Future Drug Research Articles

Strategic behavior and entry deterrence by branded drug firms: the case of authorized generic drugs.

Pharmaceutical firms that market brand-name drugs lose substantial market share to generic manufacturers after patent expiration. As a response to the threat of generic competition, branded manufacturers pursue defensive strategies. One such strategy is the launch of authorized generic drugs. Authorized generic drugs are produced by branded manufacturers to compete against other generic drug entrants. Such competition may lower the expected profits of generic drug manufacturers and hence deter future generic drug entry. This paper models and empirically examines whether the introduction of authorized generic drugs changes the independent generic firms' decisions on entering the market. We use an instrumental variable approach to evaluate the effect of authorized generic drugs on the responses of generic manufacturers. The results show that the entry of authorized generic drugs deters and delays the entry of generic drugs.

An Advanced Mechanically Active Osteoarthritis-on-Chip Model to Test Injectable Therapeutic Formulations: The SYN321 Case Study.

Current treatments for osteoarthritis (OA) often fail to address the underlying pathophysiology and may have systemic side effects, particularly associated with long-term use of non-steroidal anti-inflammatory drugs (NSAIDs). Thus, researchers are currently directing their efforts toward innovative polymer-drug combinations, such as mixtures of hyaluronic acid viscoelastic hydrogels and NSAIDs like diclofenac, to ensure sustained release of the NSAID within the joint following intra-articular injection. However, the progress of novel injectable therapies for OA is hindered by the absence of preclinical models that accurately represent the pathology of the disease. The uBeat® MultiCompress platform is here presented as a novel approach for studying anti-OA injectable therapeutics on human mechanically-damaged OA cartilage microtissues, in a physiologically relevant environment. This platform can accommodate injectable therapeutic formulations and is successfully tested with SYN321, a novel diclofenac-sodium hyaluronate conjugate under development as a treatment for knee OA. Results indicate the platform's effectiveness in evaluating therapeutic potential, showing downregulation of inflammatory markers and reduction in matrix degradation in OA cartilage micro-tissues treated with SYN321. The uBeat® MultiCompress platform thus represents a valuable tool for OA research, offering a bridge between traditional in vitro studies and potential clinical applications, with implications for future drug discovery.

Fungal endophytes isolated from Withania somnifera Markedly exhibit antitumor activity against human glioblastoma

In the current study, five fungal endophytes (WR-1, WR-2, WR-3, WR-4, WS-6) were isolated from the roots and stem of Withania somnifera (L.) Dunal, and tested fungal culture filtrates (FCF) against the brain tumour (glioblastoma) cell line (U-87). All FCFs showed anti-tumour activity with an IC50 value of 3.5, 6.0, 3.2, 6.0, and 0.95 µg/mL, respectively. HPLC fractionation of WS-6 showed the presence of 11 compounds (A1–A11), all with good anti-tumour activities (IC 50 3.5, 5.0, 5.0, 3.6, 2.5, 1.7, 2.3, 2.7, 0.9, 1.8 and 0.4 µg/mL, respectively). We report for the first time, the anti-tumour activity of 1-Docosene, Phenol, 2,4-bis(1,1-dimethylethyl), 1,2-Benzenedicarboxylic acid, diisooctyl ester, Hexadecane, 1,1-bis(dodecyloxy)-, Benzene, 1,1'-(2-methyl-2-(phenylthio)cyclopropylidene) bis-, Naphthalene, 1,2-dihydro-1-phenyl- (A1–A6), identified by GC-MS. The rest (A7–A11) had earlier reports of anticancer activities on cell lines other than U-87. We conclude that endophytic WS-6 (Aspergillus fumigatus) produces antitumor compounds that might be helpful in future drug development against brain tumours, especially glioblastoma.

Molecular toxicological prediction of the ethanolic extract of the species Siparuna guianensis

The species Siparuna guianensis has anti-inflammatory, analgesic and anti-infectious potential, but there is a lack of safety and toxicity parameters for the medicinal use of the plant. The aim of this study was to identify the phytochemical compounds and carry out the molecular toxicological prediction of the ethanolic extract of the species Siparuna guianensis. The ethanolic extract of the leaves of S. guianensis was obtained and GC-MS gas chromatography was carried out to identify the secondary metabolites, for subsequent quantification of the in silico toxicological properties in terms of carcinogenicity in rodents, Ames mutagenicity, eye irritation, skin irritation and sensitization. The molecules 2-undecanone, decanoic acid, ethyl ester of decanoic acid and 2-tetradecanone were the most satisfactory, with no risk of carcinogenicity in female mice, mutagenicity, skin sensitization or eye irritation, which suggests that the plant could be a promising and safe source for the development of future drugs with low toxicological potential.

Atomistic simulations reveal impacts of missense mutations on the structure and function of SynGAP1.

De novo mutations in the synaptic GTPase activating protein (SynGAP) are associated with neurological disorders like intellectual disability, epilepsy, and autism. SynGAP is also implicated in Alzheimer's disease and cancer. Although pathogenic variants are highly penetrant in neurodevelopmental conditions, a substantial number of them are caused by missense mutations that are difficult to diagnose. Hence, in silico mutagenesis was performed for probing the missense effects within the N-terminal region of SynGAP structure. Through extensive molecular dynamics simulations, encompassing three 150-ns replicates for 211 variants, the impact of missense mutations on the protein fold was assessed. The effect of the mutations on the folding stability was also quantitatively assessed using free energy calculations. The mutations were categorized as potentially pathogenic or benign based on their structural impacts. Finally, the study introduces wild-type-SynGAP in complex with RasGTPase at the inner membrane, while considering the potential effects of mutations on these key interactions. This study provides structural perspective to the clinical assessment of SynGAP missense variants and lays the foundation for future structure-based drug discovery.

Perspectives on drug development in chronic myelomonocytic leukemia: changing the paradigm

AbstractDrug development for chronic myelomonocytic leukemia (CMML) has failed to parallel the recent success observed in related myeloid neoplasms. To address these shortcomings, the US Food and Drug Administration (FDA) held a “Mini-symposium on CMML: Current State of the Art and Trial Design” in September 2023. This symposium brought together a panel of key FDA regulators and academic experts in CMML drug development to discuss challenges and provide perspectives on future drug development for this disease. The panel explored unique challenges that underlie the lack of therapeutic advances in CMML to date and discussed relevant topics such as clinical trial design, study end points, and key regulatory considerations. This article summarizes the key points of discussion from this symposium to facilitate advancements in the field.

Hederagenin inhibits mitochondrial damage in Parkinson’s disease via mitophagy induction

BackgroundParkinson's disease (PD) is a neurodegenerative disorder marked by the loss of dopaminergic neurons and the formation of α-synuclein aggregates. Mitochondrial dysfunction and oxidative stress are pivotal in PD pathogenesis, with impaired mitophagy contributing to the accumulation of mitochondrial damage. Hederagenin (Hed), a natural triterpenoid, has shown potential neuroprotective effects; however, its mechanisms of action in PD models are not fully understood. MethodWe investigated the effects of Hed on 6-hydroxydopamine (6-OHDA)-induced cytotoxicity in SH-SY5Y cells by assessing cell viability, mitochondrial function, and oxidative stress markers. Mitophagy induction was evaluated using autophagy and mitophagy inhibitors and fluorescent staining techniques. Additionally, transgenic Caenorhabditis elegans (C. elegans) models of PD were used to validate the neuroprotective effects of Hed in vivo by focusing on α-synuclein aggregation, mobility, and dopaminergic neuron integrity. ResultsHed significantly enhanced cell viability in 6-OHDA-treated SH-SY5Y cells by inhibiting cell death and reducing oxidative stress. It ameliorated mitochondrial damage, evidenced by decreased mitochondrial superoxide production, restored membrane potential, and improved mitochondrial morphology. Hed also induced mitophagy, as shown by increased autophagosome formation and reduced oxidative stress; these effects were diminished by autophagy and mitophagy inhibitors. In C. elegans models, Hed activated mitophagy and reduced α-synuclein aggregation, improved mobility, and mitigated the loss of dopaminergic neurons. RNA interference targeting the mitophagy-related genes pdr-1 and pink-1 partially reversed these benefits, underscoring the role of mitophagy in Hed's neuroprotective actions. ConclusionHed exhibits significant neuroprotective effects in both in vitro and in vivo PD models by enhancing mitophagy, reducing oxidative stress, and mitigating mitochondrial dysfunction. These findings suggest that Hed holds promise as a therapeutic agent for PD, offering new avenues for future research and potential drug development.

Synthesis, cytotoxic evaluation, and in silico studies of novel benzenesulfonamide-thiazolidinone derivatives against colorectal carcinoma

Thirteen new benzenesulfonamide derivatives containing 4-thiazolidinone were synthesized. Their cytotoxic properties were tested on colorectal carcinoma (HT-29, DLD-1, COLO-205) and normal colon fibroblast (CCD-986Sk) cell lines. Compounds 3l (IC50=114.62 µM), 3a (IC50=25.82 µM), 3k (IC50=30.99 µM), and 3i (IC50=62.94 µM) showed the highest cytotoxicity on HT-29, DLD-1, COLO-205, and CCD-986Sk cell lines, respectively. Compound 3e (IC50=1075.4 µM) exhibited the least cytotoxicity against CCD-986Sk. The apoptosis profile of 5-FU at 5 µM was similar to that of compound 3e at 30 µM. Molecular docking and MD simulations showed stable interactions for compounds 3i and 3e. Molecular docking and MD simulations revealed that compounds 3i and 3e exhibit stable interactions with key cancer-related protein targets, particularly TGFβ2. These interactions suggest their potential as therapeutic agents. The predicted ADME parameters further highlighted compounds 3e and 3i for their favorable lipophilicity, solubility, permeability, and oral absorption profiles, supporting their promise as candidates for future drug development.

Theoretical and experimental investigation on newly synthesized pyrazolopyridine derivatives: Insight into the compound activity, NLO response, and molecular dynamics

Pyrazolopyridine derivatives exhibiting biological activity are widely present in drug molecules. The title compound, ethyl 3-amino-6-methyl-4-(thiophen-2-yl)-1H-pyrazolo[3,4-b]pyridine-5-carboxylate (II), was designed and synthesized and the structure characterized by spectroscopic techniques and confirmed by single-crystal X-ray diffraction. The pyrazolopyridine moiety is not quite planar and the thiophene and ester groups are rotated well out of the mean plane of the pyridine ring. N—H···N and C—H···O hydrogen bonds plus π-stacking interactions form thick layers of molecules parallel to (001). Based on structural activity relationship studies, II exhibits potent activity against fibroblast collagenase-1 complexed to a diphenyl-ether sulphone-based hydroxamic acid or Matrix Metalloproteinase (MMP-1). Theoretical simulations were performed to probe the reactivity and electronic properties of II where the quantum theory of atoms in molecules and NBO analysis was used to describe the bonding nature and charge transfer excitation. The optical and nonlinear characteristics of II are also evidenced by its hyperpolarizability response. The kinetic and thermodynamic stability of II was monitored through a computed ab-initio molecular dynamics study. In addition, a Hirshfeld surface analysis was performed to assess the intermolecular interactions. Efficient binding of II in the MMP-1 complex system has been achieved through classical molecular dynamics and molecular docking calculations. An ADMET analysis was also carried out to explore the potential future drug candidacy of II.

Clinicopathologic and molecular characterization of stages II-IV gastric cancer with Claudin 18.2 expression

Abstract Background Claudin 18.2 (CLDN18.2) is a promising target for targeted therapies in gastric cancer (GC). This study investigated the prevalence of CLDN18.2 expression in patients with stages II-IV GC or gastroesophageal junction (GEJ) adenocarcinoma and its correlation with clinicopathologic features and other crucial GC biomarkers. Methods We enrolled 1000 patients diagnosed with stages II-IV GC after surgical treatment. Immunohistochemistry for CLDN18 (43-14A clone), PD-L1 (22C3 pharmDx), HER2, and FGFR2 was performed. CLDN18.2 positivity was defined as moderate-to-strong (2+/3+) membranous staining in ≥75% of tumor cells. CLDN18.2 expression was compared with biomarker expression, Epstein-Barr virus (EBV) association and microsatellite instability status, and clinicopathologic features. Result CLDN18.2 was positive in 34.4% of the patients. CLDN18.2 positivity was significantly higher in the middle and upper thirds than in the lower third gastric location (P < .001), but there was no correlation with age, sex, or stage (P > .05). CLDN18.2 positivity was rare (2.8%) in mucinous adenocarcinoma but frequent (90.9%) in a majority of gastric carcinomas with lymphoid stroma. CLDN18.2 positivity was higher in EBV-associated (P < .001) and PD-L1-positive (PD-L1 CPS ≥ 5) GC (P = .014) but lower in HER2 positive GC (P = .005). CLDN18.2 positivity was not significantly associated with overall survival and disease-free survival. Conclusion This study provides a comprehensive evaluation of CLDN18.2 status and its correlation with the clinicopathologic characteristics of patients with stages II-IV GC in Korea and with crucial biomarkers. It may be valuable for guiding future drug development, expanding treatment options, and ultimately improving patient outcomes in GC.

The Application of Bicyclo[1.1.1]pentane as a Bioisostere of the Phenyl Ring in Pharmaceutical Chemistry

AbstractBicyclo[1.1.1]pentane (BCP) is a bridging ring skeleton with three-dimensional structure. BCP is a bioisostere of the phenyl ring, tert-butyl group, and alkynes; it has excellent physical and chemical properties compared with phenyl ring, so it has been widely considered by the pharmaceutical chemistry. This short review examines related reports of BCP as a bioisostere of the phenyl ring, and the changes in physicochemical properties and biological activity after substitution. The solubility, clogP, and metabolic toxicity of the drug are improved by BCP bioisosteres, but the biological activity of BCP is lower than the phenyl ring. The application of BCP in drug research and development will be further expanded to provide more possibilities for future drug innovation and development.1 Introduction2 Replacement of Phenyl Rings by BCP3 Conclusion

Mechanism of enterovirus VP0 maturation cleavage based on the structure of a stabilised assembly intermediate.

Molecular details of genome packaging are little understood for the majority of viruses. In enteroviruses (EVs), cleavage of the structural protein VP0 into VP4 and VP2 is initiated by the incorporation of RNA into the assembling virion and is essential for infectivity. We have applied a combination of bioinformatic, molecular and structural approaches to generate the first high-resolution structure of an intermediate in the assembly pathway, termed a provirion, which contains RNA and intact VP0. We have demonstrated an essential role of VP0 E096 in VP0 cleavage independent of RNA encapsidation and generated a new model of capsid maturation, supported by bioinformatic analysis. This provides a molecular basis for RNA-dependence, where RNA induces conformational changes required for VP0 maturation, but that RNA packaging itself is not sufficient to induce maturation. These data have implications for understanding production of infectious virions and potential relevance for future vaccine and antiviral drug design.

Unveiling the multifaceted interactions of antitumor drug mitoxantrone with ct-DNA through biophysical and in silico studies

Mitoxantrone, an anthraquinone derivative, is a widely used anticancer drug with its well-known ability to engage in complex interactions with DNA. Although known for its intercalating ability, the enigma surrounding its binding modes with DNA persists. The existing corpus of literature primarily focuses on mitoxantrone-DNA interactions with short DNA sequences, thereby yielding insights into its interactive nature is limited to this specific sequence. This study aims to elucidate the diverse modes with which mitoxantrone interacts with calf thymus DNA using a combination of spectroscopy, calorimetry and in silico studies. The findings from spectroscopic, calorimetric and molecular dynamic results in correlation with existing literature, unveil a fascinating narrative: mitoxantrone intercalates at lower concentrations but promotes condensation at higher concentrations. Although intercalation with side chains positioned in the minor/major groove is the major binding mode in GC-rich sequences, molecular modelling studies hint at an alternative binding mode in AT-rich sequences where it exclusively displays pure electrostatic interaction. These findings underscore the pivotal role of both drug structure and base sequence in dictating binding mode and affinity. Such insights not only deepen the understanding of structure-activity relationships but also hold promise for guiding future drug design strategies.

Deciphering Chemical Rules for Drug Penetration into Strongyloides.

Background: Strongyloidiasis, a parasitic infection, presents a significant public health challenge in tropical regions due to the limited repertoire of effective treatments. The screening of chemical libraries against the therapeutically relevant third-stage larvae (L3) of the model parasite Strongyloides venezuelensis yielded meager success rates. This situation is reminiscent of Gram-negative bacteria, where drug entry is a limiting factor. Methods: Here, we set out to determine whether similar barriers are in place and establish whether structural and property requirements exist for anti-strongyloides drug discovery. We focused on dyes as their uptake and effects on viability can be independently assessed in the multicellular parasite, thus providing a means to study the possibility of similar entry rules. We tested different dyes in in vitro assays on L3s. Results: We found that staining was necessary to reduce parasite viability, with some dyes achieving anti-strongyloides effects at concentrations similar to those of the reference drug, ivermectin (IV). Some dyes also showed activity against female adults at concentrations well below that of ivermectin. Unfortunately, the most potent dye, Methylene Blue, was unable to prevent the infection in a preliminary in vivo mouse model assay, presumably due to fast dye clearance. Structural analysis showed that positive charges facilitated the access of the compounds to the L3 tissue, thus providing a structural tool for the introduction of activity. For female adults, low globularity is additionally required. As a proof of concept, we added a positive charge to an inactive compound of one of our chemical libraries and re-determined the activity. Conclusions: These findings allow us to establish structural rules for parasite entry that could be of interest for future drug screening or drug development campaigns. These rules might also be applicable to other related parasites.

Mechanism Actions of Coniferyl Alcohol in Improving Cardiac Dysfunction in Renovascular Hypertension Studied by Experimental Verification and Network Pharmacology.

Renovascular hypertension (RH), a secondary hypertension, can significantly impact heart health, resulting in heart damage and dysfunction, thereby elevating the risk of cardiovascular diseases. Coniferol (CA), which has vascular relaxation properties, is expected to be able to treat hypertension-related diseases. However, its potential effects on cardiac function after RH remain unclear. In this study, in combination with network pharmacology, the antihypertensive and cardioprotective effects of CA in a two-kidney, one-clip (2K1C) mice model and its ability to mitigate angiotensin II (Ang II)-induced hypertrophy in H9C2 cells were investigated. The findings revealed that CA effectively reduced blood pressure, myocardial tissue damage, and inflammation after RH. The possible targets of CA for RH treatment were screened by network pharmacology. The interleukin-17 (IL-17) and tumor necrosis factor (TNF) signaling pathways were identified using a Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. The inflammatory response was identified using a Gene Ontology (GO) enrichment analysis. Western blot analysis confirmed that CA reduced the expression of IL-17, matrix metallopeptidase 9 (MMP9), cyclooxygenase 2 (COX2), and TNF α in heart tissues and the H9C2 cells. In summary, CA inhibited cardiac inflammation and fibrohypertrophy following RH. This effect was closely linked to the expression of MMP9/COX2/TNF α/IL-17. This study sheds light on the therapeutic potential of CA for treating RH-induced myocardial hypertrophy and provides insights into its underlying mechanisms, positioning CA as a promising candidate for future drug development.

Whole-exome sequencing study of opioid dependence offers novel insights into the contributions of exome variants.

Opioid dependence (OD) is epidemic in the United States and it is associated with a variety of adverse health effects. Its estimated heritability is ∼50%, and recent genome-wide association studies have identified more than a dozen common risk variants. However, there are no published studies of rare OD risk variants. In this study, we analyzed whole-exome sequencing data from the Yale-Penn cohort, comprising 2,100 participants of European ancestry (EUR; 1,321 OD cases) and 1,790 of African ancestry (AFR; 864 cases). A novel low-frequency variant (rs746301110) in the RUVBL2 gene was identified in EUR ( p =6.59×10 -10 ). Suggestive associations ( p <1×10 -5 ) were observed in TMCO3 in EUR, in NEIL2 and CFAP44 in AFR, and in FAM210B in the cross-ancestry meta-analysis. Gene-based collapsing tests identified SLC22A10 , TMCO3 , FAM90A1 , DHX58 , CHRND , GLDN , PLAT , H1-4 , COL3A1 , GPHB5 and QPCTL as top genes ( p <1×10 -4 ) with most associations attributable to rare variants and driven by the burden of predicted loss-of-function and missense variants. This study begins to fill the gap in our understanding of the genetic architecture of OD, providing insights into the contribution of rare coding variants and potential targets for future functional studies and drug development.

Current Formulation Strategies to Design Novel Carriers for Targeted Drug Delivery and Management of Infectious Keratitis: A Comprehensive Review on the Present State of the Art

Objective: Infectious keratitis is a pernicious disease that affects the anterior segment of the eye and is one the leading causes of blindness worldwide. This disease may cause severe visual impairment or permanent vision damage if left untreated. Discussion: No doubt there are many conventional drug delivery systems to treat ocular keratitis, yet it is the fifth leading cause of blindness globally. This is the result of the eye's complex anatomy and barrier system, which restricts the total ocular contact time of the conventional formulations resulting in underdosing. The widely used traditional formulations to treat keratitis, like antibiotic eye drops and ointments, are rendered useless due to less ocular contact time and low therapeutic drug levels at the target ocular site. The main requirement of the present time is to develop novel drug delivery-backed stratagems to overcome the shortcomings of conventional formulations, which will reduce the morbidity associated with infectious keratitis and improve clinical outcomes. It is worth mentioning that there are documented incidents of Herpetic keratitis of the cornea followed by COVID-19 infection and vaccination. Conclusion: This paper is a rigorous review of all the novel drug delivery strategies to combat ocular keratitis. These future drug delivery strategies will pave the way for the present time researcher and formulation chemists to develop multi-dimensional novel formulations that are safe, patient-compliant, and surpass the ocular barriers to maintain therapeutic drug levels in ocular tissues.

Identifying new biomarkers and potential therapeutic targets for breast cancer through the integration of human plasma proteomics: a Mendelian randomization study and colocalization analysis.

The proteome is a crucial reservoir of targets for cancer treatment. While some targeted therapies have been developed, there are still significant challenges in early diagnosis and treatment, highlighting the need to identify new biomarkers and therapeutic targets for breast cancer. Therefore, we conducted a comprehensive proteome-wide Mendelian randomization (MR) study to identify novel biomarkers and potential therapeutic targets for breast cancer. Protein quantitative trait locus (pQTL) data were extracted from two published plasma proteome-wide association studies. Genetic variants associated with breast cancer were obtained from the Breast Cancer Association Consortium, which included 133,384 cases and 113,789 controls, and the Finnish cohort study, comprising 18,786 cases and 182,927 controls. We employed summary-based MR and colocalization methods to identify potential drug targets for breast cancer, which were subsequently validated using a two-sample MR approach. Finally, a protein-protein interaction (PPI) network was constructed to detect interactions between the identified proteins and existing cancer drug targets. Gene-predicted levels of ten proteins were associated with breast cancer risk. Decreased levels of CASP8, DDX58, CPNE1, ULK3, PARK7, and BTN2A1, as well as increased levels of TNFRSF9, TNXB, DNPH1, and TLR1, were linked to an elevated risk of breast cancer. Among these, CASP8 and DDX58 were supported by tier-one evidence, while CPNE1, ULK3, PARK7, and TNFRSF9 received tier-two evidence support. The remaining proteins, TNXB, BTN2A1, DNPH1, and TLR1, were supported by tier-three evidence. CASP8, DDX58, CPNE1, ULK3, PARK7, and TNFRSF9 have already been identified as targets in drug development and potential therapeutic targets for breast cancer treatment. Additionally, ULK3 showed promise as a prognostic biomarker for breast cancer. The present study identified several novel potential drug targets and biomarkers for breast cancer, providing new insights into its diagnosis and treatment. The integration of PPI and druggability evaluations enhances the prioritization of these therapeutic targets, paving the way for future drug development efforts.

Comparative Analysis of Hepatitis C virus Genotype 1a (Isolate 1) using Multiple Regression Algorithms and Fingerprinting Techniques

Approximately 70 million people worldwide have been infected with Hepatitis C virus (HCV), presenting a critical global health challenge. As a member of the Flaviviridae family, HCV can cause severe liver diseases such as cirrhosis, acute hepatitis, and chronic hepatitis. The Hepatitis C virus (HCV) genome encodes a single polyprotein consisting of 3010 amino acids, which when processed contains 10 polypeptides derived from cellular and viral proteases. These include structural proteins such as core protein, E1 and E2 envelope glycoproteins, and nonstructural proteins such as NS1, NS2, NS3, NS4A, NS4B, NS5A, and NS5B. Nonstructural proteins will be released by HCV NS2-3 and NS3-4A proteases, however, structural proteins will be released by host ER signaling peptidases. co-translationally and post-translationally form 10 individual structural proteins: 5'-C-E1-E2-p7-NS2-NS3-NS4A-NS4B-NS5A-NS5B-3'. Despite extensive research, there are significant gaps in predictive and analytical approaches to managing HCV, particularly in understanding the polyprotein structure and its implications for drug discovery. This study addresses these gaps by employing machine learning techniques to analyze HCV polyprotein using various fingerprinting methods and regression algorithms. The data was sourced from the ChEMBL database, and fingerprinting techniques such as PubChem, MACCS, and E-State were utilized. Regression algorithms, including Gradient Boosting Regression (GBR), Random Forest Regression (RFR), AdaBoost Regression (ABR), and Hist Gradient Boosting Regression (HSR), were applied. Model performance was evaluated using R² and Adjusted R² metrics, comparing default models with those enhanced by hyperparameter tuning. Feature importance analysis was conducted to identify key features influencing model performance, aiding in model simplification. The results show that although hyperparameter tuning does not significantly improve the predictive power of a model, it can provide an insight into model optimization. In particular, the default model showed higher R² and Adjusted R² values across different fingerprinting techniques compared to models with hyperparameterized features. Gradient Boosting Regression (GBR) and Random Forest Regression (RFR) consistently performed well, with GBR showing the highest R² values when using PubChem fingerprints. Although there was no significant improvement through hyperparameter tuning, this study was able to find out the features that strongly influenced the model performance by conducting a feature importance analysis. This analysis helped simplify the model and highlighted the potential of machine learning in improving the understanding of HCV polyprotein structure. This research identifies optimal regression models and fingerprinting techniques, providing a strong framework for future drug discovery efforts aimed at improving global health outcomes. The research also shows that it is important to date to advance drug discovery using machine learning.

Abstract IA-01: Targeting autophagy in pancreatic cancer

Abstract Pancreatic ductal adenocarcinoma (PDAC) is one of the most vexing problems in cancer with 5-year overall survival rates of 13%, thus there is a need for new therapeutic targets. PDAC have a distinct dependence on autophagy, a conserved eukaryotic catabolic pathway that serves to degrade proteins, other macromolecules, and organelles via the lysosome as part of a recycling process to maintain cellular homeostasis during basal and stress conditions. The unique importance of autophagy in PDAC suggests that there may be a subset of proteins that are specifically targeted by autophagy for degradation, which would promote proliferation and survival, and that these may represent new targets for therapy. Using a quantitative PDAC cellular autophagosomal proteomics approach, we identified NCOA4 as the autophagy receptor for ferritin, the cellular iron storage complex, and demonstrated that ferritin autophagy (ferritinophagy) is a highly regulated process and plays a central role in the larger context of cellular and organismal iron homeostasis. Given the reliance of PDAC, on both high levels of autophagy as well as iron, we studied the role of NCOA4 and ferritinophagy in PDAC thereby identifying NCOA4-mediated ferritinophagy and more broadly lysosomal iron metabolism as a PDAC dependency and therapeutic target. We recently determined the cryo-EM structure of the NCOA4-Ferritin complex for future drug design. To identify the role of autophagy and the lysosome in PDAC metastatic progression, we co-developed an in vivo capable lysosomal enrichment that enables capture and proteomic profiling of lysosomes at different stages of tumor evolution, including early stage, late stage, and metastatic disease. Employing this strategy, we successfully captured lysosomal proteins from primary tumors (pancreas), as well as lung and liver metastases. Our preliminary analysis revealed an enrichment of resident lysosomal membrane and luminal proteins in the datasets, confirming successful isolation of intact lysosomes from these complex tissues. Additionally, we identified non-resident lysosomal proteins (termed cargo) that are enriched and co-evolve with advancing tumor stages. Notably, our results reveal distinct differences in the lysosomal proteome of tumor cells across different tissues. These findings emphasize the critical role of lysosomal function in tumor progression and suggest that targeting lysosomal components could be a promising therapeutic strategy for treating metastatic PDAC. Finally, given the challenging pharmacokinetic and pharmacodynamic properties and limited clinical efficacy of hydroxychloroquine as an autophagy/lysosomal inhibition strategy, we are now exploring novel autophagy inhibition strategies in PDAC to effectively target this pathway for clinical benefit. Citation Format: Joseph D. Mancias. Targeting autophagy in pancreatic cancer [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Pancreatic Cancer Research; 2024 Sep 15-18; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2024;84(17 Suppl_2):Abstract nr IA-01.