Conformational Differences Research Articles

Induced Chirality in Sulfasalazine by Complexation With Albumins: Theoretical and Experimental Study.

Through molecular recognition, drugs can interact and complex with macromolecules circulating in the body. The serum albumin transport protein, found in several mammals, has several interaction sites where these molecules can be located. The drug sulfasalazine (SSZ) is known in the literature to complex at drug site 1 (DS1) in human serum (HSA) and bovine serum (BSA) proteins. This complexation can be studied using various spectroscopic techniques. With the techniques used in this work, absorption in the ultraviolet and visible regions (UV-Vis) and electronic circular dichroism (ECD), a significant difference was observed in the results involving HSA and BSA. The application of theoretical methodologies, such as TD-DFT and molecular docking, suggests that the conformation that SSZ assumes in DS1 of the two proteins is different, which exposes it to different amino acid residues and different hydrophobicities. This difference in conformation may be related to the location of DS1 where the drug interacts or to the possibility of SSZ moving in the BSA site, due to its larger size, and moving less freely in HSA.

A Bicyclic Analog of the Linear Peptide Arodyn Is a Potent and Selective Kappa Opioid Receptor Antagonist.

Kappa opioid receptor (KOR) antagonists have potential therapeutic applications in the treatment of stress-induced relapse to substance abuse and mood disorders. The dynorphin A analog arodyn (Ac[Phe1,2,3,Arg4,D-Ala8]dynorphin A-(1-11)-NH2) exhibits potent and selective kappa opioid receptor antagonism. Multiple cyclizations in longer peptides, such as dynorphin and its analogs, can extend the conformational constraint to additional regions of the peptide beyond what is typically constrained by a single cyclization. Here, we report the design, synthesis, and pharmacological evaluation of a bicyclic arodyn analog with two constraints in the opioid peptide sequence. The peptide, designed based on structure-activity relationships of monocyclic arodyn analogs, was synthesized by solid-phase peptide synthesis and cyclized by sequential ring-closing metathesis (RCM) in the C- and N-terminal sequences. Molecular modeling studies suggest similar interactions of key aromatic and basic residues in the bicyclic peptide with KOR as found in the cryoEM structure of KOR-bound dynorphin, despite substantial differences in the backbone conformations of the two peptides. The bicyclic peptide's affinities at KOR and mu opioid receptors (MOR) were determined in radioligand binding assays, and its KOR antagonism was determined in the [35S]GTPγS assay in KOR-expressing cells. The bicyclic analog retains KOR affinity and selectivity (Ki = 26 nM, 97-fold selectivity over MOR) similar to arodyn and exhibits potent KOR antagonism in the dynorphin-stimulated [35S]GTPγS assay. This bicyclic peptide represents a promising advance in preparing cyclic opioid peptide ligands and opens avenues for the rational design of additional bicyclic opioid peptide analogs.

The surface charge of electroactive materials governs cell behaviour through its effect on protein deposition

The precise mechanisms underlying the cellular response to static electric cues remain unclear, limiting the design and development of biomaterials that utilize this parameter to enhance specific biological behaviours. To gather information on this matter we have explored the interaction of collagen type-I, the most abundant mammalian extracellular protein, with poly(vinylidene fluoride) (PVDF), an electroactive polymer with great potential for tissue engineering applications. Our results reveal significant differences in collagen affinity, conformation, and interaction strength depending on the electric charge of the PVDF surface, which subsequently affects the behaviour of mesenchymal stem cells seeded on them. These findings highlight the importance of surface charge in the establishment of the material–protein interface and ultimately in the biological response to the material. Statement of significanceThe development of new tissue engineering strategies relies heavily on the understanding of how biomaterials interact with biological tissues. Although several factors drive this process and their driving principles have been identified, the relevance and mechanism by which the surface potential influences cell behaviour is still unknown. In our study, we investigate the interaction between collagen, the most abundant component of the extracellular matrix, and poly(vinylidene fluoride) with varying surface charges. Our findings reveal substantial variations in the binding forces, structure and adhesion of collagen on the different surfaces, which collectively explain the differential cellular responses. By exposing these differences, our research fills a critical knowledge gap and paves the way for innovations in material design for advanced tissue regeneration strategies.

AlphaFold2 structures guide prospective ligand discovery.

AlphaFold2 (AF2) models have had wide impact but mixed success in retrospective ligand recognition. We prospectively docked large libraries against unrefined AF2 models of the σ2 and serotonin 2A (5-HT2A) receptors, testing hundreds of new molecules and comparing results with those obtained from docking against the experimental structures. Hit rates were high and similar for the experimental and AF2 structures, as were affinities. Success in docking against the AF2 models was achieved despite differences between orthosteric residue conformations in the AF2 models and the experimental structures. Determination of the cryo-electron microscopy structure for one of the more potent 5-HT2A ligands from the AF2 docking revealed residue accommodations that resembled the AF2 prediction. AF2 models may sample conformations that differ from experimental structures but remain low energy and relevant for ligand discovery, extending the domain of structure-based drug design.

Characterize and Mediate Assembly of Triptycenes on Au(111) Surface.

Herein, we report the assembly behavior of triptycenes with aldehyde (Trip-1) and amino (Trip-2) groups on pristine and iodine-passivated Au(111) surfaces by a combination of scanning tunneling microscopy (STM), X-ray photoelectron spectroscopy (XPS), Raman spectroscopy, and density functional theory (DFT) calculation. On Au(111) surface, Trip-1 forms long trimer chains and two-dimensional islands via aldehyde-aldehyde hydrogen bonding in one dimension and π-π stacking of adjacent benzene rings in the other dimension. In contrast, Trip-2 lies as individuals or in disorderly stacked islands. Trip-2 and Trip-1 can be mixed in an arbitrary ratio. And Trip-2 molecules disrupt the ordered self-assembly structure of Trip-1 due to the formation of stronger aldehyde-amino hydrogen bonding. DFT, XPS, and Raman spectra confirm the conformational difference of Trip-1 and -2, as well as the aldehyde-amino hydrogen bonding formation in Trip-1 and Trip-2 mixture. On the iodine-passivated Au(111) surface, Trip-1 forms single-molecule chains and a hexagonal closely packed structure due to iodine interlayer mediation. Trip-2 molecules disrupt the hexagonal closely packed structure of Trip-1.

Applying Flow Virometry to Study the HIV Envelope Glycoprotein and Differences Across HIV Model Systems.

The HIV envelope glycoprotein (Env) is a trimeric protein that facilitates viral binding and fusion with target cells. As the sole viral protein on the HIV surface, Env is important both for immune responses to HIV and in vaccine designs. Targeting Env in clinical applications is challenging due to its heavy glycosylation, high genetic variability, conformational camouflage, and its low abundance on virions. Thus, there is a critical need to better understand this protein. Flow virometry (FV) is a useful methodology for phenotyping the virion surface in a high-throughput, single virion manner. To demonstrate the utility of FV to characterize Env, we stained HIV virions with a panel of 85 monoclonal antibodies targeting different regions of Env. A broad range of antibodies yielded robust staining of Env, with V3 antibodies showing the highest quantitative staining. A subset of antibodies tested in parallel on viruses produced in CD4+ T cell lines, HEK293T cells, and primary cells showed that the cellular model of virus production can impact Env detection. Finally, in addition to being able to highlight Env heterogeneity on virions, we show FV can sensitively detect differences in Env conformation when soluble CD4 is added to virions before staining.

Exploring coaggregation mechanisms involved in biofilm formation in drinking water through a proteomic-based approach.

Coaggregation, a highly specific cell-cell interaction mechanism, plays a pivotal role in multispecies biofilm formation. While it has been mostly studied in oral environments, its occurrence in aquatic systems is also acknowledged. Considering biofilm formation's economic and health-related implications in engineered water systems, it is crucial to understand its mechanisms. Here, we hypothesized that traceable differences at the proteome level might determine coaggregation ability. Two strains of Delftia acidovorans, isolated from drinking water were studied. First, in vitro motility assays indicated more swarming and twitching motility for the coaggregating strain (C+) than non-coaggregating strain (C-). By transmission electronic microscopy, we confirmed the presence of flagella for both strains. By proteomics, we detected a significantly higher expression of type IV pilus twitching motility proteins in C+, in line with the motility assays. Moreover, flagellum ring proteins were more abundant in C+, while those involved in the formation of the flagellar hook (FlE and FilG) were only detected in C-. All the results combined suggested structural and conformational differences between stains in their cell appendages. This study presents an alternative approach for identifying protein biomarkers to detect coaggregation abilities in uncharacterized strains.

Antioxidative Triplet Excitation Energy Transfer in Bacterial Reaction Center Using a Screened Range Separated Hybrid Functional.

Excess energy absorbed by photosystems (PSs) can result in photoinduced oxidative damage. Transfer of such energy within the core pigments of the reaction center in the form of triplet excitation is important in regulating and preserving the functionality of PSs. In the bacterial reaction center (BRC), the special pair (P) is understood to act as the electron donor in a photoinduced charge transfer process, triggering the charge separation process through the photoactive branch A pigments that experience a higher polarizing environment. At this work, triplet excitation energy transfer (TEET) in BRC is studied using a computational perspective to gain insights into the roles of the dielectric environment and interpigment orientations. We find in agreement with experimental observations that TEET proceeds through branch B. The TEET process toward branch B pigment is found to be significantly faster than the hypothetical process proceeding through branch A pigments with ps and ms time scales, respectively. Our calculations find that conformational differences play a major role in this branch asymmetry in TEET, where the dielectric environment asymmetry plays only a secondary role in directing the TEET to proceed through branch B. We also address TEET processes asserting the role of carotenoid as the final triplet energy acceptor and in a mutant form, where the branch pigments adjacent to P are replaced by bacteriopheophytins. The necessary electronic excitation energies and electronic state couplings are calculated by the recently developed polarization-consistent framework combining a screened range-separated hybrid functional and a polarizable continuum mode. The polarization-consistent potential energy surfaces are used to parametrize the quantum mechanical approach, implementing Fermi's golden rule expression of the TEET rate calculations.

Why Does One Measure Resonance Raman Optical Activity? A Unique Case of Measurements under Strong Resonance versus Far-from-Resonance Conditions.

Raman optical activity (ROA) spectroscopy exhibits significant potential in the study of (bio)molecules as it encodes information on their molecular structure, chirality, and conformations. Furthermore, the method reveals details on excited electronic states when applied under resonance conditions. Here, we present a combined study of the far from resonance (FFR)-ROA and resonance ROA (RROA) of a single relatively small molecular system. Notably, this study is the first to employ the density functional theory (DFT) analysis of both FFR-ROA and RROA spectra. This is illustrated for cobalamin derivatives using near-infrared and visible light excitation. Although the commonly observed monosignate RROA spectra lose additional information visible in bisignate nonresonance ROA spectra, the RROA technique acts as a complement to nonresonance ROA spectroscopy. In particular, the combination of these methods integrated with DFT calculations can reveal a complete spectral picture of the structural and conformational differences between tested compounds.

Two 5-Methoxyindole Carboxylic Acid-Derived Hydrazones of Neuropharmacological Interest: Synthesis, Crystal Structure, and Chemiluminescent Study of Radical Scavenging Properties

Given the importance of molecular structure in pharmacological activity and interaction with biological receptors, we conducted a study on the 3,4-dihydroxybenzaldehyde hydrazone derivative of 5-methoxy-indole carboxylic acid (5MICA) and a newly synthesised analogue bearing a 2-methoxy-4-hydroxyphenyl ring using single-crystal X-ray diffraction. We studied the ability of the two compounds to scavenge hypochlorite ions using luminol-enhanced chemiluminescence and their potential to modulate oxidative damage induced by iron on the biologically significant molecules lecithin and deoxyribose in order to evaluate possible antioxidant and prooxidant effects. The X-ray study revealed highly conserved geometry and limited rotation and deformation freedom of the respective indole and phenyl fragments. Interestingly, a conformational difference between the two independent molecules in the asymmetric unit of 3b was found. The X-ray study revealed a combination of hydrogen bonding interactions, short contacts, and π–π stacking stabilizing the specific three-dimensional packing of the molecules of 3a and 3b in the crystal structures. The three-dimensional packing of the molecules of 3b produced a zigzag layering projected along the c-axis. Both compounds effectively decreased luminol-dependent chemiluminescence in model systems with KO2-produced superoxide. They displayed opposite effects when applied in a xanthine/xanthine oxidase system. The hydrazones of 5MICA do not trigger a prooxidant effect or subsequent toxicity under conditions of iron-induced oxidative stress. The 3,4-dihydroxy-substituted derivative demonstrated excellent radical scavenging properties in all model systems, making it the lead compound for the development of compounds with combined neuroprotective and antioxidant properties.

Comparison between a complete preconditioning programme and conventional conduct on behaviour, health and performance of young bulls from small cow-calf herds

Bovine respiratory diseases (BRDs) have major socioeconomic impacts in the beef sector. Antimicrobials have been traditionally used to prevent the development of BRDs upon arrival in fattening units. Currently, from a “One Health and One Welfare” perspective, alternative solutions are being investigated. Preconditioning programmes that aim at reducing stress and reinforcing immune functions have been proposed to decrease BRDs incidence. In this study, we assessed the effect of a preconditioning protocol set up in nine commercial beef herds on young bulls’ behaviour, health, and performance. Preconditioned bulls (PREC) were weaned indoors 50 days before departure, and progressively fed a concentrate diet supplemented with vitamins and trace elements. They also received an anthelmintic treatment, and two doses of a trivalent vaccine against respiratory pathogens at 4-week intervals. In contrast, controls (CTRL) were kept on pasture with their dams with no vaccination or particular diets. All calves were transported together to a single sorting facility to be sorted by experimental groups, origins, and BW, forming new groups before dispatch to four fattening units. At arrival, CTRL were treated with anthelmintic drugs and received one injection of the same BRDs vaccine. No intervention was performed on PREC bulls. BRD-scores were 0.73 in PREC versus 0.07 in CTRL (P = 0.01) during the preconditioning period and 0.96 in PREC versus 0.54 in CTRL (P = 0.41) after 15 days in the fattening units. Morbidity estimates were 18% in PREC versus 1% in CTRL (P < 0.001) during the preconditioning period and 32% in PREC versus 19% (P = 0.07) in CTRL after 15 days in the fattening units. Poor housing conditions during preconditioning and a different aetiology could partly explain these results. At arrival to fattening, the average daily gain (ADG) was 1 605 g for PREC versus 1 140 g (P = 0.012) for CTRL. After fattening for 180 days, differences in BW, ADG, carcass weight and conformation were inconclusive. In Europe, preconditioning programmes including vaccination must be set up coherently with good husbandry practices and with a global adaptation of batch management of the beef sector otherwise, they may be less effective than expected.

CryoEM structures reveal how the bacterial flagellum rotates and switches direction

Bacterial chemotaxis requires bidirectional flagellar rotation at different rates. Rotation is driven by a flagellar motor, which is a supercomplex containing multiple rings. Architectural uncertainty regarding the cytoplasmic C-ring, or ‘switch’, limits our understanding of how the motor transmits torque and direction to the flagellar rod. Here we report cryogenic electron microscopy structures for Salmonella enterica serovar typhimurium inner membrane MS-ring and C-ring in a counterclockwise pose (4.0 Å) and isolated C-ring in a clockwise pose alone (4.6 Å) and bound to a regulator (5.9 Å). Conformational differences between rotational poses include a 180° shift in FliF/FliG domains that rotates the outward-facing MotA/B binding site to inward facing. The regulator has specificity for the clockwise pose by bridging elements unique to this conformation. We used these structures to propose how the switch reverses rotation and transmits torque to the flagellum, which advances the understanding of bacterial chemotaxis and bidirectional motor rotation.

Ethnic differences in meat consumption attitudes, norms and behaviors: A survey of White, South Asian and Black ethnic groups in the UK

A reduction in meat consumption is necessary to mitigate negative impacts of climate change and adverse health outcomes. The UK has an increasingly multi-ethnic population, yet there is little research on meat consumption habits and attitudes among ethnic groups in the UK. We ran a survey (N = 1014) with quota samples for ethnic groups and analyzed attitudes, behaviors and norm perceptions of White, South Asian and Black British respondents. Most respondents believe overconsumption of red and processed meat has negative impacts on health (73.3%) and the environment (64.3%).South Asian respondents were statistically significantly less likely to be meat eaters than White respondents (OR = 0.44, 95% CIs: 0.30-0.65, t = −4.15, p = 0.000), while there was no significant difference between White and Black respondents (OR = 1.06, 95% CIs: 0.63–1.76, t = 0.21, p = 0.834). Both South Asian (OR = 2.76, 95% CIs: 1.89–4.03 t = 5.25, p = 0.000) and Black respondents (OR = 2.09, 95% CIs: 0.1.30–3.35, t = 3.06, p = 0.002) were significantly more likely to express being influenced by friends and family in their food choices than White respondents. South Asian (OR = 3.24,95% CIs: 2.17–4.84, t = 5.74, p = 0.000) and Black (OR = 2.02,95% CIs: 1.21–3.39, t = 2.69, p = 0.007) respondents were also both significantly more likely to report they would want to eat similarly to their friends and family than White respondents. Statistical analyses suggested some gender and socioeconomic differences across and among ethnic groups, which are reported and discussed. The differences in meat consumption behaviors and norm conformity between ethnic groups raises the prospect that interventions that leverage social norms may be more effective in South Asian groups than Black and White groups in the UK.

Clinical Viability of an Active Spot Scanning Beam Delivery System With a Newly Developed Carbon-Ion Treatment Planning System

PurposeAlthough active spot scanning irradiation technique is theoretically superior to passive-scattered broad beam irradiation with respect to normal tissue sparing, corroborations of the clinical benefit of carbon-ion spot scanning have remained scarce. This study aims to investigate the feasibility and clinical implementation of an active spot scanning beam calculation algorithm in a homemade carbon-ion treatment planning system (TPS) by comparing it with a conventional passive uniform scanning technique. Materials and methodsCarbon-ion plans were initially formulated using spot/uniform scanning methods in 22 participants enrolled in a prospective observational clinical trial. Subsequently, two additional plans were designed, resulting in three carbon-ion plans for each participant: uniform and spot scanning with mini-ridge filters (MRFs) of 2mm and 4mm, respectively. ResultsThe findings revealed no significant differences in dose homogeneity; however, significant differences in dose conformity were found between the active and passive scanning plans. For dose drop-off outside the target volume, the average gradient index (GI) values were 1.94 (95% confidence interval (CI): 1.79%-2.09%), 1.87 (95% CI: 1.73%-2.01%), and 3.20 (95% CI: 2.80%-3.61%) for the MRF4, MRF2, and uniform scanning plans, respectively. The pre-treatment tumor volume was 124.7 cm3 (range, 54.2-234 cm3), and the average shrinkage observed was 38.4% (95% CI: 17.6%-59.4%). Seven participants experienced grade 1 acute toxicity, and four experienced grade 2 acute toxicity. However, none of the patients developed grade 3 acute toxicity. ConclusionsIncreasing evidence suggests that potential clinical advantages of spot scanning delivery underlie its technical characteristics. As one among the few institutions currently utilizing carbon-ion radiotherapy, the investigation also provides promising safety and efficacy outcomes from the initial groups of treated participants, thereby contributing to the established clinical evidence supporting the effectiveness and superiority of carbon-ion therapy.

Polymorphism Dependent Cytotoxicity, Cellular Uptake, and Live Cell Imaging Studies on Napthalimide-Vinyl-Phenothiazine Conjugate.

Polymorphism-dependent cytotoxicity and cellular uptake of drug molecules have been studied for the past two decades. However, the visualization of polymorph-dependent cellular uptake and cytotoxicity using microscopy imaging techniques has not yet been reported. The luminescent polymorph is an ideal candidate to validate the above hypothesis. Herein, we report the polymorph-dependent cellular uptake, cytotoxicity, and bio-imaging functions of polymorphs 1Y and 1R of a naphthalimide-phenothiazine dyad. These polymorphs show different luminescence colors in the solid state and exhibit aggregation-induced enhanced emission (AIEE) in the DMSO-Water mixture. Bioimaging, cytotoxicity assay, and fluorescence-activated cell sorting (FACS) studies revealed that these polymorphs show different levels of cytotoxicity, cellular uptake, localization, and imaging potential. Detailed photophysical, morphological, and biological studies revealed that the difference in molecular conformation in these polymorphs enables them to form aggregates of different sizes and morphology, which leads to the differential uptake of these into the cells and consequently shows different cytotoxicity and imaging potentials.

Abstract ND12: Discovery of PF-07220060, a potent and selective CDK4 inhibitor

Abstract PF-07220060 was developed based on the clinical need to improve efficacy and safety outcomes in patients treated with currently approved dual CDK4/6 inhibitors, including Palbociclib. Although all dual CDK4/6 inhibitors increase response rates and prolong disease control, they show common dose-limiting hematologic toxicities, foremost neutropenia. This poses challenges to provide these agents at doses necessary to extinguish cell cycling in tumors. Human ER+ breast cancer cells are highly dependent on CDK4 but not CDK6. By contrast, CDK4 is dispensable for human bone marrow derived cells, or cells enriched for neutrophil precursors or hematopoietic stem cells. This is primarily due to the compensatory role of CDK6 in these compartments. These observations prompted us to develop PF-07220060, an aminopyrimidine-based inhibitor, endowed with 20-fold and 4-fold increased selectivity for CDK4 over CDK6 when compared to Palbociclib and Abemaciclib/Ribociclib, respectively. CDK4-over-CDK6 selectivity is explained by G-loop conformational differences between the two kinases, with the G-loop of CDK4 being more flexible, assuming a more open conformation when bound to CDK4 selective versus non-selective inhibitors. PF-07220060 reduces dose-limiting neutropenia in beagle dogs by 15-fold when compared with Palbociclib, consistent with early clinical data obtained with PF-07220060. Higher tolerated plasma concentrations of PF-07220060 versus dual CDK4/6 inhibitors enable increased inhibition of CDK4 kinase activity in tumors. This translates to improved tumor growth inhibition across CDK4-driven models of human breast and prostate cancer at clinically relevant doses. Our work establishes proof-of-concept for CDK4 selective inhibition and introduces a best-in-class CDK4 inhibitor for treatment of HR+ HER2- breast cancer and other CDK4 dependent tumor types. Citation Format: Lars Anders, Gary Gallego. Discovery of PF-07220060, a potent and selective CDK4 inhibitor [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr ND12.

Fabrication of soy protein microgels via two top-down methods and characterization of the foaming behavior

The aim of this study was to design and characterize soy protein microgels (SPM) using heat-induced (H-SPM) and enzyme cross-linking (E-SPM) methods, and then compared their conformational differences with soy protein isolate (SPI) and explored their foaming behavior. The results showed that transglutaminase-induced covalent cross-linking could fabricate SPM more effectively than that of simple heat treatment, resulting in larger particle sizes, higher surface charge and lower surface hydrophobicity, as well as more robust internal integrity and more ordered structure. Compared with SPI and H-SPM, the foamability of E-SPM decreased by 18.60% and 25.53%, respectively, while the short-term foam stability (60 min) increased by 20.50% and 5.81%, respectively. In terms of long-term foam stability, the foam volume of SPI and H-SPM eventually disappeared after standing for 300 min, while E-SPM still had a considerable foam volume (11.33 mL). Microstructure evaluation suggested that E-SPM stabilized foams via a Pickering-type mechanism. This study will facilitate the applications of SPM as a plant protein-based Pickering-type foam stabilizer in terms of generating aerated foods with long-term foam stability.

Collagen type I mimicking peptide additives to functionalize synthetic supramolecular hydrogels

Small bioactive peptide sequences derived from extracellular matrix proteins possess the ability to interact with cell receptors. As such, these peptide additives are excellent mimics to develop materials for 3D cell culture. Two types of supramolecular modified collagen type I mimicking peptide additives are presented; UPy-GFOGER (39 amino acids), with a novel superstructure, and the more simplistic UPy-DGEA (7 amino acids). Here, we studied the impact of the conformational differences between both peptide additives, on their biological performance. Various analyzing techniques demonstrated the ability of the supramolecular UPy-GFOGER to self-assemble into short nanofibers with brush-like outer features, suggesting trimerization into a triple helix. UPy-DGEA is a short additive without a complex structure. Since, collagen type I is a major component of the human corneal stroma, primary keratocytes (PKs) are encapsulated within the functionalized hydrogels to provide insights in the induced bioactivity of both additives. Incorporation of UPy-GFOGER supported an elongated morphology and (re-)differentiation of the encapsulated PKs, while tiny round-shaped cells were observed within the hydrogels functionalized with UPy-DGEA. This difference in biological success between UPy-GFOGER and UPy-DGEA indicates the difficulty of using short peptide additives without a complex structure to mimic the complex structure of natural collagen.

Studying the ssDNA loaded adeno-associated virus aggregation using coarse-grained molecular dynamics simulations

The aggregation of adeno-associated viral (AAV) capsids in an aqueous environment was investigated via coarse-grained molecular dynamics (CG-MD) simulations. The primary driving force and mechanism of the aggregation were investigated with or without single-strand DNA (ssDNA) loaded at various process temperatures. Capsid aggregation appeared to involve multiple residue interactions (i.e., hydrophobic, polar and charged residues) leading to complex protein aggregation. In addition, two aggregation mechanisms (i.e., the fivefold face-to-face contact and the edge-to-edge contact) were identified from this study. The ssDNA with its asymmetric structure could be the reason for destabilizing protein subunits and enhancing the interaction between the charged residues, and further result in the non-reversible face-to-face contact. At higher temperature, the capsid structure was found to be unstable with the significant size expansion of the loaded ssDNA which could be attributed to reduced number of intramolecular hydrogen bonds, the increased conformational deviations of protein subunits and the higher residue fluctuations. The CG-MD model was further validated with previous experimental and simulation data, including the full capsid size measurement and the capsid internal pressure. Thus, a good understanding of AAV capsid aggregation, instability and the role of ssDNA were revealed by applying the developed computational model.

Exploring Various Crystal and Molecular Structures of Gabapentin—A Review

Novel antiepileptic drugs have been developed at an unparalleled rate during the past 15 years. Gabapentin (GBP), which was approved for the treatment of refractory localization-related epilepsies in the U.K. and Europe in 1993, was one of the first drugs to come out of this era. Since then, GBP has become well-known across the world, not only for its antiepileptic qualities but also for its effectiveness in the treatment of chronic pain disorders, particularly neuropathic pain. In this review, the crystal structures of GBP and GBP-related compounds have been analyzed and compared. Particular attention has been paid to the polymorphism of GBP and its hydrates, their thermodynamic stability, and conformational differences. In addition, the puckering parameters for the cyclohexane ring of a total of 118 molecules of GBP found in the analyzed crystal structures have been calculated and analyzed. The results of recent high-pressure crystallization studies and quantum chemical calculations indicate that the entire landscape of GBP has not been revealed yet.