As the size of existing and novel chemical libraries is growing exponentially, finding new ways to leverage both legacy and enterprise information as well as existing resources and tools will become critical to ingeniously navigate and exploit these massive libraries. More often than not, new visions of evergreen tools and data infrastructures quickly become impractical in the Big Data paradigm that aims to more selectively navigate new agrochemical targets and chemical space in effective ways. Although many filtering technologies currently exist (ex. DEL, uHTS, AI/ML) to identify novel target binders/inhibitors, we are still limited in being able to pre-emptively weed out critical interactions, bad actors, and causes of attrition in agrochemical development (cost-of-goods, freedom-to-operate, agrokinetics, toxicity liabilities, environmental/ecological and human safety) early on in the discovery and development process. Advancements in this arena will provide a benefit to enhance discovery and reduce economic impacts to research and development, industry, and society. Despite the huge implications, not all of these aspects and technology of computer assisted agrochemical discovery and de-risking have come to fruition ((Figure 1)) . Here we present a workflow that comprises multiple playbooks for different strategies of the de-risking process that may hold value to agrochemical discovery and innovation. Moving in the direction of federated modeling with the use of functional playbooks and workflows can potentially eliminate some R&D bottlenecks by providing industry with increased innovation pipelines that reduce liabilities earlier in the discovery phase and provide consumers with accelerated access to safer agrochemical solutions. Figure 1 Symbolic representation of diverse focus areas of modern and computer assisted agrochemical discovery and de-risking, with emphasis on technology gaps.
A mutation analysis of SARS-CoV-2 genomes collected around the world sorted by sequence, date, geographic location, and species has revealed a large number of variants from the initial reference sequence in Wuhan. This analysis also reveals that humans infected with SARS-CoV-2 have infected mink populations in the Netherlands, Denmark, United States, and Canada. In these animals, a small set of mutations in the spike protein receptor binding domain (RBD), often occurring in specific combinations, has transferred back into humans. The viral genomic mutations in minks observed in the Netherlands and Denmark show the potential for new mutations on the SARS-CoV-2 spike protein RBD to be introduced into humans by zoonotic transfer. Our data suggests that close attention to viral transfer from humans to farm animals and pets will be required to prevent build-up of a viral reservoir for potential future zoonotic transfer.
The common aldehyde dehydrogenase 2 ( ALDH2 ) alcohol flushing variant known as ALDH2*2 affects ∼8% of the world’s population. Even in heterozygous carriers, this missense variant leads to a severe loss of ALDH2 enzymatic activity and has been linked to an increased risk of coronary artery disease (CAD). Endothelial cell (EC) dysfunction plays a determining role in all stages of CAD pathogenesis, including early-onset CAD. However, the contribution of ALDH2*2 to EC dysfunction and its relation to CAD are not fully understood. In a large genome-wide association study (GWAS) from Biobank Japan, ALDH2*2 was found to be one of the strongest single-nucleotide polymorphisms associated with CAD. Clinical assessment of endothelial function showed that human participants carrying ALDH2*2 exhibited impaired vasodilation after light alcohol drinking. Using human induced pluripotent stem cell–derived ECs (iPSC-ECs) and CRISPR-Cas9–corrected ALDH2*2 iPSC-ECs, we modeled ALDH2*2 -induced EC dysfunction in vitro, demonstrating an increase in oxidative stress and inflammatory markers and a decrease in nitric oxide (NO) production and tube formation capacity, which was further exacerbated by ethanol exposure. We subsequently found that sodium-glucose cotransporter 2 inhibitors (SGLT2i) such as empagliflozin mitigated ALDH2*2 -associated EC dysfunction. Studies in ALDH2*2 knock-in mice further demonstrated that empagliflozin attenuated ALDH2*2 -mediated vascular dysfunction in vivo. Mechanistically, empagliflozin inhibited Na + /H + -exchanger 1 (NHE-1) and activated AKT kinase and endothelial NO synthase (eNOS) pathways to ameliorate ALDH2*2 -induced EC dysfunction. Together, our results suggest that ALDH2*2 induces EC dysfunction and that SGLT2i may potentially be used as a preventative measure against CAD for ALDH2*2 carriers.
Direct-acting antivirals are needed to combat coronavirus disease 2019 (COVID-19), which is caused by severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2). The papain-like protease (PLpro) domain of Nsp3 from SARS-CoV-2 is essential for viral replication. In addition, PLpro dysregulates the host immune response by cleaving ubiquitin and interferon-stimulated gene 15 protein (ISG15) from host proteins. As a result, PLpro is a promising target for inhibition by small-molecule therapeutics. Here we have designed a series of covalent inhibitors by introducing a peptidomimetic linker and reactive electrophile onto analogs of the noncovalent PLpro inhibitor GRL0617. The most potent compound inhibited PLpro with kinact/KI = 10,000 M - 1 s - 1 , achieved sub-µM EC 50 values against three SARS-CoV-2 variants in mammalian cell lines, and did not inhibit a panel of human deubiquitinases at > 30 µM concentrations of inhibitor. An X-ray co-crystal structure of the compound bound to PLpro validated our design strategy and established the molecular basis for covalent inhibition and selectivity against structurally similar human DUBs. These findings present an opportunity for further development of covalent PLpro inhibitors.
Abstract Cardiac troponin I (cTnI) is a sarcomeric protein critical to myocyte contraction. Unexpectedly, we found that some cTnI localized to the mitochondrial matrix in the heart, inhibited mitochondrial functions when stably expressed in non-cardiac cells and increased opening of the mitochondrial permeability transition pore under oxidative stress. Direct, specific, and saturable binding of cTnI to ATP synthase was demonstrated in vitro , using immune-captured ATP synthase, and in cells using proximity ligation assay. cTnI binding doubled F 1 F 0 ATPase activity, whereas skeletal troponin I and several human mutant cTnI variants associated with familial hypertrophic cardiomyopathy did not. A rationally-designed ten amino acid peptide, P888, inhibited cTnI binding to ATP synthase, inhibited cTnI-induced increase in ATPase activity in vitro , and reduced cardiac injury following transient ischemia in vivo . We therefore suggest that mitochondria-associated cTnI may inhibit cardiac ATP synthase under basal conditions; pharmacological agents that release this inactivating effect of cTnI and thus preventing ATP hydrolysis during cardiac ischemia may increase the reservoir of functional mitochondria to reduce cardiac injury. Significance Statement Cardiac troponin I (cTnI) is a key sarcomeric protein involved in the regulation of myocardial contractility. We found that some cTnI is present in the mitochondrial matrix where it binds to ATP synthase, disrupting mitochondrial function; inhibition of the cTnI-ATP synthase interaction with a selective peptide inhibitor reduces cardiac dysfunction following ischemia and reperfusion injury. Several pathogenic cTnI mutations associated with hypertrophic cardiomyopathy do not affect ATP synthase activity, suggesting a potential mechanism that contributes to the diverse pathologies associated with these mutations.
Abstract A mutation analysis of SARS-CoV-2 genomes collected around the world sorted by sequence, date, geographic location, and species has revealed a large number of variants from the initial reference sequence in Wuhan. This analysis also reveals that humans infected with SARS-CoV-2 have infected mink populations in the Netherlands, Denmark, United States, and Canada. In these animals, a small set of mutations in the spike protein receptor binding domain (RBD), often occurring in specific combinations, has transferred back into humans. The viral genomic mutations in minks observed in the Netherlands and Denmark show the potential for new mutations on the SARS-CoV-2 spike protein RBD to be introduced into humans by zoonotic transfer. Our data suggests that close attention to viral transfer from humans to farm animals and pets will be required to prevent build-up of a viral reservoir for potential future zoonotic transfer.
COVID-19 emergency use authorizations and approvals for vaccines were achieved in record time. However, there remains a need to develop additional safe, effective, easy-to-produce, and inexpensive prevention to reduce the risk of acquiring SARS-CoV-2 infection. This need is due to difficulties in vaccine manufacturing and distribution, vaccine hesitancy, and, critically, the increased prevalence of SARS-CoV-2 variants with greater contagiousness or reduced sensitivity to immunity. Antibodies from eggs of hens (immunoglobulin Y; IgY) that were administered the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein were developed for use as nasal drops to capture the virus on the nasal mucosa. Although initially raised against the 2019 novel coronavirus index strain (2019-nCoV), these anti-SARS-CoV-2 RBD IgY surprisingly had indistinguishable enzyme-linked immunosorbent assay binding against variants of concern that have emerged, including Alpha (B.1.1.7), Beta (B.1.351), Delta (B.1.617.2), and Omicron (B.1.1.529). This is different from sera of immunized or convalescent patients. Culture neutralization titers against available Alpha, Beta, and Delta were also indistinguishable from the index SARS-CoV-2 strain. Efforts to develop these IgY for clinical use demonstrated that the intranasal anti-SARS-CoV-2 RBD IgY preparation showed no binding (cross-reactivity) to a variety of human tissues and had an excellent safety profile in rats following 28-day intranasal delivery of the formulated IgY. A double-blind, randomized, placebo-controlled phase 1 study evaluating single-ascending and multiple doses of anti-SARS-CoV-2 RBD IgY administered intranasally for 14 days in 48 healthy adults also demonstrated an excellent safety and tolerability profile, and no evidence of systemic absorption. As these antiviral IgY have broad selectivity against many variants of concern, are fast to produce, and are a low-cost product, their use as prophylaxis to reduce SARS-CoV-2 viral transmission warrants further evaluation.https://www.clinicaltrials.gov/ct2/show/NCT04567810, identifier NCT04567810.
The heart relies on mitochondria for its extensive energetic demands, and some cytoskeletal elements can regulate mitochondrial function. Cardiac troponin I (cTnI) is a structural protein involved in sarcomeric contraction. Here we demonstrate that some cTnI localizes to mitochondria, inhibits mitochondrial functions, and increases opening of the mitochondrial permeability transition pore under oxidative stress. Purified cTnI directly binds immune-captured ATP synthase in saturable fashion and doubles "reverse" F 1 F 0 -ATPase activity in vitro , whereas skeletal troponin I (ssTnI) does not. Relevant to human disease, several pathogenic variants of cTnI associated with hypertrophic cardiomyopathy do not increase F 1 F 0 -ATPase activity. Using a rational search, we identified the d subunit of ATP synthase as a potential cTnI-binding partner, and a ten-amino acid peptide inhibitor of cTnI’s interaction with ATP synthase, peptide P888, inhibited cTnI binding to ATP synthase and abolished the cTnI-induced increase in ATPase activity. P888 treatment greatly reduced cardiac LDH release and improved fractional shortening in vivo after transient coronary artery occlusion in rats, indicating that mitochondrial cTnI exacerbates cardiac ischemia-reperfusion injury. We explore the mechanisms governing cTnI’s mitochondrial localization and additional mitochondrial binding partners for cTnI. Together, our studies suggest that mitochondria-associated cTnI inhibits ATP synthase under basal conditions. Preventing cTnI from binding to ATP synthase during cardiac ischemia may increase the reservoir of functional mitochondria to mitigate post-ischemic cardiac injury. We also suggest that cTnI has additional roles in regulating mitochondrial functions. Finally, pathogenic cTnI mutations associated with hypertrophic cardiomyopathy do not affect ATP synthase activity, suggesting a potential mechanism that contributes to the diverse pathologies associated with these mutations.
Significance Of all cyanobacteria on Earth, marine Synechococcus are those displaying the greatest pigment diversity. The most sophisticated pigment type is cells able to reversibly modify their color by a phenomenon called type IV chromatic acclimation or CA4. Two genetically distinct CA4 types (CA4-A and CA4-B) have evolved in different lineages. Together, they represent almost half of all Synechococcus cells in oceanic areas and are equally abundant but occupy complementary ecological niches. While the molecular mechanism of CA4-A has recently started to be deciphered, the CA4-B mechanism was so far uncharacterized. Here, by unveiling this mechanism and demonstrating its singularity relative to CA4-A, we provide highlights on the evolutionary history of Synechococcus acclimation to light color in the oceans.
