UNRES-GPU for physics-based coarse-grained simulations of protein systems at biological time- and size-scales.

SUMMARY: The UNited RESisdue (UNRES) package for coarse-grained simulations, which has recently been optimized to treat large protein systems, has been implemented on Graphical Processor Units (GPUs). An over 100-time speed-up of the GPU code (run on an NVIDIA A100) with respect to the sequential code and an 8.5 speed-up with respect to the parallel Open Multi-Processing (OpenMP) code (run on 32 cores of 2 AMD EPYC 7313 Central Processor Units (CPUs)) has been achieved for large proteins (with size over 10 000 residues). Due to the averaging over the fine-grain degrees of freedom, 1 time unit of UNRES simulations is equivalent to about 1000 time units of laboratory time; therefore, millisecond time scale of large protein systems can be reached with the UNRES-GPU code. AVAILABILITY AND IMPLEMENTATION: The source code of UNRES-GPU along with the benchmarks used for tests is available at https://projects.task.gda.pl/eurohpcpl-public/unres.

Long-time scale simulations of virus-like particles from three human-norovirus strains.

The dynamics of the virus like particles (VLPs) corresponding to the GII.4 Houston, GII.2 SMV, and GI.1 Norwalk strains of human noroviruses (HuNoV) that cause gastroenteritis was investigated by means of long-time (about 30 µs in the laboratory timescale) molecular dynamics simulations with the coarse-grained UNRES force field. The main motion of VLP units turned out to be the bending at the junction between the P1 subdomain (that sits in the VLP shell) and the P2 subdomain (that protrudes outside) of the major VP1 protein, this resulting in a correlated wagging motion of the P2 subdomains with respect to the VLP surface. The fluctuations of the P2 subdomain were found to be more pronounced and the P2 domain made a greater angle with the normal to the VLP surface for the GII.2 strain, which could explain the inability of this strain to bind the histo-blood group antigens (HBGAs).

Optimization of parallel implementation of UNRES package for coarse-grained simulations to treat large proteins.

We report major algorithmic improvements of the UNRES package for physics-based coarse-grained simulations of proteins. These include (i) introduction of interaction lists to optimize computations, (ii) transforming the inertia matrix to a pentadiagonal form to reduce computing and memory requirements, (iii) removing explicit angles and dihedral angles from energy expressions and recoding the most time-consuming energy/force terms to minimize the number of operations and to improve numerical stability, (iv) using OpenMP to parallelize those sections of the code for which distributed-memory parallelization involves unfavorable computing/communication time ratio, and (v) careful memory management to minimize simultaneous access of distant memory sections. The new code enables us to run molecular dynamics simulations of protein systems with size exceeding 100,000 amino-acid residues, reaching over 1 ns/day (1 µs/day in all-atom timescale) with 24 cores for proteins of this size. Parallel performance of the code and comparison of its performance with that of AMBER, GROMACS and MARTINI 3 is presented.

Visual Features for Improving Endoscopic Bleeding Detection Using Convolutional Neural Networks.

The presented paper investigates the problem of endoscopic bleeding detection in endoscopic videos in the form of a binary image classification task. A set of definitions of high-level visual features of endoscopic bleeding is introduced, which incorporates domain knowledge from the field. The high-level features are coupled with respective feature descriptors, enabling automatic capture of the features using image processing methods. Each of the proposed feature descriptors outputs a feature activation map in the form of a grayscale image. Acquired feature maps can be appended in a straightforward way to the original color channels of the input image and passed to the input of a convolutional neural network during the training and inference steps. An experimental evaluation is conducted to compare the classification ROC AUC of feature-extended convolutional neural network models with baseline models using regular color image inputs. The advantage of feature-extended models is demonstrated for the Resnet and VGG convolutional neural network architectures.

Chiral Iminophosphoranes-An Emerging Class of Superbase Organocatalysts.

Chiral Brønsted base catalysis is a fascinating and highly explored field of research. For many years catalysts based on chincona alkaloid chiral scaffolds have constituted privileged systems widely employed in numerous base-promoted organic transformations. Recently, a novel group of chiral base catalysts has been successfully introduced. The application of organosuperbases, namely cyclopropenimines, guanidines, and iminophosphoranes, as chiral catalysts is receiving increasing attention. The aim of this Concept article is to summarize recent progress in the field of chiral iminophosphorane superbase organocatalysis. Catalysts design, different approaches to their synthesis, and applications in asymmetric synthesis are outlined and discussed in detail.

Synthesis and biological evaluation of α-methylidene-δ-lactones with 3,4-dihydrocoumarin skeleton.

A series of new 3-methylidenechroman-2-ones bearing various aromatic moieties and various substituents at position 4 were synthesized in a three step reaction sequence. Friedel-Crafts alkylation of phenols or naphthols using ethyl 3-methoxy-2-diethoxyphosphorylacrylate in the presence of trifluoromethanesulphonic acid gave 3-diethoxyphosphorylchromen-2-ones. These compounds were employed as Michael acceptors in the reaction with Grignard reagents to give adducts which were finally used as Horner-Wadsworth-Emmons reagents for the olefination of formaldehyde. All obtained 3-methylidenechroman-2-ones were tested against two human leukemia cell lines NALM-6 and HL-60 as well as MCF-7 breast cancer and HT-29 colon cancer adenocarcinomas. Several obtained methylidenechromanones displayed high cytotoxic activity with IC(50) values below 1 µM, mainly against leukemia and MCF-7 cell lines. Investigation of structure-activity relationships revealed that the presence of additional, ortho-fused benzene ring and n-butyl or i-propyl group in position 4 enhances the activity. Selected methylidenechromanones were also tested on normal human umbilical vein endothelial cells (HUVEC) and chromanone 14o was found to be eightfold more toxic against MCF-7 than normal cells. Furthermore, antimicrobial assays revealed that chromanone 14n is highly active and bactericidal at concentration equal to MIC or 2MIC against nosocomial and community-associated staphylococci (MRSA) which are resistant to most or all available therapeutic classes of antimicrobial drugs.

Organocatalytic asymmetric synthesis of organophosphorus compounds.

240 Years have passed since the discovery of elemental phosphorus. During that time organophosphorus chemistry has emerged as an interesting and exciting field of research. Recently organophosphorus chemistry has been raised to a new level. Organophosphorus compounds have found applications in asymmetric organocatalysis for the synthesis of optically active compounds of synthetic or biological importance. The aim of this review article is to present recent contributions to this developing field of chemistry and to point out synthetic advantages of methodologies developed so far.

Organocatalytic domino Michael-Knoevenagel condensation reaction for the synthesis of optically active 3-diethoxyphosphoryl-2-oxocyclohex-3-enecarboxylates.

Versatile dominoes: A novel, organocatalytic, Michael-Knoevenagel condensation domino reaction of ethyl 4-diethoxyphosphoryl-3-oxobutanoate with various aryl- and aliphatic-substituted alpha,beta-unsaturated aldehydes catalyzed by a chiral diarylprolinol ether has been successfully performed. The reaction proceeds in a highly enantio- and diastereoselective manner giving access to optically active 6-substituted-3-diethoxyphosphoryl-2-oxocyclohex-3-enecarboxylates (see scheme).A novel, organocatalytic, highly enantio- and diastereoselective synthetic approach towards optically active 6-substituted-3-diethoxyphosphoryl-2-oxocyclohex-3-enecarboxylates is presented. Our methodology utilizes a Michael-Knoevenagel domino reaction sequence of ethyl 4-diethoxyphosphoryl-3-oxobutanoate and alpha,beta-unsaturated aldehydes catalyzed by a chiral diarylprolinol ether. The cyclohexenecarboxylates obtained are particularly well suited for the preparation of highly functionalized cyclohexene and cyclohexane derivatives, with up to four chiral centers and high levels of stereocontrol.

Enantioselective organocatalytic approach to alpha-methylene-delta-lactones and delta-lactams.

We present the first enantioselective organocatalytic approach for the synthesis of alpha-methylene-delta-lactones and delta-lactams. Our methodology utilizes the Michael addition of unmodified aldehydes to ethyl 2-(diethoxyphosphoryl)acrylate as the key step affording highly enantiomerically enriched adducts, which can be transformed into the target compounds maintaining the high stereoselectivity achieved in the first step. This methodology has been shown to be general and various optically active gamma-substituted alpha-methylene-delta-lactones and delta-lactams can be easily accessed.

trans-(1R,2R)-1-benzyl-2-phenylcyclopropanecarboxylic acid.

The cyclopropane ring of the title compound, C17H16O2, shows a high level of substituent-induced bond-length asymmetry. The carboxyl group adopts a conformation that prompts electron-density transfer from the ring towards the carbonyl pi system.

rac-(1S,2R)-Diethyl 6-hydr-oxy-1-(4-methoxy-phen-yl)-3-oxo-2,3-di-hydro-1H-benzo[f]chromen-2-yl]-phospho-nate.

In the title compound, C(24)H(25)O(7)P, the δ-valerolactonyl ring exists in a distorted screw-boat conformation with the diethoxy-phosphoryl substituent occupying an axial position. The latter adopts an almost syn-periplanar conformation around the P-C bond. The mol-ecules form centrosymmetric dimers connected by O-H⋯O hydrogen bonds.

Anticancer Properties of a New Hybrid Analog AD-013 Combining a Coumarin Scaffold with an α-methylene-δ-lactone Motif.

BACKGROUND: Coumarin is a natural phytochemical but as such has no medical uses. However, various natural and synthetic coumarin analogs attract attention due to their interesting biological properties. OBJECTIVE: Here, we evaluated and compared anticancer properties of a new synthetic hybrid compound AD- 013, which integrates a coumarin moiety and an α-methylene-δ-lactone motif, with novobiocin, a natural antibiotic bearing a coumarin scaffold. METHODS: Cytotoxic activities of compound AD-013 and novobiocin were assessed by the MTT assay. In order to explore the mechanism of anticancer activity of analog AD-013, we performed quantitative real-time PCR analysis of apoptosis- and cell cycle-related genes. The ability of AD-013 and novobiocin to induce apoptosis and DNA damage was studied by flow cytometry. RESULTS: The cytotoxic activity of this new compound was compared with the activity of a coumarin-based antibiotic novobiocin against two cancer cell lines, MCF-7 and HL-60 and also against normal human cells, MCF- 10A and HUVEC. AD-013 was much more cytotoxic than novobiocin in both cancer cell lines and showed some selectivity against MCF-7 cancer cells as compared with MCF-10A healthy cells. Expression levels of the pro-apoptotic genes significantly increased while the anti-apoptotic genes, were down-regulated for both compounds in both cancer cell lines. AD-013 was able to inhibit cell proliferation, generate DNA damage and induce apoptosis. The obtained data showed that this compound caused the cell cycle arrest in subG0/G1 in both cancer cell lines. CONCLUSION: The new hybrid analog was a much stronger apoptosis inducer than novobiocin and activated the intrinsic pathway of apoptosis.

Synthesis and cytotoxic evaluation of beta-alkyl or beta-aryl-delta-methyl-alpha-methylene-delta-lactones. Comparison with the corresponding gamma-lactones.

We present a simple and general strategy for the synthesis of beta,delta-disubstituted-alpha-methylene-delta-lactones starting from easily available tert-butyl 2-(diethoxyphosphoryl)alk-2-enoates. The elaborated synthetic protocol includes pyrrolidine-catalyzed Michael addition of acetone, diastereoselective reduction of the carbonyl group, lactonization and finally the Horner-Wadsworth-Emmons reaction with formaldehyde. All alpha-methylene-delta-lactones were evaluated in vitro against mouse leukemia cell line L-1210 and two human leukemia cell lines HL-60 and NALM-6. Comparison of cytotoxic activity with corresponding alpha-methylene-gamma-lactones is also discussed.

A general stereoselective method for the synthesis of cyclopropanecarboxylates. A new version of the homologous Horner-Wadsworth-Emmons reaction.

The synthesis of alpha-, beta- and gamma-substituted alpha-phosphono-gamma-lactones was accomplished using different ring closure and ring homologation strategies. It was found that the lactones could be selectively transformed into the corresponding ethyl cyclopropanecarboxylates by treatment with sodium ethoxide in boiling THF. The reported reaction provides an attractive alternative to the classical homologous Horner-Wadsworth-Emmons approach to the construction of cyclopropanes with electron-withdrawing functionalities.

X-ray investigations of bicyclic alpha-methylene-delta-valerolactones. V. (4aS,7R,8aR)-7-isopropenyl-4a-methyl-3-methyleneperhydrochromen-2-one.

The title compound, C(14)H(20)O(2), adopts a conformation in which the delta-valerolactone and cyclohexane rings are almost coplanar with one another. The gamma-methyl substituent occupies an axial position with respect to the cyclohexane ring. The delta-valerolactone moiety adopts an envelope arrangement, while the cyclohexane ring exists in a chair conformation.

X-ray investigations of bicyclic alpha-methylene-delta-valerolactones. III. trans-(4aR,8aR)-4a-Methoxy-3-methyleneperhydrochromen-2-one.

The title compound, C11H16O3, adopts a conformation in which the delta-valerolactone and cyclohexane rings are almost coplanar with one another. The beta-methoxy substituent occupies an axial position with respect to the cyclohexane ring. The delta-valerolactone moiety adopts a half-chair arrangement, while the cyclohexane ring exists in a chair conformation.

X-ray investigations of bicyclic alpha-methylene-delta-valerolactones. II. (4aS,8aS)-4a-methyl-3-methyleneperhydrochromen-2-one.

The title compound, C(11)H(16)O(2), adopts a semifolded conformation with the delta-lactone and cyclohexane rings almost perpendicular to one another. The beta-methyl substituent occupies an axial position with respect to the cyclohexane ring. The delta-lactone moiety adopts a slightly distorted half-chair arrangement, while the cyclohexane ring exists in an almost ideal chair conformation.