron affinities (EA(a)s) of NE, C(2)H(5)NO(2), and its clusters, (C(2)H(5)NO(2))(n), n=2-5, are estimated using vibrationally unresolved PES to be 0.3+/-0.2 eV (n=1), 0.9+/-0.2 eV (n=2), 1.5+/-0.2 eV (n=3), 1.9+/-0.2 eV (n=4), and 2.1+/-0.2 eV (n=5). These energies were then used to determine stepwise anion-neutral solvation energies and compared with previous literature values. Vertical detachment energies for (C(2)H(5)NO(2))(n)(-) were also measured to be 0.92+/-0.10 eV (n=1), 1.63+/-0.10 eV (n=2), 2.04+/-0.10 eV (n=3), and 2.3+/-0.1 eV (n=4). RET experiments show that Rydberg electrons can be attached to NE both as dipole-bound and valence bound anion states. The results are similar to those found for nitromethane (NM), where it was argued that the diffuse dipole state act as a "doorway state" to the more tightly bound valence anion. Using previous models for relating the maximum in the RET dependence of the Rydberg effective principle number n(max)(*), the dipole-bound electron affinity is predicted to be approximately 25 meV. However, a close examination of the RET cross section data for NE and a re-examination of such data for NM finds a much broader dependence on n(*) than is seen for RET in conventional dipole bound states and, more importantly, a pronounced [l] dependence is found in n(max)(*) (n(max)(*) increases with [l]). Ab initio calculations agree well with the experimental results apart from the vertical electron affinity value associated with the dipole bound state which is predicted to be 8 meV. Moreover, the calculations help to visualize the dramatic difference in the distributions of the excess electron for dipole-bound and valence states, and suggest that NE clusters form only anions where the excess electron localizes on a single monomer.     

Modulation of intramolecular heterodimer-induced fluorescence quenching of tricarbocyanine dye for the development of fluorescent sensor

Various approaches have been used to modulate the fluorescence changes of sensors in the presence of target analytes, including intramolecular interaction between fluorophores or between fluorophore and other molecular species, like resonance energy transfer (RET). Here, we focus on fluorescence quenching by intramolecular heterodimer complex formation, which can be modulated over a shorter distance range than RET. We synthesized several conjugates of tricarbocyanine, which is a near-infrared fluorophore, with several quencher candidates via flexible short linker structure, and examined their fluorescence properties. Of our synthesized compounds, the dabcyl group proved to be the best quencher via heterodimer complex formation. The fluorescence of tricarbocyanine-dabcyl conjugates in aqueous media was almost completely quenched, and there was a dramatic fluorescence enhancement when heterodimer formation was blocked. These results suggested a design approach to develop fluorescence sensors for probing proximity relationships and structural transitions.     

Spin,orbit, and parity conservation in rotation changing collisions

Three series of paradoxical experiments on diatom-atom rotational energy transfer (RET) are reviewed. Resolution of the paradoxes leads to two propensity rules governing parity changes in RET collisions: (i) electronic spin orientation is conserved; and (ii) orbital angular momentum orientation is preserved in polar molecule-atom RET.     

Spin‐Resolved Rotational Energy Transfer for the CH B 2Σ−(v=0, N,F) State by Collisions with Ar

An experimental and theoretical investigation of rotational energy transfers (RET) of CH involving the B ²Σ^? (v=0, 0≤N≤5, F) state by collisions with Ar is undertaken, using the photolysis‐probe technique. Time‐resolved laser‐induced fluorescence resulting from an initially prepared fine‐structure label is dispersed using a step‐scan Fourier transform spectrometer. The spin‐resolved RET rate constants are evaluated with the simulation of a kinetic model. The quantum‐scattering method is used for the calculation of the fine‐structure‐resolved cross sections and rate constants in the rotationally inelastic collisions. The theoretical values are generally consistent with our experimental findings, both in the order of magnitude and trend of N and ΔN dependence. The propensity rules obtained from the experiments are essentially obeyed by theoretical calculations, and are also in accordance with those reported by Kind and Stuhl. The RET rate constants obtained for the v=0 level are smaller than those obtained previously for v=1. The discrepancy in the RET behavior may be caused by an anisotropy difference of the interaction potential resulting from vibrational excitation.     

靶向RET抑制剂塞尔帕替尼的合成进展

塞尔帕替尼是一种高选择性转染过程中重排(RET)受体酪氨酸激酶抑制剂,由Loxo Oncology公司研发于2020年5月在美国获批上市用于治疗RET融合阳性非小细胞肺癌、RET融合阳性甲状腺癌和RET突变甲状腺髓样癌。本文综述了目前报道的有关塞尔帕替尼的合成方法研究进展,并讨论了各方法的特点,以期对其工业化生产提供参考。     

Unified treatment of coherent and incoherent electronic energy transfer dynamics using classical electrodynamics

Recent experiments on resonance energy transfer (RET) in photosynthetic systems have found evidence of quantum coherence between the donor and the acceptor. Under these conditions, Fo?rster's theory of RET is no longer applicable and no theory of coherent RET advanced to date rivals the intuitive simplicity of Fo?rster's theory. Here, we develop a framework for understanding RET that is based on classical electrodynamics but still captures the essence of the quantum coherence between the molecules. Our theory requires only a knowledge of the complex polarizabilities of the two molecules participating in the transfer as well as the distance between them. We compare our results to quantum mechanical calculations and show that the results agree quantitatively.     

The investigation of the resolution enhancement transformation and the analysis of complex overlapping peaks in gamma-ray spectra

A method is proposed for the resolution enhancement transformation (RET) of the γ-ray spectrum, which is not only a simple convolution operation but also have a definite analytical significance because of the introduction of the parameter ω representing the degree of the resolution enhancement. We apply the RET to the peak detection method for complex overlapping peaks. The validity of this method is ascertained by the analysis of X-ray overlapping peaks.     

The smallest resonance energy transfer acceptor for tryptophan

The utility of diazirine ligands as acceptors in resonance energy transfer (RET) distance measurements with tryptophan or tryptophan analogues as donor is reported. The principle is demonstrated for a diazirine derivative of d-mannitol, 2-azi-2-deoxy-d-arabino-hexitol, and single-tryptophan-containing mutants of the mannitol transporter, EIImtl, from E. coli. The F?rster distance is 10 A for the tryptophan-diazirine donor-acceptor couple, allowing the measurement of distances up to 17 A. The versatility of tryptophan as an intrinsic spectroscopic probe in protein chemistry and the small size of the diazirine group makes this a very attractive donor-acceptor couple for accurate RET distance information in protein chemistry.     

Doublet rotational energy transfer of the SH (X ²Π, v'=0) state by collisions with Ar

The rotational energy transfer (RET) by Ar collisions within the SH X?(2)Π (v' = 0, J' = 0.5-10.5) state is characterized. The integral cross sections as a function of collision energy for each rotational transition are calculated using a quantum scattering method in which the constructed potential energy functions are based on a ground state potential energy surface (PES) reported previously. On the other hand, a laser-induced excitation fluorescence technique is employed to monitor the relaxation of the rotational population as a function of photolysis-probe delay time following the photodissociation of H(2)S at 248 nm. The rotational population evolution is comparable to its theoretical counterpart based on calculated Λ-resolved RET rate constants. The propensity in Λ-resolved RET transitions is found to approximately resemble the case of OH(X?(2)Π, v' = 0) + Ar. The Λ-averaged RET collisions are also analyzed and result in several propensity rules in the transitions. Most propensity rules are similar to those observed in the collisions of SH(A?(2)Σ(+)) by Ar. However, the behavior of the conserving ratio, defined as rate constants for spin-orbit conserving transition divided by those for spin-orbit changing transition, shows distinct difference from those described by Hund's case (b).     

Rate of excitation energy transfer between fluorescent dyes and nanoparticles

Because of the sensitivity of the rate of Coulomb interaction induced long range resonance energy transfer (RET) on the distance between the donor (D) and the acceptor (A) molecules, the technique of FRET (fluorescence resonance energy transfer) is popularly termed as “spectroscopic ruler” and is increasingly being used in many areas of biological and material science. For example, the phenomenon is used to monitor the in vivo separation between different (bio)polymers/units of (bio)polymers and hence the dynamics of various biomolecular processes. In this work, we examine the distance and the orientation dependence of RET in three different systems: (i) between a conjugated polymer and a fluorescent dye, (ii) between a nanometal particle (NMP) and a fluorescent dye and (iii) between two NMP. We show that in all the three cases, the rate of RET follows a distance dependence of d^−σ where exponent σ approaches 6 at large distance d (Förster type dependence) but has a value varying from 3–4 at short to intermediate distances.     

Rotational energy transfer in NO (A 2Sigma+,v'=0) by N2 and O2 at room temperature

State-to-state rotational energy transfer (RET) rate coefficients for NO (A 2Sigma+, v'=0, J=5.5, 11.5, 17.5) were measured for N2 and O2 at room temperature using a pump-probe method. The NO A 2Sigma+ state is prepared by 226 nm light and the RET is monitored by fluorescence from the D 2Sigma+ v'=0 state, following excitation by a time-delayed laser at approximately 1.1 microm. Additionally, total collisional removal and final state distributions were measured exciting in the Q1+P21 band head, to simulate an NO laser-induced fluorescence atmospheric monitoring scheme. Time-resolved modeling is used to understand relaxation mechanisms and predict relaxation times in ambient air. H2O at atmospherically relevant concentrations does not affect the degree of RET in ambient air.