Base-promoted cyclization of ortho-hydroxyacetophenones with in situ generated cyclopropenes: diastereoselective access to spirobenzo[b]oxepines and related precursors.

An unprecedented [5 + 2] spirocyclization route to obtain a vital class of functionalized spirobenzo[b]oxepine-cyclopropanes in good to high yields with excellent diastereoselectivities is reported. This domino reaction proceeds through a regioselective oxa-Michael addition of ortho-hydroxyacetophenones as 1,5-binucleophiles to in situ produced highly reactive cyclopropenes from 2-aroyl-1-chlorocyclopropanecarboxylates triggered by Cs2CO3 and the subsequent intramolecular aldol reaction under heating conditions, enabling the formation of new C-O and C-C bonds for benzo[b]oxepine ring synthesis. Moreover, at ambient temperature, the above C-O/C-C bond-forming event takes place preferentially via a [4 + 2] annulation path over a spirocyclization route, leading to substituted fused-cyclopropanes with good diastereoselectivities. Gratifyingly, further alterations of the obtained spirobenzo[b]oxepines and tetrahydrocyclopropa[b]chromenes afford fascinating classes of 4H-chromen-4-ones and cyclopenta[c]chromenes, respectively, under metal-free conditions.

A substrate-dependent reaction of 1-aryl-2-alkyl-1,2-diketones with 2-aroyl-1-chlorocyclopropanecarboxylates: selective access to 2',5'-dicyclopropoxy-1,1':4',1''-teraryls and pentafulvenes.

An interesting substrate-controlled one-pot approach to highly substituted 2',5'-dicyclopropoxy-1,1':4',1''-teraryls and 6-hydroxypentafulvenes involving various 1,2-diketones and 2-aroyl-1-chlorocyclopropanecarboxylates as 3C Michael acceptors triggered by Cs2CO3 has been developed. We noticed that 1,2-diketones play a decisive role in this reaction to determine the product's selectivity. For example, aryl rings having electron-poor functionalities at the para and meta-positions of 1,2-diketones led to 2,5-diarylhydroquinones selectively via a cyclodimerization/double oxa-Michael process with highly strained cyclopropenes. However, when 1-naphthyl/electron-donating aryl/ortho-aryl-substituted 1,2-diketones were chosen, the Michael-initiated ring expansion reaction (C-C and CC bonds) took place under the same conditions that gave the corresponding pentafulvenes predominately. Moreover, this reaction has several imperative features such as good to high diastereoselectivities, wide substrate scope, good functional group tolerance, transition metal-free process, etc.

Cu(OAc)2/DABCO-mediated domino reaction of vinyl malononitriles with cyclic sulfamidate imines: access to 6-hydroxyaryl-2-aminonicotinonitriles.

A novel Cu(II)-salt/DABCO-mediated one-pot access to a myriad of highly substituted biologically relevant 2-aminonicotinonitriles possessing a resourceful phenolic moiety with satisfactory yields is reported. This method involves cyclic sulfamidate imines as 1C1N sources and different kinds of acyclic/cyclic vinyl malononitriles as 4C sources for pyridine synthesis via a vinylogous Mannich-cycloaromatization sequence process, creating two new C-N bonds under mild conditions. Importantly, this de novo strategy is applicable to gram-scale syntheses, underlining the method's practicability and allowing for a wide range of substrates with excellent functional group tolerance.

Substrate-Controlled Domino Reaction of N-Sulfonyl Ketimines with 2-Aroyl-1-chlorocyclopropanecarboxylates: Access to Cyclopenta[c]chromenes and Benzo[f]cyclopenta[d][1,2]thiazepine Dioxides.

An unprecedented substrate-controlled annulation method for the synthesis of fascinating classes of angularly fused cyclopenta[c]chromenes and benzo[f]cyclopenta[d][1,2]thiazepine 5,5-dioxide derivatives in good to high chemical yields is reported. This Michael-initiated ring-expansion reaction would enable two C-C and one C-O or C-N bonds by a judicious choice of carbonucleophiles, either 4-alkyl or 3-alkyl-substituted N-sulfonyl ketimines, respectively, with a series of donor-acceptor cyclopropane scaffolds as 4C sources promoted by DBU. Moreover, this eco-friendly method is mild enough to protect different kinds of functionalities. Importantly, the prepared fused fulvene scaffolds were smoothly transformed into a special class of hexahydrocyclopenta[c]chromenes as single cis-cis-cis-cis diastereomers in excellent yields by a simple catalytic hydrogenation reaction.

Diastereoselective desymmetrization reactions of prochiral para-quinamines with cyclopropenes generated in situ: access to fused hydroindol-5-one scaffolds.

Interesting desymmetric [3 + 2] annulation reactions between p-quinamines as prochiral N-donors and 2-aroyl-1-chlorocyclopropanecarboxylates facilitated by a base are reported. This successive double Michael reaction delivered a unique class of cyclopropane-fused hydoindol-5-one frameworks, each having four contiguous stereogenic centers, with three of them being fully substituted. Moreover, this method was found to provide acceptable chemical yields with promising diastereoselectivities (dr of up to ≤95 : 5) and to work with a variety of substrates. Importantly, a polycyclic tacrine analogue used to treat Alzheimer's disease was synthesized using our developed method.

Disentangling the Contribution of Each Descriptive Characteristic of Every Single Mutation to Its Functional Effects.

Mutational effects predictions continue to improve in accuracy as advanced artificial intelligence (AI) algorithms are trained on exhaustive experimental data. The next natural questions to ask are if it is possible to gain insights into which attribute of the mutation contributes how much to the mutational effects and if one can develop universal rules for mapping the descriptors to mutational effects. In this work, we mainly address the former aspect using a framework of interpretable AI. Relations between the physicochemical descriptors and their contributions to the mutational effects are extracted by analyzing the data on 29,832 variants from eight systematic deep mutational scan studies. An opposite trend in the dependence of fitness and solubility on the distance of the amino acid from the catalytic sites could be extracted and quantified. The dependence of the mutational effect contributions on the position-specific scoring matrix (PSSM) score for the amino acid after mutation or the BLOSUM score of the substitution showed universal trends. Our attempts in the present work to explain the quantitative differences in the dependence on conservation and SASA across proteins were not successful. The work nevertheless brings transparency into the predictions and development of rules, and will hopefully lead to empirically uncovering the universalities among these rules.

NH4OAc-Promoted Domino Route to Hydroxyarylated Unsymmetrical Pyridines under Neat Conditions.

A new metal-, oxidant-, and solvent-free ecofriendly domino method has been established for modular synthesis of a diverse range of medicinally promising hydroxyarylated unsymmetrical pyridines in good to high chemical yields with an excellent regioselectivity. This domino process involves a range of N-sulfonyl ketimines as C,N-binucleophiles, enolizable ketones, and aromatic/heteroaromatic aldehydes using ammonium acetate as an ideal promoter under neat conditions, which creates two new C-C bonds and one C-N bond. Notably, the neutral reaction conditions are mild enough to tolerate a range of functionalities and cover a variety of substrates, thus bestowing a powerful avenue to access tri- and tetrasubstituted pyridines including carbo- and heterocyclic fused ones. Interestingly, a practical, scalable, and high-yielding synthesis of pyridylphenol derivatives was successfully accomplished by our unique method.

Modelling a pandemic with asymptomatic patients, impact of lockdown and herd immunity, with applications to SARS-CoV-2.

The SARS-CoV-2 is a type of coronavirus that has caused the pandemic known as the Coronavirus Disease of 2019, or COVID-19. In traditional epidemiological models such as SEIR (Susceptible, Exposed, Infected, Removed), the exposed group E does not infect the susceptible group S. A distinguishing feature of COVID-19 is that, unlike with previous viral diseases, there is a distinct "asymptomatic" group A, which does not show any symptoms, but can nevertheless infect others, at the same rate as infected symptomatic patients. This situation is captured in a model known as SAIR (Susceptible, Asymptomatic, Infected, Removed), introduced in Robinson and Stillianakis (2013). The dynamical behavior of the SAIR model is quite different from that of the SEIR model. In this paper, we use Lyapunov theory to establish the global asymptotic stabililty of the SAIR model, both without and with vital dynamics. Then we develop compartmental SAIR models to cater to the migration of population across geographic regions, and once again establish global asymptotic stability. Next, we go beyond long-term asymptotic analysis and present methods for estimating the parameters in the SAIR model. We apply these estimation methods to data from several countries including India, and demonstrate that the predicted trajectories of the disease closely match actual data. We show that "herd immunity" (defined as the time when the number of infected persons is maximum) can be achieved when the total of infected, symptomatic and asymptomatic persons is as low as 25% of the population. Previous estimates are typically 50% or higher. We also conclude that "lockdown" as a way of greatly reducing inter-personal contact has been very effective in checking the progress of the disease.

CMOST: an open-source framework for the microsimulation of colorectal cancer screening strategies.

BACKGROUND: Colorectal cancer (CRC) is a leading cause of cancer-related mortality. CRC incidence and mortality can be reduced by several screening strategies, including colonoscopy, but randomized CRC prevention trials face significant obstacles such as the need for large study populations with long follow-up. Therefore, CRC screening strategies will likely be designed and optimized based on computer simulations. Several computational microsimulation tools have been reported for estimating efficiency and cost-effectiveness of CRC prevention. However, none of these tools is publicly available. There is a need for an open source framework to answer practical questions including testing of new screening interventions and adapting findings to local conditions. METHODS: We developed and implemented a new microsimulation model, Colon Modeling Open Source Tool (CMOST), for modeling the natural history of CRC, simulating the effects of CRC screening interventions, and calculating the resulting costs. CMOST facilitates automated parameter calibration against epidemiological adenoma prevalence and CRC incidence data. RESULTS: Predictions of CMOST were highly similar compared to a large endoscopic CRC prevention study as well as predictions of existing microsimulation models. We applied CMOST to calculate the optimal timing of a screening colonoscopy. CRC incidence and mortality are reduced most efficiently by a colonoscopy between the ages of 56 and 59; while discounted life years gained (LYG) is maximal at 49-50 years. With a dwell time of 13 years, the most cost-effective screening is at 59 years, at $17,211 discounted USD per LYG. While cost-efficiency varied according to dwell time it did not influence the optimal time point of screening interventions within the tested range. CONCLUSIONS: Predictions of CMOST are highly similar compared to a randomized CRC prevention trial as well as those of other microsimulation tools. This open source tool will enable health-economics analyses in for various countries, health-care scenarios and CRC prevention strategies. CMOST is freely available under the GNU General Public License at https://gitlab.com/misselwb/CMOST.

Product Release Pathways in Human and Plasmodium falciparum Phosphoribosyltransferase.

Atomistic molecular dynamics (MD) simulations coupled with the metadynamics technique were carried out to delineate the product (PPi.2Mg and IMP) release mechanisms from the active site of both human (Hs) and Plasmodium falciparum (Pf) hypoxanthine-guanine-(xanthine) phosphoribosyltransferase (HG(X)PRT). An early movement of PPi.2Mg from its binding site has been observed. The swinging motion of the Asp side chain (D134/D145) in the binding pocket facilitates the detachment of IMP, which triggers the opening of flexible loop II, the gateway to the bulk solvent. In PfHGXPRT, PPi.2Mg and IMP are seen to be released via the same path in all of the biased MD simulations. In HsHGPRT too, the product molecules follow similar routes from the active site; however, an alternate but minor escape route for PPi.2Mg has been observed in the human enzyme. Tyr 104 and Phe 186 in HsHGPRT and Tyr 116 and Phe 197 in PfHGXPRT are the key residues that mediate the release of IMP, whereas the motion of PPi.2Mg away from the reaction center is guided by the negatively charged Asp and Glu and a few positively charged residues (Lys and Arg) that line the product release channels. Mutations of a few key residues present in loop II of Trypanosoma cruzi (Tc) HGPRT have been shown to reduce the catalytic efficiency of the enzyme. Herein, in silico mutation of corresponding residues in loop II of HsHGPRT and PfHGXPRT resulted in partial opening of the flexible loop (loop II), thus exposing the active site to bulk water, which offers a rationale for the reduced catalytic activity of these two mutant enzymes. Investigations of the product release from these HsHGPRT and PfHGXPRT mutants delineate the role of these important residues in the enzymatic turnover.

Presenting symptoms predict local staging of anal cancer: a retrospective analysis of 86 patients.

BACKGROUND: Incidence of anal carcinoma (AC) is increasing and timely diagnosis is critical for efficient therapy. However, there is a paucity of recent studies addressing clinical symptoms and physical findings of anal carcinoma. METHODS: We performed a retrospective study reviewing history, symptoms and physical findings from 86 patients with newly diagnosed AC. We analyzed frequency of symptoms and physical findings according to T and TNM stage and their predictive value regarding tumor stage. RESULTS: Most patients presented with T2 (37 %) or T3 (29 %) cancer. 85 of 86 patients were symptomatic with anal bleeding (78 %), anal/perianal pain (63 %), weight loss (31 %) and foreign body sensation (22 %). 95 % of patients had ≥1 finding on physical examination including a visible tumor, palpable resistance and pain/blood during digital rectal examination. Patients with locally advanced disease (T3/T4) presented with more symptoms (p < 0.01) and more physical findings (p = 0.04) than patients with T1/T2 disease. On multivariate regression analysis perianal pain, painful defecation and weight loss were significantly associated with T3/T4 disease. CONCLUSION: Clinical symptoms and physical findings are present in nearly all AC patients. Pain referred to the perianal region, painful defecation and weight loss have predictive value for locally advanced disease.

Free-energy landscape of protein oligomerization from atomistic simulations.

In the realm of protein-protein interactions, the assembly process of homooligomers plays a fundamental role because the majority of proteins fall into this category. A comprehensive understanding of this multistep process requires the characterization of the driving molecular interactions and the transient intermediate species. The latter are often short-lived and thus remain elusive to most experimental investigations. Molecular simulations provide a unique tool to shed light onto these complex processes complementing experimental data. Here we combine advanced sampling techniques, such as metadynamics and parallel tempering, to characterize the oligomerization landscape of fibritin foldon domain. This system is an evolutionarily optimized trimerization motif that represents an ideal model for experimental and computational mechanistic studies. Our results are fully consistent with previous experimental nuclear magnetic resonance and kinetic data, but they provide a unique insight into fibritin foldon assembly. In particular, our simulations unveil the role of nonspecific interactions and suggest that an interplay between thermodynamic bias toward native structure and residual conformational disorder may provide a kinetic advantage.

Microgravity Simulated by the 6° Head-Down Tilt Bed Rest Test Increases Intestinal Motility but Fails to Induce Gastrointestinal Symptoms of Space Motion Sickness.

BACKGROUND: Space motion sickness (SMS) is the most relevant medical problem during the first days in microgravity. Studies addressing pathophysiology in space face severe technical challenges and microgravity is frequently simulated using the 6° head-down tilt bed rest test (HDT). AIM: We were aiming to test whether SMS could be simulated by HDT, identify related changes in gastrointestinal physiology and test for beneficial effects of exercise interventions. METHODS: HDT was performed in ten healthy individuals. Each individual was tested in three study campaigns varying by a 30-min daily exercise intervention of either standing, an upright exercise regimen, or no intervention. Gastrointestinal symptoms, stool characteristics, gastric emptying time, and small intestinal transit were assessed using standardized questionnaires, (13)C octanoate breath test, and H2 lactulose breath test, respectively, before and at day 2 and 5 of HDT. RESULTS: Individuals described no or minimal gastrointestinal symptoms during HDT. Gastric emptying remained unchanged relative to baseline data collection (BDC). At day 2 of HDT the H2 peak of the lactulose test appeared earlier (mean ± standard error for BDC-1, HDT2, HDT5: 198 ± 7, 139 ± 18, 183 ± 10 min; p: 0.040), indicating accelerated small intestinal transit. Furthermore, during HDT, stool was softer and stool mass increased (BDC: 47 ± 6, HDT: 91 ± 12, recovery: 53 ± 8 g/day; p: 0.014), indicating accelerated colonic transit. Exercise interventions had no effect. CONCLUSION: HDT did not induce symptoms of SMS. During HDT, gastric emptying remained unchanged, but small and large intestinal transit was accelerated.

On the recombination of hydronium and hydroxide ions in water.

The recombination of hydronium and hydroxide ions following water ionization is one of the most fundamental processes determining the pH of water. The neutralization step once the solvated ions are in close proximity is phenomenologically understood to be fast, but the molecular mechanism has not been directly probed by experiments. We elucidate the mechanism of recombination in liquid water with ab initio molecular dynamics simulations, and it emerges as quite different from the conventional view of the Grotthuss mechanism. The neutralization event involves a collective compression of the water-wire bridging the ions, which occurs in approximately 0.5 ps, triggering a concerted triple jump of the protons. This process leaves the neutralized hydroxide in a hypercoordinated state, with the implications that enhanced collective compressions of several water molecules around similarly hypercoordinated states are likely to serve as nucleation events for the autoionization of liquid water.

Optimal timing of a colonoscopy screening schedule depends on adenoma detection, adenoma risk, adherence to screening and the screening objective: A microsimulation study.

Colonoscopy-based screening provides protection against colorectal cancer (CRC), but the optimal starting age and time intervals of screening colonoscopies are unknown. We aimed to determine an optimal screening schedule for the US population and its dependencies on the objective of screening (life years gained or incidence, mortality, or cost reduction) and the setting in which screening is performed. We used our established open-source microsimulation model CMOST to calculate optimized colonoscopy schedules with one, two, three or four screening colonoscopies between 20 and 90 years of age. A single screening colonoscopy was most effective in reducing life years lost from CRC when performed at 55 years of age. Two, three and four screening colonoscopy schedules saved a maximum number of life years when performed between 49-64 years; 44-69 years; and 40-72 years; respectively. However, for maximum incidence and mortality reduction, screening colonoscopies needed to be scheduled 4-8 years later in life. The optimum was also influenced by adenoma detection efficiency with lower values for these parameters favoring a later starting age of screening. Low adherence to screening consistently favored a later start and an earlier end of screening. In a personalized approach, optimal screening would start earlier for high-risk patients and later for low-risk individuals. In conclusion, our microsimulation-based approach supports colonoscopy screening schedule between 45 and 75 years of age but the precise timing depends on the objective of screening, as well as assumptions regarding individual CRC risk, efficiency of adenoma detection during colonoscopy and adherence to screening.

Swapping Copper-Catalytic Process: Selective Access to Pyrazoles and Conjugated Ketimines from Oxime Acetates and Cyclic Sulfamidate Imines.

A powerful CuCl-catalyzed sequential one-pot reaction of aryl methyl ketoxime acetates with cyclic N-sulfonyl imines followed by elimination in the presence of base is reported. This hydrazine-free method conveniently makes C-C and N-N bonds via a radical cleavage of the N-O bond, delivering a special class of C3-hydroxyarylated pyrazoles in good yields. Surprisingly, while employing CuI as a catalyst instead of CuCl, the reaction proceeds through a non-radical pathway which embodies a new tactic for the high-yielding access to value-added conjugated N-unsubstituted ketimines. Moreover, additive-free approach to sulfamidate-fused-pyrazoles was achieved by successfully catalyzing addition and oxidative N-N bond-making reactions by CuI and CuCl, respectively. Significantly, our novel technique could convert the prepared ketimines into the pharmacologically recognized 6H-benzo[c]chromene frameworks.

Using Atomistic Simulations to Explore the Role of Methylation and ATP in Chemotaxis Signal Transduction.

A bacterial chemotaxis mechanism is activated when nutrients bind to surface receptors. The sequence of intra- and interprotein events in this signal cascade from the receptors to the eventual molecular motors has been clearly identified. However, the atomistic details remain elusive, as in general may be expected of intraprotein signal transduction pathways, especially when fibrillar proteins are involved. We performed atomistic calculations of the methyl accepting chemoprotein (MCP)-CheA-CheW multidomain complex from Escherichia coli, simulating the methylated and unmethylated conditions in the chemoreceptors and the ATP-bound and apo conditions of the CheA. Our results indicate that these atomistic simulations, especially with one of the two force fields we tried, capture several relevant features of the downstream effects, such as the methylation favoring an intermediate structure that is more toward a dipped state and increases the chance of ATP hydrolysis. The results thus suggest the sensitivity of the model to reflect the nutrient signal response, a nontrivial validation considering the complexity of the system, encouraging even more detailed studies on the thermodynamic quantification of the effects and the identification of the signaling networks.

Early Bioinformatic Implication of Triacidic Amino Acid Motifs in Autophagy-Dependent Unconventional Secretion of Mammalian Proteins.

Several proteins are secreted outside the cell, and in many cases, they may be identified by a characteristic signal peptide. However, more and more studies point to the evidence for an "unconventional" secretion, where proteins without a hitherto unknown signal are secreted, possibly in conditions of starvation. In this work, we analyse a set of 202 RNA binding mammalian proteins, whose unconventional secretion has recently been established. Analysis of these proteins secreted by LC3 mediation, the largest unconventionally secreted dataset to our knowledge, identifies the role of KKX motif as well as triacidic amino acid motif in unconventional secretion, the latter being an extension of the recent implicated diacidic amino acid motif. Further data analysis evolves a hypothesis on the sequence or structural proximity of the triacidic or KKX motifs to the LC3 interacting region, and a phosphorylatable amino acid such as serine as a statistically significant feature among these unconventionally secreted proteins. This hypothesis, although needs to be validated in experiments that challenge the specific details of each of these aspects, appears to be one of the early steps in defining what may be a plausible signal for unconventional protein secretion.

Insights on the role of (dis)order from protein-protein interaction linear free-energy relationships.

Protein-protein interactions (PPIs) are remarkably diverse and form the basis for various cellular functions. PPIs can be classified as ordered or disordered; the disordered ones do not have a well-defined structure prior to association, which is an exception to the conventional structure-function relationship. The occurrence of disordered proteins in functional roles is not explained by the conventional structure-function paradigm, and at present there is no clear understanding of the differences between the natures of these two PPIs. In this work, we studied the relationship between the kinetics and thermodynamics in PPIs to provide insights into the latter, with possible implications for the former. Analyzing the experimental data for various protein complexes, we found linear free-energy behavior with a striking kinetic difference between these two types of interactions. Binding affinities of (dis)ordered proteins are correlated with their (association) dissociation rates. Our observation, combined with the correspondence between biological activity and affinity, suggests that selection pressure on the dissociation or association kinetics in a functional context necessitates the presence of (dis)order in the structure.

Probing the mechanism of pH-induced large-scale conformational changes in dengue virus envelope protein using atomistic simulations.

One of the key steps in the infection of the cell by dengue virus is a pH-induced conformational change of the viral envelope proteins. These envelope proteins undergo a rearrangement from a dimer to a trimer, with large conformational changes in the monomeric unit. In this article, metadynamics simulations were used to enable us to understand the mechanism of these large-scale changes in the monomer. By using all-atom, explicit solvent simulations of the monomers, the stability of the protein structure is studied under low and high pH conditions. Free energy profiles obtained along appropriate collective coordinates demonstrate that pH affects the domain interface in both the conformations of E monomer, stabilizing one and destabilizing the other. These simulations suggest a mechanism with an intermediate detached state between the two monomeric structures. Using further analysis, we comment on the key residue interactions responsible for the instability and the pH-sensing role of a histidine that could not otherwise be studied experimentally. The insights gained from this study and methodology can be extended for studying similar mechanisms in the E proteins of the other members of class II flavivirus family.