The influence of backbone fluorination on the helicity of α/γ-hybrid peptides.

Peptides that are composed of an alternating pattern of α- and γ-amino acids are potentially valuable as metabolism-resistant bioactive agents. For optimal function, some kind of conformational restriction is usually required to either stabilize the dominant 12-helix, or else to divert the peptide away from this conformation in a controlled way. Herein, we explore stereoselective fluorination as a method for controlling the conformations of α/γ-hybrid peptides. We show through a combination of X-ray, NMR and CD analyses that fluorination can either stabilize or disrupt the 12-helix, depending on the fluorine stereochemistry. These findings could inform the ongoing development of diverse functional hybrid peptides.

The potential and shortcomings of mitochondrial DNA analysis for cheetah conservation management.

There are only about 7,100 adolescent and adult cheetahs (Acinonyx jubatus) remaining in the wild. With the majority occurring outside protected areas, their numbers are rapidly declining. Evidence-based conservation measures are essential for the survival of this species. Genetic data is routinely used to inform conservation strategies, e.g., by establishing conservation units (CU). A commonly used marker in conservation genetics is mitochondrial DNA (mtDNA). Here, we investigated the cheetah's phylogeography using a large-scale mtDNA data set to refine subspecies distributions and better assign individuals to CUs. Our dataset mostly consisted of historic samples to cover the cheetah's whole range as the species has been extinct in most of its former distribution. While our genetic data largely agree with geography-based subspecies assignments, several geographic regions show conflicting mtDNA signals. Our analyses support previous findings that evolutionary forces such as incomplete lineage sorting or mitochondrial capture likely confound the mitochondrial phylogeography of this species, especially in East and, to some extent, in Northeast Africa. We caution that subspecies assignments solely based on mtDNA should be treated carefully and argue for an additional standardized nuclear single nucleotide polymorphism (SNP) marker set for subspecies identification and monitoring. However, the detection of the A. j. soemmeringii specific haplogroup by a newly designed Amplification-Refractory Mutation System (ARMS) can already provide support for conservation measures. Supplementary Information: The online version contains supplementary material available at 10.1007/s10592-022-01483-1.

Tinker, Tailor, Soldier, Spy: The Diverse Roles That Fluorine Can Play within Amino Acid Side Chains.

Side chain-fluorinated amino acids are useful tools in medicinal chemistry and protein science. In this review, we outline some general strategies for incorporating fluorine atom(s) into amino acid side chains and for elaborating such building blocks into more complex fluorinated peptides and proteins. We then describe the diverse benefits that fluorine can offer when located within amino acid side chains, including enabling 19F NMR and 18F PET imaging applications, enhancing pharmacokinetic properties, controlling molecular conformation, and optimizing target-binding.

Genomic analyses show extremely perilous conservation status of African and Asiatic cheetahs (Acinonyx jubatus).

We live in a world characterized by biodiversity loss and global environmental change. The extinction of large carnivores can have ramifying effects on ecosystems like an uncontrolled increase in wild herbivores, which in turn can have knock-on impacts on vegetation regeneration and communities. Cheetahs (Acinonyx jubatus) serve important ecosystem functions as apex predators; yet, they are quickly heading towards an uncertain future. Threatened by habitat loss, human-wildlife conflict and illegal trafficking, there are only approximately 7100 individuals remaining in nature. We present the most comprehensive genome-wide analysis of cheetah phylogeography and conservation genomics to date, assembling samples from nearly the entire current and past species' range. We show that their phylogeography is more complex than previously thought, and that East African cheetahs (A. j. raineyi) are genetically distinct from Southern African individuals (A. j. jubatus), warranting their recognition as a distinct subspecies. We found strong genetic differentiation between all classically recognized subspecies, thus refuting earlier findings that cheetahs show only little differentiation. The strongest differentiation was observed between the Asiatic and all the African subspecies. We detected high inbreeding in the Critically Endangered Iranian (A. j. venaticus) and North-western (A. j. hecki) subspecies, and show that overall cheetahs, along with snow leopards, have the lowest genome-wide heterozygosity of all the big cats. This further emphasizes the cheetah's perilous conservation status. Our results provide novel and important information on cheetah phylogeography that can support evidence-based conservation policy decisions to help protect this species. This is especially relevant in light of ongoing and proposed translocations across subspecies boundaries, and the increasing threats of illegal trafficking.

Strategies for Fine-Tuning the Conformations of Cyclic Peptides.

Cyclic peptides are promising scaffolds for drug development, attributable in part to their increased conformational order compared to linear peptides. However, when optimizing the target-binding or pharmacokinetic properties of cyclic peptides, it is frequently necessary to "fine-tune" their conformations, e.g., by imposing greater rigidity, by subtly altering certain side chain vectors, or by adjusting the global shape of the macrocycle. This review systematically examines the various types of structural modifications that can be made to cyclic peptides in order to achieve such conformational control.

Fluorinated quorum sensing inhibitors: enhancement of potency through conformational control.

The bacterial quorum sensing (QS) system is a target for non-lethal antibacterial agents that do not encourage the development of resistance. QS inhibitors commonly contain a polar "head" moiety and a lipidic "tail" moiety. In this work, we synthesised novel QS inhibitor candidates in which the lipidic "tail" is decorated with stereospecifically positioned fluorine atoms. The presence of fluorine is shown to bias the molecules into distinctive conformations that are pre-organised for binding to the QS receptor. This translates into significant increases in QS inhibitory potency.

Discovery of neuroprotective agents that inhibit human prolyl hydroxylase PHD2.

Prolyl hydroxylase (PHD) enzymes play a critical role in the cellular responses to hypoxia through their regulation of the hypoxia inducible factor α (HIF-α) transcription factors. PHD inhibitors show promise for the treatment of diseases including anaemia, cardiovascular disease and stroke. In this work, a pharmacophore-based virtual high throughput screen was used to identify novel potential inhibitors of human PHD2. Two moderately potent new inhibitors were discovered, with IC50 values of 4 µM and 23 µM respectively. Cell-based studies demonstrate that these compounds exhibit protective activity in neuroblastoma cells, suggesting that they have the potential to be developed into clinically useful neuroprotective agents.

The variable spectrum of anterior mitral valve leaflet restriction in rheumatic heart disease screening.

INTRODUCTION: The World Heart Federation (WHF) screening criteria do not incorporate a strict, reproducible definition of anterior mitral valve leaflet (AMVL) restriction. Using a novel definition, we have identified two distinct AMVL restriction configurations. The first, called "distal tip" AMVL restriction is associated with additional morphological features of rheumatic heart disease (RHD), while the second, "gradual bowing" AMVL restriction is not. This "arch-like" leaflet configuration involves the base to tip of the medial MV in isolation. We hypothesize that this configuration is a normal variant. METHODOLOGY: The prevalence and associated leaflet configurations of AMVL restriction were assessed in schoolchildren with an established "very low" (VLP), "high" (HP), and "very high" prevalence (VHP) of RHD. RESULTS: 936 studies were evaluated (HP 577 cases; VLP 359 cases). Sixty-five cases of "gradual bowing" AMVL restriction were identified in the HP cohort (11.3%, 95% CI 8.9-14.1) and 35 cases (9.7%, 95% CI 7-13.2) in the VLP cohort (P = .47). In the second analyses, an enriched cohort of 43 studies with proven definite RHD were evaluated. "Distal tip" AMVL restriction was identified in all 43 VHP cases (100%) and affected the central portion of the AMVL in all cases. CONCLUSION: "Gradual bowing" AMVL restriction appears to be a normal, benign variant of the MV, not associated with RHD risk nor with any other morphological features of RHD. Conversely, "Distal tip" AMVL restriction was present in all cases in the VHP cohort with no cases exhibiting a straight, nonrestricted central portion of the AMVL. This novel finding requires further investigation as a potential RHD rule-out test of the MV.

More than $1 billion needed annually to secure Africa's protected areas with lions.

Protected areas (PAs) play an important role in conserving biodiversity and providing ecosystem services, yet their effectiveness is undermined by funding shortfalls. Using lions (Panthera leo) as a proxy for PA health, we assessed available funding relative to budget requirements for PAs in Africa's savannahs. We compiled a dataset of 2015 funding for 282 state-owned PAs with lions. We applied three methods to estimate the minimum funding required for effective conservation of lions, and calculated deficits. We estimated minimum required funding as $978/km2 per year based on the cost of effectively managing lions in nine reserves by the African Parks Network; $1,271/km2 based on modeled costs of managing lions at ≥50% carrying capacity across diverse conditions in 115 PAs; and $2,030/km2 based on Packer et al.'s [Packer et al. (2013) Ecol Lett 16:635-641] cost of managing lions in 22 unfenced PAs. PAs with lions require a total of $1.2 to $2.4 billion annually, or ∼$1,000 to 2,000/km2, yet received only $381 million annually, or a median of $200/km2 Ninety-six percent of range countries had funding deficits in at least one PA, with 88 to 94% of PAs with lions funded insufficiently. In funding-deficit PAs, available funding satisfied just 10 to 20% of PA requirements on average, and deficits total $0.9 to $2.1 billion. African governments and the international community need to increase the funding available for management by three to six times if PAs are to effectively conserve lions and other species and provide vital ecological and economic benefits to neighboring communities.

The Effect of Vicinal Difluorination on the Conformation and Potency of Histone Deacetylase Inhibitors.

Histone deacetylase enzymes (HDACs) are potential targets for the treatment of cancer and other diseases, but it is challenging to design isoform-selective agents. In this work, we created new analogs of two established but non-selective HDAC inhibitors. We decorated the central linker chains of the molecules with specifically positioned fluorine atoms in order to control the molecular conformations. The fluorinated analogs were screened against a panel of 11 HDAC isoforms, and minor differences in isoform selectivity patterns were observed.

Ecological opportunity drives individual dietary specialization in leopards.

Individual specialization, when individuals exploit only a subset of resources utilized by the population, is a widespread phenomenon. It provides the basis for evolutionary diversification and can impact population and community dynamics. Both phenotypic traits and environmental conditions are predicted to influence individual specialization; however, its adaptive consequences are poorly understood, particularly among large mammalian carnivores that play an important role in shaping ecosystems. We used observations of 2,960 kills made by 49 leopards Panthera pardus in the Sabi Sand Game Reserve, South Africa, to quantify the magnitude of individual dietary specialization in a solitary large carnivore, and to examine the proximate and ultimate drivers of this behaviour. We found evidence of individual specialization in leopard diet, with respect to both the species and size of prey killed. Males tended to be more specialized than females, likely because they could access a wider range of prey due to larger body size. Similarly, individuals that encountered a greater diversity of prey tended to be more specialized. Our results confirmed that ecological opportunity was a key determinant of individual specialization; however, contrary to predictions, per capita resource availability (and by extension, intraspecific competition) did not affect the degree of specialization exhibited by individuals. Surprisingly, dietary specialization appeared to disadvantage male leopards. Specialist males overlapped with fewer resident females, had fewer cubs born on their home ranges and had fewer cubs survive to independence on their home ranges than generalist males. This may have resulted from the high degree of environmental stochasticity experienced during our study, as dietary specialization is expected to advantage individuals more during periods of resource predictability. In summary, we showed that a species usually considered to be a dietary generalist was in fact a heterogeneous collection of specialist and generalist individuals. Individual specialization is typically assumed to be maintained by disruptive and/or fluctuating selection; hence, the somewhat paradoxical coexistence of both in the same population might be explained by a dynamic evolutionary equilibrium that exists between specialists and generalists, in which each benefit under different conditions.

Context dependency of top-down, bottom-up and density-dependent influences on cheetah demography.

Research on drivers of demographic rates has mostly focused on top predators and their prey, and comparatively less research has considered the drivers of mesopredator demography. Of those limited studies, most focused on top-down effects of apex predators on mesopredator population dynamics, whereas studies investigating alternative mechanisms are less common. In this study, we tested hypotheses related to top-down, bottom-up and density-dependent regulation of demographic rates in an imperilled mesopredator, the cheetah (Acinonyx jubatus). We used a 25-year dataset of lion density, cheetah density and prey density from the Mun-Ya-Wana Conservancy in South Africa and assessed the effects of top-down, bottom-up and density-dependent drivers on cheetah survival and reproduction. In contrast to the top-down and bottom-up predictions, both adult and juvenile cheetahs experienced the lowest survival during months with high prey densities and low lion densities. We observed support only for a density-dependent response in juvenile cheetahs, where they had a higher probability of reaching independence during times with low cheetah density and low prey density. We did not identify any strong drivers of litter size. Collectively, our results indicate that high apex predator abundance might not always have negative effects on mesopredator populations, and suggest that context dependency in top-down, bottom-up and density-dependent factors may regulate demographic rates of cheetahs and other mesopredators. Our results highlight the complexities of population-level drivers of cheetah demographic rates and the importance of considering multiple hypotheses of mesopredator population regulation.

Diastereoselective synthesis and conformational analysis of 4,5-difluoropipecolic acids.

Stereoselectively-fluorinated analogs of pipecolic acid have been investigated through a combined theoretical and experimental approach. Three of the four possible diastereoisomers of 4,5-difluoropipecolic acid were successfully synthesized via deoxyfluorination chemistry, navigating a complex reaction network that included neighboring group participation, rearrangement, and elimination pathways. A DFT-based conformational study, supported by NMR J-based analysis, revealed that the different diastereoisomers of 4,5-difluoropipecolic acid preferentially adopt different puckers of the six-membered ring. These findings could have future relevance for the conformational control of biologically active peptides.

Screening for rheumatic heart disease: The reliability of anterior mitral valve leaflet thickness measurement.

BACKGROUND: Studies determining the reliability of the World Heart Federation (WHF) anterior mitral valve leaflet (AMVL) measurement are limited by the introduction of bias in their test-retest analyses. This study sought to determine the reliability of the current AMVL measurement while controlling for systematic bias. METHODS: Retrospective analysis of echocardiographic data from 16 patients with previous acute rheumatic fever was performed. Included in this study was an optimized cine loop of the mitral valve (MV) [reader-optimized measurement (ROM]) in the parasternal long-axis view and an optimized still image of the MV obtained from the same cine loop [specialist-optimized image (SOI)]. Each still image and associated cine loop was quadruplicated and randomized to determine intra- and inter-rater agreement and quantify the impact of zoom on AMVL measurement. RESULTS: Specialist-optimized image without zoom reflected the highest degree of agreement in both cohorts with an ICC of 0.29 and 0.46. The agreement in ROM images without zoom was ICC of 0.23 and 0.45. The addition of zoom to SOI decreased agreement further to an ICC of 0.20 and 0.36. The setting associated with the poorest agreement profile was ROI with zoom with an ICC of 0.13 and 0.34, respectively. The intra-rater agreement between readers in both cohorts was moderate across all settings with an ICC ranging between 0.64 and 0.86. CONCLUSIONS: The WHF AMVL measurement is only moderately repeatable within readers and demonstrates poor reproducibility that was not improved by the addition of a zoom-optimized protocol. Given our study findings, we cannot advocate the current WHF AMVL measurement as a reliable assessment for RHD.

The global decline of cheetah Acinonyx jubatus and what it means for conservation.

Establishing and maintaining protected areas (PAs) are key tools for biodiversity conservation. However, this approach is insufficient for many species, particularly those that are wide-ranging and sparse. The cheetah Acinonyx jubatus exemplifies such a species and faces extreme challenges to its survival. Here, we show that the global population is estimated at ∼7,100 individuals and confined to 9% of its historical distributional range. However, the majority of current range (77%) occurs outside of PAs, where the species faces multiple threats. Scenario modeling shows that, where growth rates are suppressed outside PAs, extinction rates increase rapidly as the proportion of population protected declines. Sensitivity analysis shows that growth rates within PAs have to be high if they are to compensate for declines outside. Susceptibility of cheetah to rapid decline is evidenced by recent rapid contraction in range, supporting an uplisting of the International Union for the Conservation of Nature (IUCN) Red List threat assessment to endangered. Our results are applicable to other protection-reliant species, which may be subject to systematic underestimation of threat when there is insufficient information outside PAs. Ultimately, conserving many of these species necessitates a paradigm shift in conservation toward a holistic approach that incentivizes protection and promotes sustainable human-wildlife coexistence across large multiple-use landscapes.

Vicinal difluorination as a C=C surrogate: an analog of piperine with enhanced solubility, photostability, and acetylcholinesterase inhibitory activity.

Piperine, a natural product derived from peppercorns, has a variety of biological activities that make it an attractive lead compound for medicinal chemistry. However, piperine has some problematic physicochemical properties including poor aqueous solubility and a susceptibility to UV-induced degradation. In this work, we designed an analog of piperine in which the central conjugated hydrocarbon chain is replaced with a vicinal difluoroalkane moiety. We show that this fluorinated analog of piperine has superior physicochemical properties, and it also has higher potency and selectivity towards one particular drug target, acetylcholinesterase. This work highlights the potential usefulness of the threo-difluoroalkane motif as a surrogate for E-alkenes in medicinal chemistry.

Correction: The value of universally available raw NMR data for transparency, reproducibility, and integrity in natural product research.

Correction for 'The value of universally available raw NMR data for transparency, reproducibility, and integrity in natural product research' by James B. McAlpine et al., Nat. Prod. Rep., 2018, DOI: .

The value of universally available raw NMR data for transparency, reproducibility, and integrity in natural product research.

Covering: up to 2018With contributions from the global natural product (NP) research community, and continuing the Raw Data Initiative, this review collects a comprehensive demonstration of the immense scientific value of disseminating raw nuclear magnetic resonance (NMR) data, independently of, and in parallel with, classical publishing outlets. A comprehensive compilation of historic to present-day cases as well as contemporary and future applications show that addressing the urgent need for a repository of publicly accessible raw NMR data has the potential to transform natural products (NPs) and associated fields of chemical and biomedical research. The call for advancing open sharing mechanisms for raw data is intended to enhance the transparency of experimental protocols, augment the reproducibility of reported outcomes, including biological studies, become a regular component of responsible research, and thereby enrich the integrity of NP research and related fields.

Tuning the properties of a cyclic RGD-containing tetrapeptide through backbone fluorination.

Stereoselective fluorination is investigated as a method for modulating the properties of a cyclic RGD-containing tetrapeptide. Three key outcomes of fluorination are assessed: (i) the effect on peptide cyclisation efficiency; (ii) the ability to fine-tune the molecular conformation; and (iii) the effect on the cyclic peptides' biological activity. Fluorination is found to exert pronounced effects against all three criteria.

Lion (Panthera leo) populations are declining rapidly across Africa, except in intensively managed areas.

We compiled all credible repeated lion surveys and present time series data for 47 lion (Panthera leo) populations. We used a Bayesian state space model to estimate growth rate-λ for each population and summed these into three regional sets to provide conservation-relevant estimates of trends since 1990. We found a striking geographical pattern: African lion populations are declining everywhere, except in four southern countries (Botswana, Namibia, South Africa, and Zimbabwe). Population models indicate a 67% chance that lions in West and Central Africa decline by one-half, while estimating a 37% chance that lions in East Africa also decline by one-half over two decades. We recommend separate regional assessments of the lion in the World Conservation Union (IUCN) Red List of Threatened Species: already recognized as critically endangered in West Africa, our analysis supports listing as regionally endangered in Central and East Africa and least concern in southern Africa. Almost all lion populations that historically exceeded ∼ 500 individuals are declining, but lion conservation is successful in southern Africa, in part because of the proliferation of reintroduced lions in small, fenced, intensively managed, and funded reserves. If management budgets for wild lands cannot keep pace with mounting levels of threat, the species may rely increasingly on these southern African areas and may no longer be a flagship species of the once vast natural ecosystems across the rest of the continent.