Antiviral Approaches against Influenza Virus.

Preventing and controlling influenza virus infection remains a global public health challenge, as it causes seasonal epidemics to unexpected pandemics. These infections are responsible for high morbidity, mortality, and substantial economic impact. Vaccines are the prophylaxis mainstay in the fight against influenza. However, vaccination fails to confer complete protection due to inadequate vaccination coverages, vaccine shortages, and mismatches with circulating strains. Antivirals represent an important prophylactic and therapeutic measure to reduce influenza-associated morbidity and mortality, particularly in high-risk populations. Here, we review current FDA-approved influenza antivirals with their mechanisms of action, and different viral- and host-directed influenza antiviral approaches, including immunomodulatory interventions in clinical development. Furthermore, we also illustrate the potential utility of machine learning in developing next-generation antivirals against influenza.

Differences in prescribing patterns of opioid dependence drugs among patients with primary alcohol use problems and opioid use disorders within New York State by social determinant factors, 2005-2018.

BACKGROUND: The increase in alcohol use problems and opioid use disorder (OUD) highlights the need for research on effective medication treatments for patients with dual diagnoses. OBJECTIVES: This study analyzed trends and social disparities in prescribing OUD medications for patients who initially had alcohol use problems and later received their first OUD diagnosis. METHODS: This study utilized merged data from the New York State Office of Addiction Services and Supports and the Medicaid to analyze individuals aged 18 and older who initially had primary alcohol use problems and later had OUD for the first time between 2005 and 2018. It examined the rates of new buprenorphine and naltrexone prescriptions across various demographic and socioeconomic groups. RESULTS: Among 27,029 clients, the average rate of new buprenorphine was 64.23 per 1,000 clients (95% CI [61.30, 67.15]), with upward trends. The 18-35 age group had the highest buprenorphine utilization (111.48 per 1,000 clients), and highest increase rates compared to other age groups. The White non-Hispanic group had the highest rates of buprenorphine (119.23 per 1000 clients) and showed larger increase over time compared to other race/ethnicity groups. Disabled patients showed slower increasing rates of buprenorphine compared to other groups. Upward trends were observed in naltrexone. All observed differences were statistically significant (P<0.05). CONCLUSIONS: Trends showed increased use of OUD medications, with varying rates of buprenorphine utilization across different ages, races, and employment statuses. Despite this, the rates of receiving new buprenorphine remained low, suggesting a need for innovative methods to expand access to treatments.

Trends in Prescribing Opioids, Benzodiazepines, and Both Among Adults with Alcohol Use Disorder in New York State.

BACKGROUND: Alcohol use disorder (AUD) is a highly prevalent public health problem that contributes to opioid- and benzodiazepine-related morbidity and mortality. Even though co-utilization of these substances is particularly harmful, data are sparse on opioid or benzodiazepine prescribing patterns among individuals with AUD. OBJECTIVE: To estimate temporal trends and disparities in opioid, benzodiazepine, and opioid/benzodiazepine co-prescribing among individuals with AUD in New York State (NYS). DESIGN/PARTICIPANTS: Serial cross-sectional study analyzing merged data from the NYS Office of Addiction Services and Supports (OASAS) and the NYS Department of Health Medicaid Data Warehouse. Subjects with a first admission to an OASAS treatment program from 2005-2018 and a primary AUD were included. A total of 148,328 subjects were identified. MEASURES: Annual prescribing rates of opioids, benzodiazepines, or both between the pre- (2005-2012) and post- (2013-2018) Internet System for Tracking Over-Prescribing (I-STOP) periods. I-STOP is a prescription monitoring program implemented in NYS in August 2013. Analyses were stratified based on sociodemographic factors (age, sex, race/ethnicity, and location). RESULTS: Opioid prescribing rates decreased between the pre- and post-I-STOP periods from 25.1% (95% CI, 24.9-25.3%) to 21.3% (95% CI, 21.2-21.4; P <.001), while benzodiazepine (pre: 9.96% [95% CI, 9.83-10.1%], post: 9.92% [95% CI, 9.83-10.0%]; P =.631) and opioid/benzodiazepine prescribing rates remained unchanged (pre: 3.01% vs. post: 3.05%; P =.403). After I-STOP implementation, there was a significant decreasing trend in opioid (change, -1.85% per year, P <.0001), benzodiazepine (-0.208% per year, P =.0184), and opioid/benzodiazepine prescribing (-0.267% per year, P <.0001). Opioid, benzodiazepine, and co-prescription rates were higher in females, White non-Hispanics, and rural regions. CONCLUSIONS: Among those with AUD, opioid prescribing decreased following NYS I-STOP program implementation. While both benzodiazepine and opioid/benzodiazepine co-prescribing rates remained high, a decreasing trend was evident after program implementation. Continuing high rates of opioid and benzodiazepine prescribing necessitate the development of innovative approaches to improve the quality of care.

A cohort of patients in New York State with an alcohol use disorder and subsequent treatment information - A merging of two administrative data sources.

OBJECTIVE: Despite the high prevalence of alcohol use disorder (AUD) in the United States, limited research is focused on the associations among AUD, pain, and opioids/benzodiazepine use. In addition, little is known regarding individuals with a history of AUD and their potential risk for pain diagnoses, pain prescriptions, and subsequent misuse. Moreover, the potential risk of pain diagnoses, prescriptions, and subsequent misuse among individuals with a history of AUD is not well known. The objective was to develop a tailored dataset by linking data from 2 New York State (NYS) administrative databases to investigate a series of hypotheses related to AUD and painful medical disorders. METHODS: Data from the NYS Office of Addiction Services and Supports (OASAS) Client Data System (CDS) and Medicaid claims data from the NYS Department of Health Medicaid Data Warehouse (MDW) were merged using a stepwise deterministic method. Multiple patient-level identifier combinations were applied to create linkage rules. We included patients aged 18 and older from the OASAS CDS who initially entered treatment with a primary substance use of alcohol and no use of opioids between January 1, 2003, and September 23, 2019. This cohort was then linked to corresponding Medicaid claims. RESULTS: A total of 177,685 individuals with a primary AUD problem and no opioid use history were included in the dataset. Of these, 37,346 (21.0%) patients had an OUD diagnosis, and 3,365 (1.9%) patients experienced an opioid overdose. There were 121,865 (68.6%) patients found to have a pain condition. CONCLUSION: The integrated database allows researchers to examine the associations among AUD, pain, and opioids/benzodiazepine use, and propose hypotheses to improve outcomes for at-risk patients. The findings of this study can contribute to the development of a prognostic prediction model and the analysis of longitudinal outcomes to improve the care of patients with AUD.

Multiscale Analysis and Validation of Effective Drug Combinations Targeting Driver KRAS Mutations in Non-Small Cell Lung Cancer.

Pharmacogenomics is a rapidly growing field with the goal of providing personalized care to every patient. Previously, we developed the Computational Analysis of Novel Drug Opportunities (CANDO) platform for multiscale therapeutic discovery to screen optimal compounds for any indication/disease by performing analytics on their interactions using large protein libraries. We implemented a comprehensive precision medicine drug discovery pipeline within the CANDO platform to determine which drugs are most likely to be effective against mutant phenotypes of non-small cell lung cancer (NSCLC) based on the supposition that drugs with similar interaction profiles (or signatures) will have similar behavior and therefore show synergistic effects. CANDO predicted that osimertinib, an EGFR inhibitor, is most likely to synergize with four KRAS inhibitors.Validation studies with cellular toxicity assays confirmed that osimertinib in combination with ARS-1620, a KRAS G12C inhibitor, and BAY-293, a pan-KRAS inhibitor, showed a synergistic effect on decreasing cellular proliferation by acting on mutant KRAS. Gene expression studies revealed that MAPK expression is strongly correlated with decreased cellular proliferation following treatment with KRAS inhibitor BAY-293, but not treatment with ARS-1620 or osimertinib. These results indicate that our precision medicine pipeline may be used to identify compounds capable of synergizing with inhibitors of KRAS G12C, and to assess their likelihood of becoming drugs by understanding their behavior at the proteomic/interactomic scales.

Identifying Protein Features and Pathways Responsible for Toxicity Using Machine Learning and Tox21: Implications for Predictive Toxicology.

Humans are exposed to numerous compounds daily, some of which have adverse effects on health. Computational approaches for modeling toxicological data in conjunction with machine learning algorithms have gained popularity over the last few years. Machine learning approaches have been used to predict toxicity-related biological activities using chemical structure descriptors. However, toxicity-related proteomic features have not been fully investigated. In this study, we construct a computational pipeline using machine learning models for predicting the most important protein features responsible for the toxicity of compounds taken from the Tox21 dataset that is implemented within the multiscale Computational Analysis of Novel Drug Opportunities (CANDO) therapeutic discovery platform. Tox21 is a highly imbalanced dataset consisting of twelve in vitro assays, seven from the nuclear receptor (NR) signaling pathway and five from the stress response (SR) pathway, for more than 10,000 compounds. For the machine learning model, we employed a random forest with the combination of Synthetic Minority Oversampling Technique (SMOTE) and the Edited Nearest Neighbor (ENN) method (SMOTE+ENN), which is a resampling method to balance the activity class distribution. Within the NR and SR pathways, the activity of the aryl hydrocarbon receptor (NR-AhR) and the mitochondrial membrane potential (SR-MMP) were two of the top-performing twelve toxicity endpoints with AUCROCs of 0.90 and 0.92, respectively. The top extracted features for evaluating compound toxicity were analyzed for enrichment to highlight the implicated biological pathways and proteins. We validated our enrichment results for the activity of the AhR using a thorough literature search. Our case study showed that the selected enriched pathways and proteins from our computational pipeline are not only correlated with AhR toxicity but also form a cascading upstream/downstream arrangement. Our work elucidates significant relationships between protein and compound interactions computed using CANDO and the associated biological pathways to which the proteins belong for twelve toxicity endpoints. This novel study uses machine learning not only to predict and understand toxicity but also elucidates therapeutic mechanisms at a proteomic level for a variety of toxicity endpoints.

cando.py: Open Source Software for Predictive Bioanalytics of Large Scale Drug-Protein-Disease Data.

Traditional drug discovery methods focus on optimizing the efficacy of a drug against a single biological target of interest for a specific disease. However, evidence supports the multitarget theory, i.e., drugs work by exerting their therapeutic effects via interaction with multiple biological targets, which have multiple phenotypic effects. Analytics of drug-protein interactions on a large proteomic scale provides insight into disease systems while also allowing for prediction of putative therapeutics against specific indications. We present a Python package for analysis of drug-proteome and drug-disease relationships implementing the Computational Analysis of Novel Drug Opportunities (CANDO) platform. The CANDO package allows for rapid drug similarity assessment, most notably via an in-house interaction scoring protocol where billions of drug-protein interactions are rapidly scored and the similarity of drug-proteome interaction signatures is calculated. The package also implements a variety of benchmarking protocols for shotgun drug discovery and repurposing, i.e., to determine how every known drug is related to every other in the context of the indications/diseases for which they are approved. Drug predictions are generated through consensus scoring of the most similar compounds to drugs known to treat a particular indication. Support for comparing and ranking novel chemical entities, as well as machine learning modules for both benchmarking and putative drug candidate prediction is also available. The CANDO Python package is available on GitHub at https://github.com/ram-compbio/CANDO, through the Conda Python package installer, and at http://compbio.org/software/.

Decomposition Products of Phosphine Under Pressure: PH2 Stable and Superconducting?

Evolutionary algorithms (EAs) coupled with density functional theory (DFT) calculations have been used to predict the most stable hydrides of phosphorus (PHn, n = 1-6) at 100, 150, and 200 GPa. At these pressures phosphine is unstable with respect to decomposition into the elemental phases, as well as PH2 and H2. Three metallic PH2 phases were found to be dynamically stable and superconducting between 100 and 200 GPa. One of these contains five formula units in the primitive cell and has C2/m symmetry (5FU-C2/m). It comprises 1D periodic PH3-PH-PH2-PH-PH3 oligomers. Two structurally related phases consisting of phosphorus atoms that are octahedrally coordinated by four phosphorus atoms in the equatorial positions and two hydrogen atoms in the axial positions (I4/mmm and 2FU-C2/m) were the most stable phases between ∼160-200 GPa. Their superconducting critical temperatures (Tc) were computed as 70 and 76 K, respectively, via the Allen-Dynes modified McMillan formula and using a value of 0.1 for the Coulomb pseudopotential, µ*. Our results suggest that the superconductivity recently observed by Drozdov, Eremets, and Troyan when phosphine was subject to pressures of 207 GPa in a diamond anvil cell may result from these, and other, decomposition products of phosphine.

Computational prediction and analysis of the (27)Al solid-state NMR spectrum of methylaluminoxane (MAO) at variable temperatures and field strengths.

Calculations of NMR shielding tensors and nuclear quadrupole coupling (NQC) tensors at the Kohn-Sham density functional level are used to simulate (27)Al magic-angle spinning (MAS) NMR spectra of the important olefin polymerization co-catalyst methylaluminoxane (MAO) at 77, 298, 398, and 498 K and spectrometer magnetic field inductions B ranging from 14.1 to 23.5 T. The calculations utilize the temperature (T) dependent distribution of species present in MAO determined recently by Zurek and coworkers from first-principles theory [Macromolecules, 2014, 47, 8556]. The NMR calculations suggest that variable-T and variable-B NMR measurements are able to quantify the ratio of free versus bound trimethyl-aluminum (TMA) in MAO via characteristic spectral features assigned to 3-coordinate and 4-coordinate Al sites in MAO as well as spectral features arising from free TMA or its dimer. The T-dependent distribution of species causes other characteristic features in the NMR spectra to appear/disappear that can be associated with different aluminum environments such as square vs. hexagonal faces in cage and tubular structures. The simulated spectra at 298 K and 19.6 T are in reasonably good agreement with the experimental solid-state NMR (SSNMR) spectra obtained previously for MAO gel. The promise and limitations of solid-state NMR to unravel the enigma surrounding the structure(s) of MAO are discussed.

High-risk use of prescription opioids among patients treated for alcohol problems in New York State. A repeated cross-sectional study, 2005-2018.

Background: Patients with alcohol use disorder (AUD) and high-risk opioid use are at risk of serious complications. The purpose of this study was to estimate the prevalence of and factors associated with high-risk opioid use in patients with an alcohol use problem from 2005 to 2018. Methods: This repeated cross-sectional study analyzed data from first admissions for alcohol treatment (2005-2018) to the NYS Office of Addiction Services and Supports merged with Medicaid Claims Data. High-risk opioid use was defined as opioid dose ≥50 morphine mg equivalents (MME) per day; opioid prescriptions overlapping ≥7 days; opioids for chronic pain >90 days or opioids for acute pain >7 days. Results: Patients receiving ≥50 MME increased from 690 to 3226 from 2005 to 2010; then decreased to 2330 in 2018. From 2005-2011, patients with opioid prescriptions overlapping ≥7 days increased from 226 to 1594 then decreased to 892 in 2018. From 2005-2010, opioid use >7 days for acute pain increased from 133 to 970 and plateaued after 2010. From 2005-2018, patients who received opioids >90 days for chronic pain trended from 186 to 1655. White patients, females, age 36-55, patients with chronic and acute pain diagnoses had the highest rates of high-risk use. Conclusions: The prevalence of high-risk opioid use in patients with alcohol use problems increased from 2005 to 2011, and generally decreased after 2010. However, prevalence of opioids >90 days for chronic pain trended up from 2005 to 2018. High-risk opioid use among patients with AUD emphasizes the need to develop interventional strategies to improve patient care.

Incidence, Timing and Social Correlates of the Development of Opioid Use Disorder Among Clients Seeking Treatment for an Alcohol Use Problem: Changes Over the Three Waves of the Opioid Epidemic.

Introduction: Opioid use disorder (OUD) and opioid overdose (OD) have shown to be strongly associated with alcohol use disorder (AUD). As a potential target population for secondary prevention, we examined the incidence and timing of OUD/OD among clients seeking treatment for alcohol problems and how this has changed over the three waves of the opioid epidemic corresponding to the primary opioid involved in fatal ODs, prescription painkillers (2007-2009), heroin (2010-2012), and fentanyl (2013-2016). We also examined social determinants of health as predictors of OUD/OD. Methods: Clients (N = 59,186) presenting for a first treatment for alcohol use problems were extracted from the Client Data System (CDS) of the New York State Office of Addiction Services and Support (OASAS) and New York State (NYS) Medicaid Data Warehouse. Using this cohort, we employed the Kaplan-Meier method to determine the survival probabilities for patients admitted in each of the three waves of the epidemic. Results: Patients in Cohort 3 (2013-2016) were diagnosed with OUD/OD more rapidly than patients in Cohort 1 (2007-2009) or Cohort 2 (2010-2012), although the overall estimated OUD/OD rate was comparable across the three cohorts. Discussion: These findings provide a useful estimate of the incidence and the expected time frame of an opioid use disorder in clients with an alcohol use problem. Moreover, it suggests that as the opioid epidemic progressed, OUD/OD developed more rapidly but the overall prevalence did not increase.

The Effect of Antidepressants on Withdrawal in Patients with Alcohol Dependence: A Retrospective Study.

The use of electronic health records has expanded in the past decades, with healthcare entities storing terabytes of patient health data. In this study, we investigated how these databases can be utilized to generate clinically relevant information. We used the Office of Addiction Services and Supports Client Data Systems data merged with the NYS Medicaid Data Warehouse to study the relationship of certain antidepressants on alcohol withdrawal (AW) rates in patients with alcohol dependence (AD). We found that in patients with AD, bupropion was associated with a significantly reduced rate of AW compared to selective serotonin reuptake inhibitors (SSRIs). This may be due to the ability of bupropion to inhibit dopaminergic reuptake. This retrospective study provides the advantage of being faster and less expensive than randomized controlled trials (RCTs).

The implications of APOBEC3-mediated C-to-U RNA editing for human disease.

Intra-organism biodiversity is thought to arise from epigenetic modification of constituent genes and post-translational modifications of translated proteins. Here, we show that post-transcriptional modifications, like RNA editing, may also contribute. RNA editing enzymes APOBEC3A and APOBEC3G catalyze the deamination of cytosine to uracil. RNAsee (RNA site editing evaluation) is a computational tool developed to predict the cytosines edited by these enzymes. We find that 4.5% of non-synonymous DNA single nucleotide polymorphisms that result in cytosine to uracil changes in RNA are probable sites for APOBEC3A/G RNA editing; the variant proteins created by such polymorphisms may also result from transient RNA editing. These polymorphisms are associated with over 20% of Medical Subject Headings across ten categories of disease, including nutritional and metabolic, neoplastic, cardiovascular, and nervous system diseases. Because RNA editing is transient and not organism-wide, future work is necessary to confirm the extent and effects of such editing in humans.

Building Chemical Intuition about Physicochemical Properties of C8-Per-/Polyfluoroalkyl Carboxylic Acids through Computational Means.

We have predicted acid dissociation constants (pK a), octanol-water partition coefficients (K OW), and DMPC lipid membrane-water partition coefficients (K lipid-w) of 150 different eight-carbon-containing poly-/perfluoroalkyl carboxylic acids (C8-PFCAs) utilizing the COnductor-like Screening MOdel for Realistic Solvents (COSMO-RS) theory. Different trends associated with functionalization, degree of fluorination, degree of saturation, degree of chlorination, and branching are discussed on the basis of the predicted values for the partition coefficients. In general, functionalization closest to the carboxylic headgroup had the greatest impact on the value of the predicted physicochemical properties.

Determination of the structures of molecularly imprinted polymers and xerogels using an automated stochastic approach.

An automated stochastic docking program with a graphical user interface, RANDOMDOCK (RD), has been developed to aid the development of molecularly imprinted polymers and xerogels. RD supports computations with ab initio and semiempirical quantum chemistry programs. The RD algorithms have been tested by searching for the most stable geometries of a varying number of methacrylic acid molecules interacting with nicotinamide. The optimal structures found are either as stable or more stable than those previously proposed for this molecularly imprinted polymer, illustrating that RD is capable of identifying the lowest-energy structures out of a potentially vast number of possible configurations. RD was subsequently applied to determine the most favorable binding sites between silane molecules and tetracycline (TC) as well as TC analogues. Hydrogen bonding between the templates and a silane is an important determinant of stability. Dispersion interactions are also sizable, sometimes dominant, especially between the largest silane and TC analogues not possessing a site readily available for hydrogen bonding. We highlight the importance of exploring the full intermolecular potential energy landscape when studying systems which may not afford highly specific interactions.

Effective holistic characterization of small molecule effects using heterogeneous biological networks.

The two most common reasons for attrition in therapeutic clinical trials are efficacy and safety. We integrated heterogeneous data to create a human interactome network to comprehensively describe drug behavior in biological systems, with the goal of accurate therapeutic candidate generation. The Computational Analysis of Novel Drug Opportunities (CANDO) platform for shotgun multiscale therapeutic discovery, repurposing, and design was enhanced by integrating drug side effects, protein pathways, protein-protein interactions, protein-disease associations, and the Gene Ontology, and complemented with its existing drug/compound, protein, and indication libraries. These integrated networks were reduced to a "multiscale interactomic signature" for each compound that describe its functional behavior as vectors of real values. These signatures are then used for relating compounds to each other with the hypothesis that similar signatures yield similar behavior. Our results indicated that there is significant biological information captured within our networks (particularly via side effects) which enhance the performance of our platform, as evaluated by performing all-against-all leave-one-out drug-indication association benchmarking as well as generating novel drug candidates for colon cancer and migraine disorders corroborated via literature search. Further, drug impacts on pathways derived from computed compound-protein interaction scores served as the features for a random forest machine learning model trained to predict drug-indication associations, with applications to mental disorders and cancer metastasis highlighted. This interactomic pipeline highlights the ability of Computational Analysis of Novel Drug Opportunities to accurately relate drugs in a multitarget and multiscale context, particularly for generating putative drug candidates using the information gleaned from indirect data such as side effect profiles and protein pathway information.

The Role of C-to-U RNA Editing in Human Biodiversity.

Intra-organism biodiversity is thought to arise from epigenetic modification of our constituent genes and post-translational modifications after mRNA is translated into proteins. We have found that post-transcriptional modification, also known as RNA editing, is also responsible for a significant amount of our biodiversity, substantively expanding this story. The APOBEC (apolipoprotein B mRNA editing catalytic polypeptide-like) family RNA editing enzymes APOBEC3A and APOBEC3G catalyze the deamination of cytosines to uracils (C>U) in specific stem-loop structures.1,2 We used RNAsee (RNA site editing evaluation), a tool developed to predict the locations of APOBEC3A/G RNA editing sites, to determine whether known single nucleotide polymorphisms (SNPs) in DNA could be replicated in RNA via RNA editing. About 4.5% of non-synonymous SNPs which result in C>U changes in RNA, and about 5.4% of such SNPs labelled as pathogenic, were identified as probable sites for APOBEC3A/G editing. This suggests that the variant proteins created by these DNA mutations may also be created by transient RNA editing, with the potential to affect human health. Those SNPs identified as potential APOBEC3A/G-mediated RNA editing sites were disproportionately associated with cardiovascular diseases, digestive system diseases, and musculoskeletal diseases. Future work should focus on common sites of RNA editing, any variant proteins created by these RNA editing sites, and the effects of these variants on protein diversity and human health. Classically, our biodiversity is thought to come from our constitutive genetics, epigenetic phenomenon, transcriptional differences, and post-translational modification of proteins. Here, we have shown evidence that RNA editing, often stimulated by environmental factors, could account for a significant degree of the protein biodiversity leading to human disease. In an era where worries about our changing environment are ever increasing, from the warming of our climate to the emergence of new diseases to the infiltration of microplastics and pollutants into our bodies, understanding how environmentally sensitive mechanisms like RNA editing affect our own cells is essential.

Optimal COVID-19 therapeutic candidate discovery using the CANDO platform.

The worldwide outbreak of SARS-CoV-2 in early 2020 caused numerous deaths and unprecedented measures to control its spread. We employed our Computational Analysis of Novel Drug Opportunities (CANDO) multiscale therapeutic discovery, repurposing, and design platform to identify small molecule inhibitors of the virus to treat its resulting indication, COVID-19. Initially, few experimental studies existed on SARS-CoV-2, so we optimized our drug candidate prediction pipelines using results from two independent high-throughput screens against prevalent human coronaviruses. Ranked lists of candidate drugs were generated using our open source cando.py software based on viral protein inhibition and proteomic interaction similarity. For the former viral protein inhibition pipeline, we computed interaction scores between all compounds in the corresponding candidate library and eighteen SARS-CoV proteins using an interaction scoring protocol with extensive parameter optimization which was then applied to the SARS-CoV-2 proteome for prediction. For the latter similarity based pipeline, we computed interaction scores between all compounds and human protein structures in our libraries then used a consensus scoring approach to identify candidates with highly similar proteomic interaction signatures to multiple known anti-coronavirus actives. We published our ranked candidate lists at the very beginning of the COVID-19 pandemic. Since then, 51 of our 276 predictions have demonstrated anti-SARS-CoV-2 activity in published clinical and experimental studies. These results illustrate the ability of our platform to rapidly respond to emergent pathogens and provide greater evidence that treating compounds in a multitarget context more accurately describes their behavior in biological systems.

Evaluating the performance of drug-repurposing technologies.

Drug-repurposing technologies are growing in number and maturing. However, comparisons to each other and to reality are hindered because of a lack of consensus with respect to performance evaluation. Such comparability is necessary to determine scientific merit and to ensure that only meaningful predictions from repurposing technologies carry through to further validation and eventual patient use. Here, we review and compare performance evaluation measures for these technologies using version 2 of our shotgun repurposing Computational Analysis of Novel Drug Opportunities (CANDO) platform to illustrate their benefits, drawbacks, and limitations. Understanding and using different performance evaluation metrics ensures robust cross-platform comparability, enabling us to continue to strive toward optimal repurposing by decreasing the time and cost of drug discovery and development.

Proteomic Network Analysis of Bronchoalveolar Lavage Fluid in Ex-Smokers to Discover Implicated Protein Targets and Novel Drug Treatments for Chronic Obstructive Pulmonary Disease.

Bronchoalveolar lavage of the epithelial lining fluid (BALF) can sample the profound changes in the airway lumen milieu prevalent in chronic obstructive pulmonary disease (COPD). We compared the BALF proteome of ex-smokers with moderate COPD who are not in exacerbation status to non-smoking healthy control subjects and applied proteome-scale translational bioinformatics approaches to identify potential therapeutic protein targets and drugs that modulate these proteins for the treatment of COPD. Proteomic profiles of BALF were obtained from (1) never-smoker control subjects with normal lung function (n = 10) or (2) individuals with stable moderate (GOLD stage 2, FEV1 50−80% predicted, FEV1/FVC < 0.70) COPD who were ex-smokers for at least 1 year (n = 10). After identifying potential crucial hub proteins, drug−proteome interaction signatures were ranked by the computational analysis of novel drug opportunities (CANDO) platform for multiscale therapeutic discovery to identify potentially repurposable drugs. Subsequently, a literature-based knowledge graph was utilized to rank combinations of drugs that most likely ameliorate inflammatory processes. Proteomic network analysis demonstrated that 233 of the >1800 proteins identified in the BALF were significantly differentially expressed in COPD versus control. Functional annotation of the differentially expressed proteins was used to detail canonical pathways containing the differential expressed proteins. Topological network analysis demonstrated that four putative proteins act as central node proteins in COPD. The drugs with the most similar interaction signatures to approved COPD drugs were extracted with the CANDO platform. The drugs identified using CANDO were subsequently analyzed using a knowledge-based technique to determine an optimal two-drug combination that had the most appropriate effect on the central node proteins. Network analysis of the BALF proteome identified critical targets that have critical roles in modulating COPD pathogenesis, for which we identified several drugs that could be repurposed to treat COPD using a multiscale shotgun drug discovery approach.