Generalizing the Concept of Specific Compound Formulation Additives towards Non‐Fluorescent Drugs: A Solubilization Study on Potential Anti‐Alzheimer‐Active Small‐Molecule Compounds

Tailor‐made compound formulation additives enable the testing of potential drugs with undesirable pharmacological profiles. A combinatorial approach using Raman microscopy as the readout method is presented to select peptide sequences from large one‐bead‐one‐compound libraries. The resulting peptide–PEG conjugates solubilize potential prophylactic and therapeutic anti‐Alzheimer compounds and can be used as specific additives not only for fluorescent but also for non‐fluorescent compounds.     

Lichens biomonitoring as feasible methodology to assess air pollution in natural ecosystems: Combined study of quantitative PAHs analyses and lichen biodiversity in the Pyrenees Mountains

The air quality in the Aragón valley, in the central Pyrenees, has been assessed by evaluation of lichen biodiversity and mapped by elaboration of the Index of Air Purity (IAP) based on observations of the presence and abundance of eight kinds of lichen with different sensitivity to air pollution. The IAP values obtained have been compared with quantitative analytical measures of 16 PAHs in the lichen Evernia prunastri, because this species was associated with a wide range of traffic exposure and levels of urbanization. Analyses of PAHs were carried out by the DSASE method followed by an SPE clean-up step and GC–MS analysis. The concentration of total PAHs found in lichen samples from the Aragón valley ranged from 692 to 6420 ng g⁻¹ and the PAHs profile showed predominance of compounds with three aromatic rings. The influence of the road traffic in the area has been shown because values over the median concentration of PAHs (>1092 ng g⁻¹), percentage of combustion PAHs (>50%), and equivalent toxicity (>169) were found in lichens collected at places exposed to the influence of traffic. The combination of both methods suggests IAP as a general method for evaluating the air pollution referenced to PAHs because it can be correlated with the content of combustion PAHs and poor lichen biodiversity can be partly explained by the air pollution caused by specific PAHs. Figure Map of the air pollution level in the Aragón valley (Pyrenees) based on the Index of Air Purity (IAP) calculation (lichen biodiversity)     

Extraction and isolation of acetylcholinesterase inhibitors from Citrus limon peel using an in vitro method

A simple and efficient ultrafiltration–liquid chromatography–mass spectrometry–based method was developed for the rapid screening and identification of ligands from Citrus limon peel, which are suitable acetylcholinesterase inhibitors. Subsequently, the anti‐Alzheimer's activity of these compounds was assessed using a PC12 cell model. Six major compounds, viz. neoeriocitrin, isonaringin, naringin, hesperidin, neohesperidin, and limonin, were identified as potent acetylcholinesterase inhibitors. A continuous and efficient online method, which involved the use of a microwave‐assisted extraction device, solvent concentration tank, and centrifugal partition chromatography column, was developed for the scale‐up of these compounds, and the obtained compounds presented high purity. Next, their bioactivity was evaluated using a PC12 cell model. This novel approach, which was based on ultrafiltration–liquid chromatography–mass spectrometry, microwave‐assisted extraction online coupled with solvent concentration tank, and centrifugal partition chromatography along with in vitro evaluation, could represent a powerful tool for the screening and extraction of acetylcholinesterase inhibitors from complex matrices, and could be a useful platform for the large‐scale production of bioactive and nutraceutical ingredients.     

Metal-binding properties of the peptide APP170-188: a model of the ZnII-binding site of amyloid precursor protein (APP)

Amyloid precursor protein (APP) plays a key role in Alzheimer's disease (AD), although the function of this membrane protein is still unclear. Metal ions are implicated in AD and they also interact with APP. APP possesses a strong ZnII binding site, which is evolutionary conserved. In this paper a synthetic peptide, APP170-188, with a sequence corresponding to the conserved ZnII-binding domain of APP, was synthesised and its metal-binding properties analysed. Titration experiments pointed to the binding of a stoichiometric amount of divalent ions. Further studies indicated that the binding of divalent metals like ZnII, CdII and CoII induces the dimerisation of the peptide. This dimer contains a dinuclear cluster in which the two divalent metals are bridged by two thiolate ligands from cysteine residues. The other two ligands of the tetrahedral coordination sites of each metal ion are terminal thiolate ligands. This structure was supported by the following arguments. The complex formed with CoII presents the characteristic features for tetrahedral tetrathiolate coordination in its UV-visible spectrum. The sequence of APP170-188 contains only three cysteine residues, which is incompatible with a monomeric CoII-APP170-188 complex. EPR measurements of the complex with one equivalent of CoII show almost no signal at 4 K, which is compatible with an antiferromagnetic spin-coupling of the metal ions in a cluster structure. Size-exclusion chromatography indicated that the elution time for the complexes with ZnII and CdII corresponds to the expected molecular weight of a dimer. The circular dichroism (CD) spectrum of the complex with one equivalent of CdII shows a band at 265 nm+, and an ellipticity similar to those observed for similar CdII-thiolate clusters. Possible biological implications of the ZnII binding site and the metal-induced dimerisation are discussed.     

Design,identification, antifungal evaluation and molecular modeling of chlorotetaine derivatives as new anti-fungal agents

Abstract

It is feasible to rationally modify existing bioactive components for new drug development, achieving molecules with improved biological activities. In this study, rational modification of chlorotetaine was carried out following in silico molecular modelling to enhance interactions between the fungal oligopeptide transmembrane transporter PTR22 and the ligand. The peptide obtained with the lowest docking energy, Lys-chlorotetaine (LC), displayed an improved antifungal effect compared with chlorotetaine. The lowest minimum inhibitory concentration observed against a tested pathogen was 1.47?µg/mL (Candida krusei CBS573), which was satisfactory. To thoroughly explore the detailed interactions between the transporter and LC, molecular dynamics simulation was also performed, which revealed that LC could bind to the transporter via different intermolecular interactions from chlorotetaine, and predicted electrostatic interactions (salt-bridges) would enable the more efficient release of LC. This study provides a simple and reliable method for the rational modification of oligopeptide antibiotics.     

Molecular mechanism of HIV-1 integrase-vDNA interactions and strand transfer inhibitor action: a molecular modeling perspective

Human immunodeficiency virus type 1 (HIV-1) integrase (IN) is an essential enzyme for splicing a viral DNA (vDNA) replica of its genome into host cell chromosomal DNA (hDNA) and has been recently recognized as a promising therapeutic target for developing anti-AIDS agents. The interaction between HIV-1 IN and vDNA plays an important role in the integration process of the virus. However, a detailed understanding about the mechanism of this interactions as well as the action of the anti-HIV drug raltegravir (RAL, approved by FDA in 2007) targeting HIV-1 IN in the inhibition of the vDNA strand transfer is still absent. In the present work, a molecular modeling study by combining homology modeling, molecular dynamics (MD) simulations with molecular mechanics Poisson-Boltzmann surface area (MM-PBSA), and molecular mechanics Generalized-Born surface area (MM-GBSA) calculations was performed to investigate the molecular mechanism of HIV-1 IN-vDNA interactions and the inhibition action of vDNA strand transfer inhibitor (INSTI) RAL. The structural analysis showed that RAL did not influence the interaction between vDNA and HIV-1 IN, but rather targeted a special conformation of HIV-1 IN to compete with host DNA and block the function of HIV-1 IN by forcing the 3'-OH of the terminal A17 nucleotide away from the three catalytic residues (Asp64, Asp116, and Glu152) and two Mg(2+) ions. Thus, the obtained results could be helpful for understanding of the integration process of the HIV-1 virus and provide some new clues for the rational design and discovery of potential compounds that would specifically block HIV-1 virus replication.     

Rapid methods for the separation of natural mixtures of beauverolides,cholesterol acyltransferase inhibitors,isolated from the fungus Isaria fumosorosea

Beauverolides (beauveriolides) are abundant, biologically active cyclodepsipeptides produced by many entomopathogenic fungi, including those that are used as biopesticides. Beauverolides act as cholesterol acyltransferase inhibitors in humans; thus, their mode of action has been the subject of pharmacological and clinical research. The cost‐effective analytical methods are needed for fast, routine laboratory analysis of beauverolides. We isolated beauverolides from the fungal strain Isaria fumosorosea PFR 97‐Apopka and opened the rings of the isolated beauverolides using a pyridine alkaline medium. We separated fractions of cyclic and linearized beauverolides by thin‐layer chromatography, and found the chloroform–acetate (9:1, v/v) and chloroform–acetonitrile–acetate (8:1:1, v/v/v) mobile phases, respectively, to be the most efficient. We examined all the fractions by liquid chromatography–mass spectrometry using ion trap and Orbitrap high resolution mass spectrometry. For rapid screening of the contents of cyclic, and, particularly, linearized beauverolides, we developed a novel analytical method that consisted of using capillary electrophoresis coupled with contactless conductivity detection. Furthermore, we improved the separation of the peptides by applying capillary micellar electrokinetic chromatography with the N‐cyclohexyl‐2‐aminoethanesulfonic acid:SDS:NaOH buffer, pH 9.8 as the background electrolyte. The described novel methods allow fast and cost‐effective separation of chemically related groups of beauverolides.     

Stabilized phosphatidylinositol-5-phosphate analogues as ligands for the nuclear protein ING2: chemistry, biology, and molecular modeling

The interaction of PtdIns(5)P with the tumor suppressor protein ING2 has been implicated in the regulation of chromatin modification. To enhance the stability of PtdIns(5)P for studies of the biological role in vivo, two phosphatase-resistant moieties were used to replace the labile 5-phosphate. The total asymmetric synthesis of the 5-methylenephosphonate (MP) and 5-phosphothionate (PT) analogues of PtdIns(5)P is described herein, and the resulting metabolically stabilized lipid analogues were evaluated in three ways. First, liposomes containing either the dioleoyl MP or PT analogues bound to recombinant ING2 similar to liposomes containing dipalmitoyl PtdIns(5)P, indicating that the replacement of the hydrolyzable 5-phosphate group does not compromise the binding. Second, the dioleoyl MP and PT PtdIns(5)P analogues were equivalent to dipalmitoyl PtdIns(5)P in augmenting cell death induced by a DNA double-strand break in HT1080 cells. Finally, molecular modeling and docking of the MP or PT analogues to the C-terminus PtdInsP-binding region of ING2 (consisting of a PHD finger and a polybasic region) revealed a number of complementary surface and electrostatic contacts between the lipids and ING2.     

Determination of chitin and protein contents during the isolation of chitin from shrimp waste

Accurate determination of chitin and protein contents in crustacean biomass and the intermediate products during the industrial isolation of chitin cannot be made directly from the total nitrogen content, unless the appropriate corrections are applied. This method, however, is affected by the presence of other nitrogen-containing chemical species that are formed endogenously or by the action of microorganisms during the handling of the sample. Therefore, an alternative rapid method to estimate the contents of these components can be very useful both in research and in various fields of application. An original method has been developed to address this problem. The method consists of the development of a set of equations based on the stoichiometric contents of nitrogen of chitin and protein whereby the amounts of each component can be estimated from the value of the total nitrogen content, provided the rest of the proximate composition of the sample is accurately known. In order to validate the procedure, a set of model mixtures of pure chitin and protein concentrate in the solid state, both extracted from shrimp head waste, are used. Excellent agreement between the predicted and real values of chitin and protein are obtained (R2=0.98, slope=0.90). When the proposed method is tested in the analysis of real samples obtained from five different processing protocols of pretreatment of raw shrimp head, it is found that in general the values of protein and chitin contents throughout the various stages of the process vary as expected. [GRAPH: SEE TEXT] Variation of the measured total nitrogen versus calculated stoichiometric total nitrogen of the chitin-protein mixtures.     

Pharmacophore based 3D-QSAR modeling,virtual screening and docking for identification of potential inhibitors of β-secretase

The enzyme β-secretase-1 is responsible for the cleavage of the amyloid precursor protein, a vital step in the process of the formation of amyloid-β peptides which are known to lead to neurodegeneration causing Alzheimer’s disease. Challenges associated with toxicity and blood brain permeation inability of potential inhibitors, continue to evade a successful therapy, thus demanding the search and development of highly active and effective inhibitors. Towards these efforts, we used a ligand based pharmacophore model generation from a dataset of known inhibitors whose activities against β-secretase hovered in the nano molar range. The identified 5 feature pharmacophore model, AHHPR, was validated via three dimensional quantitative structure activity relationship as indicated by r², q² and Pearson R values of 0.9013, 0.7726 and 0.9041 respectively. For a dataset of compounds with nano molar activity, the important pharmacophore features present in the current model appear to be similar with those observed in the models resulting from much wider activity range of inhibitors. Virtual screening of the ChemBridge CNS-Set™, a database having compounds with a better suitability for central nervous system based disorders followed by docking and analysis of the ligand protein interactions resulted in the identification of eight prospective compounds with considerable diversity. The current pharmacophore model can thus be useful for the identification, design and development of potent β-secretase inhibitors which by optimization can be potential therapeutics for Alzheimer’s disease.     

Dual inhibitors of Interleukin-6 and acetylcholinesterase for treatment of Alzheimer's disease: Design,docking, synthesis and biological evaluation

Multitarget compounds intercept two or more functionally complementary pathways simultaneously, and are therefore considered to have potential in effectively treating complex multifactorial diseases like Alzheimer's disease (AD). In the present study, novel molecules are designed by coupling a chromone and a N,N-disubstituted carbamoyl amine as pharmacophore for interleukin-6 (IL-6) and acetylcholinesterase (AChE) inhibition, respectively. Four series (Y1–Y4) of 40 compounds are designed by using alkyl linkers of different lengths (1–4 carbon atoms) for the coupling of the two selected pharmacophore. Docking of all designed compounds in AChE leads to the identification of twelve best fit compounds (Docking score >8.3). The data suggests that a 1- or 2-carbon atom linker is the most conducive to orient the pharmacophore for optimum binding with AChE active site. The predicted ADME properties of the 12 selected compounds suggest that these can cross the blood brain barrier (BBB) with good oral bioavailability. These compounds are synthesised and evaluated for anti-AChE activity. Five compounds, showing >45% inhibition of AChE, are further evaluated for IL-6 inhibitory activity. Compound Y1f is found to be the most potent inhibitor of both AChE and IL-6 (IC₅₀ 0.7 and 0.8 ​μM, respectively). It suggests that a chromone moiety connected to a piperidine ring through a 1-carbon atom linker may provide a useful template to medical chemists for the development of new chemical entities effective against AD.     

From brain to food: analysis of phosphatidylcholins, lyso-phosphatidylcholins and phosphatidylcholin-plasmalogens derivates in Alzheimer's disease human post mortem brains and mice model via mass spectrometry

Alzheimer's disease (AD) is a devastating neurodegenerative disorder characterized by extracellular senile plaques mainly consisting of Aβ, a 40-42 amino acid long peptide, and intracellular neurofibrillary tangles, accompanied by an excessive loss of synapses. Recently evidence accumulated that nutrition, especially polyunsaturated fatty acids, influences AD pathogenesis. Especially mid-life food habits with the consumption of specific fatty acids (FA) appear to influence the disease risk. The timely separation between food intake and disease makes a direct correlation with detailed analysis of eating habits combined with accurate food analysis nearly unattainable. A possible solution to circumvent these difficulties is to investigate the FA composition in human post mortem brain. In this study we focused on the main phospholipids phosphatidylcholin (PC), phosphatidylcholin-plasmalogen (PC-PL) and lyso-phosphatidylcholin (lyso-PC) in AD brains compared to control brains. Frontal cortices, temporal cortices and cerebellum of 30 AD (mean 78 years) and 14 control aged matched brains (mean 77.4 years) as well as APP transgenic mice compared to control mice were analyzed using an AB Sciex 4000 Qtrap mass spectrometer utilizing a FIA MS/MS method. PC, PC-PL and lyso-PC metabolites were analyzed in respect to saturation level and FA composition. As expected, the majority of the lipid species showed no significant differences, but interestingly a few species revealed a highly significant reduction in AD brains. These FAs are potential candidates for further food analysis in respect to AD pathology. Additionally, we show that the method applied with multiple reaction monitoring (MRM) used for this study is suitable for semi quantitative analysis of small amounts (10 μl) of brain tissue.     

Characterization of phosphate solubilizing bacteria in sediments from a shallow eutrophic lake and a wetland: isolation, molecular identification and phosphorus release ability determination

The transformation of phosphorus (P) is a major factor of lake eutrophication, and phosphate releasing bacteria play an important role in the release process. Experiments were conducted to investigate P content and characterize phosphate solubilizing bacterial composition at the molecular level in a shallow eutrophic lake and a wetland. Results showed that P concentrations were relatively high and derived from agricultural runoff and domestic or industrial pollution. Enumeration and molecular identification of these strains indicated that these bacterial groups were abundant in the ecosystem and various kinds of bacteria participated in the phosphorus release process. Twelve phosphate solubilizing bacteria, including eight organic P-solubilizing bacteria (OPBs) and four inorganic P-solubilizing bacteria (IPBs), which belonged to three different families, were isolated and identified. Cupriavidus basilensis was found for the first time to have the ability to mineralize organic P (OP). Laboratory tests on P release ability revealed that IPBs were more effective at releasing P than OPBs. The most efficient IPB strain could accumulate over 170 mg·L-1 orthophosphate, while the equivalent OPB strain only liberated less than 4 mg·L-1 orthophosphate in liquid culture. The results obtained from this investigation should help clarify the roles of microorganisms in aquatic systems and the mechanisms of eutrophication.     

Role of protein flexibility in the design of Bcl-XL targeting agents: insight from molecular dynamics

Detailed understanding of protein–ligand interactions is crucial to the design of more effective drugs. This is particularly true when targets are protein interfaces which have flexible, shallow binding sites that exhibit substantial structural rearrangement upon ligand binding. In this study, we use molecular dynamics simulations and free energy calculations to explore the role of ligand-induced conformational changes in modulating the activity of three generations of Bcl-X_L inhibitors. We show that the improvement in the binding affinity of each successive ligand design is directly related to a unique and measurable reduction in local flexibility of specific regions of the binding groove, accompanied by the corresponding changes in the secondary structure of the protein. Dynamic analysis of ligand–protein interactions reveals that the latter evolve with each new design consistent with the observed increase in protein stability, and correlate well with the measured binding affinities. Moreover, our free energy calculations predict binding affinities which are in qualitative agreement with experiment, and indicate that hydrogen bonding to Asn100 could play a prominent role in stabilizing the bound conformations of latter generation ligands, which has not been recognized previously. Overall our results suggest that molecular dynamics simulations provide important information on the dynamics of ligand–protein interactions that can be useful in guiding the design of small-molecule inhibitors of protein interfaces. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Physicochemical evaluation of new tetrahydroacridine and iodobenzoic acid hybrids as the next step in the design of potential drugs for treating Alzheimer's disease

Tacrine derivatives containing iodobenzoic acid were developed as a novel multitarget-directed ligand and find potential application in the treatment of Alzheimer's disease. The aim of this study is to perform a physicochemical profile of this series. Experimental log P and pK_a values were determined and compared with those already calculated. The results indicated better values of the tested compounds than the values predicted using computer software. The stability report was obtained using the developed HPLC method. The stability assay in different environment conditions provided information about the photosensitivity of these compounds and a proper method for the storage of this series of compounds.     

Parsing disease‐relevant protein modifications from epiphenomena: perspective on the structural basis of SOD1‐mediated ALS

Conformational change and modification of proteins are involved in many cellular functions. However, they can also have adverse effects that are implicated in numerous diseases. How structural change promotes disease is generally not well‐understood. This perspective illustrates how mass spectrometry (MS), followed by toxicological and epidemiological validation, can discover disease‐relevant structural changes and therapeutic strategies. We (with our collaborators) set out to characterize the structural and toxic consequences of disease‐associated mutations and post‐translational modifications (PTMs) of the cytosolic antioxidant protein Cu/Zn‐superoxide dismutase (SOD1). Previous genetic studies discovered >180 different mutations in the SOD1 gene that caused familial (inherited) amyotrophic lateral sclerosis (fALS). Using hydrogen–deuterium exchange with mass spectrometry, we determined that diverse disease‐associated SOD1 mutations cause a common structural defect – perturbation of the SOD1 electrostatic loop. X‐ray crystallographic studies had demonstrated that this leads to protein aggregation through a specific interaction between the electrostatic loop and an exposed beta‐barrel edge strand. Using epidemiology methods, we then determined that decreased SOD1 stability and increased protein aggregation are powerful risk factors for fALS progression, with a combined hazard ratio > 300 (for comparison, a lifetime of smoking is associated with a hazard ratio of ~15 for lung cancer). The resulting structural model of fALS etiology supported the hypothesis that some sporadic ALS (sALS, ~80% of ALS is not associated with a gene defect) could be caused by post‐translational protein modification of wild‐type SOD1. We developed immunocapture antibodies and high sensitivity top‐down MS methods and characterized PTMs of wild‐type SOD1 using human tissue samples. Using global hydrogen–deuterium exchange, X‐ray crystallography and neurotoxicology, we then characterized toxic and protective subsets of SOD1 PTMs. To cap this perspective, we present proof‐of‐concept that post‐translational modification can cause disease. We show that numerous mutations (N➔D; Q➔E), which result in the same chemical structure as the PTM deamidation, cause multiple diseases. Copyright © 2017 John Wiley & Sons, Ltd.     

Influence of temperature, friction, and random forces on folding of the B-domain of staphylococcal protein A: all-atom molecular dynamics in implicit solvent

The influences of temperature, friction, and random forces on the folding of protein A have been analyzed. A series of all-atom molecular dynamics folding simulations with the Amber ff99 potential and Generalized Born solvation, starting from the fully extended chain, were carried out for temperatures from 300 to 500 K, using (a) the Berendsen thermostat (with no explicit friction or random forces) and (b) Langevin dynamics (with friction and stochastic forces explicitly present in the system). The simulation temperature influences the relative time scale of the major events on the folding pathways of protein A. At lower temperatures, helix 2 folds significantly later than helices 1 and 3. However, with increasing temperature, the folding time of helix 2 approaches the folding times of helices 1 and 3. At lower temperatures, the complete formation of secondary and tertiary structure is significantly separated in time whereas, at higher temperatures, they occur simultaneously. These results suggest that some earlier experimental and theoretical observations of folding events, e.g., the order of helix formation, could depend on the temperature used in those studies. Therefore, the differences in temperature used could be one of the reasons for the discrepancies among published experimental and computational studies of the folding of protein A. Friction and random forces do not change the folding pathway that was observed in the simulations with the Berendsen thermostat, but their explicit presence in the system extends the folding time of protein A.     

Polymer complexes: supramolecular modeling for determination and identification of the bond lengths in novel polymer complexes from their infrared spectra

Synthesis and characterization of allyl propenyl‐2‐(4‐derivatives phenylazo)butan‐3‐one (HL_n) are described. The monomers obtained contain N?N and carbonyl functional groups in different positions with respect to the allyl group. This structural difference affects the stereochemical structure of the uranyl polymer complexes prepared by the direct reaction of uranyl acetate with the monomers. The polymer complexes are characterized by elemental analyses, ¹H and ¹³C NMR, electronic and vibrational spectroscopy and other theoretical methods. The bonding sites of the hydrazone are deduced from IR and NMR spectra and each of the ligands were found to bond to the UO₂²⁺ ion in a bidentate fashion. The monomers obtained contain N?N and carbonyl functional groups in different positions with respect to the allyl group. IR spectra show that the allyl azo homopolymer (HL_n) acts as a neutral bidentate ligand by coordinating via the two oxygen atom of the carbonyl group, thereby forming a six‐membered chelating ring. The υ₃ frequency of UO₂²⁺ has been shown to be a good molecular probe for studying the coordinating power of the ligands. The υ₃‐values of UO₂²⁺ from IR spectra have been used to calculate the force constant, F_UO (in 10^?8 N/Å) and the bond length R_UO (in Å) of the U? O bond. We adopted a strategy based upon both theoretical and experimental investigations. The theoretical aspects are described in terms of the well‐known theory of 5d–4f transitions. The necessary structural data (coordination geometries and electronic structures) are determined from a framework for the modeling of novel polymer complexes. The Wilson, G. F. matrix method, Badger's formula and the Jones and El‐Sonbati equations were used to determine the stretching and interaction force constants from which the U? O bond distances were calculated. The bond distances of these complexes were also investigated. The effect of Hamett's constant is also discussed. Copyright © 2006 John Wiley & Sons, Ltd.     

Tightening up the structure,lighting up the pathway: application of molecular constraints and light to manipulate protein folding,self-assembly and function

Chemical cross-linking provides an effective avenue to reduce the conformational entropy of polypeptide chains and hence has become a popular method to induce or force structural formation in peptides and proteins.Recently,other types of molecular constraints,especially photoresponsive linkers and functional groups,have also found increased use in a wide variety of applications.Herein,we provide a concise review of using various forms of molecular strategies to constrain proteins,thereby stabilizing their native states,gaining insight into their folding mechanisms,and/or providing a handle to trigger a conformational process of interest with light.The applications discussed here cover a wide range of topics,ranging from delineating the details of the protein folding energy landscape to controlling protein assembly and function.