Studying Lipophilicity Trends of Phosphorus Compounds by 31P-NMR Spectroscopy: A Powerful Tool for the Design of P-Containing Drugs

Systematically studying the lipophilicity of phosphorus compounds is of great importance for many chemical and biological fields and particularly for medicinal chemistry. Here, we report on the study of trends in the lipophilicity of a wide set of phosphorus compounds relevant to drug design including phosphates, thiophosphates, phosphonates, thiophosphonates, bis-phosphonates, and phosphine chalcogenides. This was enabled by the development of a straightforward log P determination method for phosphorus compounds based on ³¹P-NMR spectroscopy. The log P values measured ranged between -3.2 and 3.6, and the trends observed were interpreted using a DFT study of the dipole moments and by H-bond basicity (pK_HB) measurements of selected compounds. Clear signal separation in ³¹P-NMR spectroscopy grants the method high tolerability to impurities. Moreover, the wide range of chemical shifts for the phosphorus nucleus (250 to -250 ppm) enables a direct simultaneous log P determination of phosphorus compound mixtures in a single shake-flask experiment and ³¹P-NMR analysis.

Nonexponential kinetics in captured in sequential unfolding of polyproteins over a range of loads

While performing under mechanical loads in vivo, polyproteins are vitally involved in cellular mechanisms such as regulation of tissue elasticity and mechano-transduction by unfolding their comprising domains and extending them. It is widely thought that the process of sequential unfolding of polyproteins follows an exponential kinetics as the individual unfolding events exhibit identical and identically distributed (iid) Poisson behavior. However, it was shown that under high loads, the sequential unfolding kinetics displays nonexponential kinetics that alludes to aging by a subdiffusion process. Statistical order analysis of this kinetics indicated that the individual unfolding events are not iid, and cannot be defined as a Poisson (memoryless) process. Based on numerical simulations it was argued that this behavior becomes less pronounced with lowering the load, therefore it is to be expected that polyproteins unfolding under lower forces will follow a Poisson behavior. This expectation serves as the motivation of the current study, in which we investigate the effect of force lowering on the unfolding kinetics of Poly-L₈ under varying loads, specifically high (150, 100 ​pN) and moderate-low (45, 30, 20 ​pN) forces. We found that a hierarchy among the unfolding events still exists even under low loads, again resulting in nonexponential behavior. We observe that analyzing the dwell-time distributions with stretched-exponentials and power laws give rise to different phenomenological trends. Using statistical order analysis, we demonstrated that even under the lowest load, the sequential unfolding cannot be considered as iid, in accord with the power law distribution. Additional free energy analysis revealed the contribution of the unfolded segments elasticity that scales with the force on the overall one-dimensional contour of the energy landscape, but more importantly, it discloses the hierarchy within the activation barriers during sequential unfolding that account for the observed nonexponentiality.

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Poly-L₈ unfolding shows nonexponential kinetics at forces ranging from 150 to 20 ​pN.

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Different phenomenological trends are observed for the dwell-time distributions.

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The unfolding events were shown to be dependent and not identically distributed.

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Free energy analysis reveals elastic impact and hierarchy in the unfolding barriers.

Theoretical investigation of pre-symptomatic SARS-CoV-2 person-to-person transmission in households

Since its emergence, the phenomenon of SARS-CoV-2 transmission by seemingly healthy individuals has become a major challenge in the effort to achieve control of the pandemic. Identifying the modes of transmission that drive this phenomenon is a perquisite in devising effective control measures, but to date it is still under debate. To address this problem, we have formulated a detailed mathematical model of discrete human actions (such as coughs, sneezes, and touching) and the continuous decay of the virus in the environment. To take into account those discrete and continuous events we have extended the common modelling approach and employed a hybrid stochastic mathematical framework. This allowed us to calculate higher order statistics which are crucial for the reconstruction of the observed distributions. We focused on transmission within a household, the venue with the highest risk of infection and validated the model results against the observed secondary attack rate and the serial interval distribution. Detailed analysis of the model results identified the dominant driver of pre-symptomatic transmission as the contact route via hand-face transfer and showed that wearing masks and avoiding physical contact are an effective prevention strategy. These results provide a sound scientific basis to the present recommendations of the WHO and the CDC.

Innate immune response in neuronopathic forms of Gaucher disease confers resistance against viral-induced encephalitis

Both monogenic diseases and viral infections can manifest in a broad spectrum of clinical phenotypes that range from asymptomatic to lethal, suggesting that other factors modulate disease severity. Here, we examine the interplay between the genetic neuronopathic Gaucher’s disease (nGD), and neuroinvasive Sindbis virus (SVNI) infection. Infection of nGD mice with SVNI had no influence on nGD severity. However, nGD mice were more resistant to SVNI infection. Significantly different inflammatory responses were seen in nGD brains when compared with SVNI brains: the inflammatory response in the nGD brains consisted of reactive astrocytes and microglia with no infiltrating macrophages, but the inflammatory response in the brains of SVNI-infected mice was characterized by infiltration of macrophages and altered activation of microglia and astrocytes. We suggest that the innate immune response activated in nGD confers resistance against viral infection of the CNS.

Correlations within polyprotein forced unfolding dwell-times introduce sequential dependency

Polyproteins, comprised from proteins arrayed in tandem, respond to mechanical loads through partial unfolding and extension. This response to tension that enables their physiological function is related to the ability to dynamically regulate their elasticity. The unique arrangement of their individual mechanical components (proteins and polymeric linkers), and the interactions between them eventually determines their performance. The sequential unfolding-times within a polyprotein are inherently assumed to be independent and identically distributed (iid), thus expected to follow an exponential distribution. Nevertheless, a large body of literature using single molecule force spectroscopy (SMFS) provides evidence that forced unfolding-times of N proteins within a polyprotein do not follow the exponential distribution. Here we use SMFS with Atomic Force Microscopy to measure the unfolding kinetics of Poly-(I91)₈ at 180 pN. The unfolding time-intervals were statistically analysed using three common approaches, all exhibiting an N-effect: hierarchical behavior with non-identical unfolding time distributions. Using continuous time random walk approach indicates that the unfolding times display subdiffusive features. Put together with free-energy reconstruction of the whole unfolding polyprotein, we provide physical explanation for this nontrivial behavior, according to which the elongating polypeptide chain with each unfolding event intervenes with the sequential unfolding probabilities and correlates them.

The Effect of Anesthetic Regimens on Intestinal Absorption of Passively Absorbed Drugs in Rats

PURPOSE

Different anesthetic regimens are used during single pass intestinal perfusion (SPIP) experiments for the study of intestinal drug absorption in rats. We examined the ketamine/xylazine anesthetic combination to evaluate its influence on drug absorption compared to older regimens. Additionally, we examined whether supplementary analgesia has any effect on drug absorption and the effect of the different anesthetic regimens on induction time and stress response.

METHODS

Rats were anesthetized using four different anesthetic regimens; ketamine/midazolam, pentobarbital, ketamine/xylazine and ketamine/xylazine/butorphanol. Three model drugs were administered to rat intestines and P_eff was calculated. Stress response was evaluated by quantifying blood corticosterone levels and induction time was recorded.

RESULTS

We found absorption under pentobarbital to be higher or similar to absorption under ketamine/midazolam. These results partly correlate with past literature data. Ketamine/xylazine was found to give similar or higher P_eff compared to pentobarbital and ketamine/midazolam. Addition of butorphanol did not affect absorption and reduced induction time and stress.

CONCLUSIONS

In studies of intestinal drug absorption, the ketamine/xylazine combination is superior to other anesthetic regimens as it is more convenient and seems to affect absorption to a lesser extent. Addition of butorphanol is highly recommended as it did not affect absorption but led to a more effective and less stress inducing experiment.

Source-receptor probability of atmospheric long-distance dispersal of viruses to Israel from the eastern Mediterranean area

Viruses that affect the health of humans and farm animals can spread over long distances via atmospheric mechanisms. The phenomenon of atmospheric long-distance dispersal (LDD) is associated with severe consequences because it may introduce pathogens into new areas. The introduction of new pathogens to Israel was attributed to LDD events numerous times. This provided the motivation for this study which is aimed to identify all the locations in the eastern Mediterranean that may serve as sources for pathogen incursion into Israel via LDD. This aim was achieved by calculating source-receptor relationship probability maps. These maps describe the probability that an infected vector or viral aerosol, once airborne, will have an atmospheric route that can transport it to a distant location. The resultant probability maps demonstrate a seasonal tendency in the probability of specific areas to serve as sources for pathogen LDD into Israel. Specifically, Cyprus' season is the summer; southern Turkey and the Greek islands of Crete, Karpathos and Rhodes are associated with spring and summer; lower Egypt and Jordan may serve as sources all year round, except the summer months. The method used in this study can easily be implemented to any other geographic region. The importance of this study is the ability to provide a climatologically valid and accurate risk assessment tool to support long-term decisions regarding preparatory actions for future outbreaks long before a specific outbreak occurs.

Using Synoptic Systems' Typical Wind Trajectories for the Analysis of Potential Atmospheric Long-Distance Dispersal of Lumpy Skin Disease Virus

Lumpy skin disease virus (LSDV) is an infectious, arthropod-borne virus that affects mostly cattle. Solitary outbreaks have occurred in Israel in 1989 and 2006. In both years, the outbreaks occurred parallel to a severe outbreak in Egypt, and LSDV was hypothesized to be transmitted from Egypt to Israel via long-distance dispersal (LDD) of infected vectors by wind. The aim of this study was to identify possible events of such transport. At the first stage, we identified the relevant synoptic systems that allowed wind transport from Egypt to Israel during the 3 months preceding each outbreak. Three-dimensional backwards Lagrangian trajectories were calculated from the receptor sites in Israel for each occurrence of such relevant synoptic system. The analysis revealed several events in which atmospheric connection routes between the affected locations in Egypt and Israel were established. Specifically, during the 1989, Damietta and Port Said stand out as likely sources for the outbreak in Israel. In 2006, different locations acted simultaneously as potential sources of the outbreak in Israel. These locations were situated in the Nile delta, the Suez Canal and in northern Sinai. The analysis pointed out Sharav low and Shallow Cyprus low to the North to be the most likely systems to enable windborne transport from Egypt to Israel. These findings are of high importance for the analysis of the risk of transmission of vectorborne viruses in the eastern Mediterranean region.

A new theoretical framework for modeling respiratory protection based on the beta distribution

The problem of modeling respiratory protection is well known and has been dealt with extensively in the literature. Often the efficiency of respiratory protection is quantified in terms of penetration, defined as the proportion of an ambient contaminant concentration that penetrates the respiratory protection equipment. Typically, the penetration modeling framework in the literature is based on the assumption that penetration measurements follow the lognormal distribution. However, the analysis in this study leads to the conclusion that the lognormal assumption is not always valid, making it less adequate for analyzing respiratory protection measurements. This work presents a formulation of the problem from first principles, leading to a stochastic differential equation whose solution is the probability density function of the beta distribution. The data of respiratory protection experiments were reexamined, and indeed the beta distribution was found to provide the data a better fit than the lognormal. We conclude with a suggestion for a new theoretical framework for modeling respiratory protection.

Frequency Analyses Can Be Improved by a Modified t-test in Sample-based Preclinical Efficacy Studies

Sample-based preclinical drug efficacy studies compare frequency (proportion) or incidences of successes within respective samples of test and control groups. The word success in principle refers to a protected (e.g., due to vaccination), recovered, or surviving animal, depending on the particular experiment. We introduce here a modified t-test for two independent groups, aimed at statistical analysis of the difference between frequencies of successes in sample based preclinical studies. The test is applicable whenever the study is based on repeating replicate experiments, as required by certain procedures such as validation. Such experiments are based on constant drug dose and performed under identical conditions and protocol. The proposed test combines the computational rules of t-test for two independent groups and analysis of variance. In the initial steps, incidences are transformed to proportions, and variance between proportions in samples of the j(th) group (s(p(j))(2)), is then transformed into theoretical weighted variance within the i(th) repetition (sample) of the j(th) group (s(i,j)(2)). The variance of proportions in samples of the size of the whole group (SE(j)(2)) is then calculated. The t-statistic is computed according to the rules of t-test for two independent groups. Significance is calculated using (N(1) - 1) + (N(2) - 1) degrees of freedom, where N(j) denotes the total number of animals in the j(th) group. The proposed model offers an important advantage over incidence or proportion distribution models, such as chi-square or normal approximation of binomial distribution, respectively, because it considers variance between replicate experiments. It moreover offers important flexibility by limiting the requirement for identical sample sizes only to samples within the control or test group. A difference between groups in sample sizes, number of samples, or both, preventing application of block designs or the standard formats of t-test, may still exist. Theoretical considerations and working examples are provided.

LAY ABSTRACT

Sample based preclinical drug efficacy studies compare frequency (proportion) or incidences of successful results (e.g., protected, recovered, or surviving animals, depending on the particular experiment) within respective samples of the test and the control groups. Certain procedures, such as validation, require replicate experiments that are identical in all controllable factors, such as drug dose, sample sizes within each group, general experimental conditions, etc. Still, the control sample size is not required to be identical to that of the respective test sample size. In such cases, t-test or block designs are not applicable for statistical analyses. Moreover, incidence or frequency distribution models, such as chi-square or normal approximation of binomial distribution, respectively, which are performed on pooled data of the examined groups, ignore variance between experiments and thereby result in impaired validity of the statistical inference. We propose here a modified t-test that limits the requirement for identical sample sizes to only within each group. This aim is achieved by combining the computational rules of t-test together with analysis of variance. The proposed t-test allows the incorporating of variance between experiments into frequency or incidence assessments. We recommend using the proposed modified t-test as a complementary test to incidence distribution models.