IU Indianapolis ScholarWorks :: Browsing by Subject "drug discovery"

Browsing by Subject "drug discovery"

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A cell-based high-throughput screening method to directly examine transthyretin amyloid fibril formation at neutral pH
(Elsevier, 2019-07-19) Ueda, Mitsuharu; Okada, Masamitsu; Mizuguchi, Mineyuki; Kluve-Beckerman, Barbara; Kanenawa, Kyosuke; Isoguchi, Aito; Misumi, Yohei; Tasaki, Masayoshi; Ueda, Akihiko; Kanai, Akinori; Sasaki, Ryoko; Masuda, Teruaki; Inoue, Yasuteru; Nomura, Toshiya; Shinriki, Satoru; Shuto, Tsuyoshi; Kai, Hirofumi; Yamashita, Taro; Matsui, Hirotaka; Benson, Merrill D.; Ando, Yukio; Pathology and Laboratory Medicine, School of Medicine
Transthyretin (TTR) is a major amyloidogenic protein associated with hereditary (ATTRm) and nonhereditary (ATTRwt) intractable systemic transthyretin amyloidosis. The pathological mechanisms of ATTR-associated amyloid fibril formation are incompletely understood, and there is a need for identifying compounds that target ATTR. C-terminal TTR fragments are often present in amyloid-laden tissues of most patients with ATTR amyloidosis, and on the basis of in vitro studies, these fragments have been proposed to play important roles in amyloid formation. Here, we found that experimentally-formed aggregates of full-length TTR are cleaved into C-terminal fragments, which were also identified in patients' amyloid-laden tissues and in SH-SY5Y neuronal and U87MG glial cells. We observed that a 5-kDa C-terminal fragment of TTR, TTR81–127, is highly amyloidogenic in vitro, even at neutral pH. This fragment formed amyloid deposits and induced apoptosis and inflammatory gene expression also in cultured cells. Using the highly amyloidogenic TTR81–127 fragment, we developed a cell-based high-throughput screening method to discover compounds that disrupt TTR amyloid fibrils. Screening a library of 1280 off-patent drugs, we identified two candidate repositioning drugs, pyrvinium pamoate and apomorphine hydrochloride. Both drugs disrupted patient-derived TTR amyloid fibrils ex vivo, and pyrvinium pamoate also stabilized the tetrameric structure of TTR ex vivo in patient plasma. We conclude that our TTR81–127–based screening method is very useful for discovering therapeutic drugs that directly disrupt amyloid fibrils. We propose that repositioning pyrvinium pamoate and apomorphine hydrochloride as TTR amyloid-disrupting agents may enable evaluation of their clinical utility for managing ATTR amyloidosis.
Differential Compound Prioritization via Bidirectional Selectivity Push with Power
(ACS, 2017-12) Liu, Junfeng; Ning, Xia; Computer and Information Science, School of Science
Effective in silico compound prioritization is a critical step to identify promising drug candidates in the early stages of drug discovery. Current computational methods for compound prioritization usually focus on ranking the compounds based on one property, typically activity, with respect to a single target. However, compound selectivity is also a key property which should be deliberated simultaneously so as to minimize the likelihood of undesired side effects of future drugs. In this paper, we present a novel machine-learning based differential compound prioritization method dCPPP. This dCPPP method learns compound prioritization models that rank active compounds well, and meanwhile, preferably rank selective compounds higher via a bidirectional selectivity push strategy. The bidirectional push is enhanced by push powers that are determined by ranking difference of selective compounds over multiple bioassays. Our experiments demonstrate that the new method dCPPP achieves significant improvement on prioritizing selective compounds over baseline models.
Drug Discovery Through Drug Perturbation Pathway Modeling and Network Analysis
(Office of the Vice Chancellor for Research, 2014-04-11) Ho, Tung; Hakola, Krista; Wagle, Pragat; Rouse, Evan; Shadmand, Mehdi; Han, Juyeon; Ibrahim, Sara
Due to intrinsic complex molecular interactions, the “one disease – one target – one drug” strategy for disease treatment is no longer the best option to treat cancers. To assess drug pharmacological effects, we assume that “ideal” drugs for a patient can treat or prevent the disease by modulating gene expression profiles of this patient to the similar level with those in healthy people. A new approach for drug-protein interactions curation, drug-drug similarity network comparison, and integrative pathway model construction and evaluation was introduced to determine optimal drugs for various cancers. Drug-protein interaction curation is conducted to discover novel drug-protein relationships and is categorized as: up regulated, down regulated, indirect up or down, ambiguous and unknown. The manual curation can be utilized for drug repurposing and examining drug mechanism on a pathway level. A drug-drug similarity network model is built by examining similar targets, therapeutic mechanisms, side effects, and chemical structures. Drug similarity analysis is useful for drug repositioning because similar drugs may have compatible therapeutic or toxic effects for a disease. Drug similarity networks are constructed and examined through a molecular network visualization platform. An integrative disease-specific pathway model is also built to gain a more holistic view of disease mechanisms by including every significant disease-specific protein. Including drugs on the pathway through target information can also offer a clear mechanism for the drug’s action. We also transform integrated pathways into network models and ranked drugs based on the network topological features of drug targets, drug-affecting genes/proteins, and curated disease-specific proteins. Combining our three approaches could potentially lead to advances in drug repurposing and repositioning.
Effective targeting of the survivin dimerization interface with small molecule inhibitors
(AACR, 2016-01) Qi, Jing; Dong, Zizheng; Liu, Jianguo; Peery, Robert C.; Zhang, Shaobo; Liu, Jingyuan; Zhang, Jian-Ting; Department of Pathology and Laboratory Medicine, IU School of Medicine
Many oncoproteins are considered undruggable because they lack enzymatic activities. In this study, we present a small-molecule–based anticancer agent that acts by inhibiting dimerization of the oncoprotein survivin, thereby promoting its degradation along with spontaneous apoptosis in cancer cells. Through a combination of computational analysis of the dimerization interface and in silico screening, we identified one compound that induced proteasome-dependent survivin degradation. Analysis of a set of structural analogues led us to identify a lead compound (LQZ-7F), which was effective in blocking the survival of multiple cancer cell lines in a low micromolar concentration range. LQZ-7F induced proteasome-dependent survivin degradation, mitotic arrest, and apoptosis, and it blocked the growth of human tumors in mouse xenograft assays. In addition to providing preclinical proof of concept for a survivin-targeting anticancer agent, our work offers novel in silico screening strategies to therapeutically target homodimeric oncogenic proteins considered undruggable.
MCAK Inhibitors Induce Aneuploidy in Triple-Negative Breast Cancer Models
(MDPI, 2023-06-23) Smith, John C.; Husted, Stefan; Pilrose, Jay; Ems-McClung, Stephanie C.; Stout, Jane R.; Carpenter, Richard L.; Walczak, Claire E.; Biochemistry and Molecular Biology, School of Medicine
Standard of care for triple-negative breast cancer (TNBC) involves the use of microtubule poisons such as paclitaxel, which are proposed to work by inducing lethal levels of aneuploidy in tumor cells. While these drugs are initially effective in treating cancer, dose-limiting peripheral neuropathies are common. Unfortunately, patients often relapse with drug-resistant tumors. Identifying agents against targets that limit aneuploidy may be a valuable approach for therapeutic development. One potential target is the microtubule depolymerizing kinesin, MCAK, which limits aneuploidy by regulating microtubule dynamics during mitosis. Using publicly available datasets, we found that MCAK is upregulated in triple-negative breast cancer and is associated with poorer prognoses. Knockdown of MCAK in tumor-derived cell lines caused a two- to five-fold reduction in the IC50 for paclitaxel, without affecting normal cells. Using FRET and image-based assays, we screened compounds from the ChemBridge 50 k library and discovered three putative MCAK inhibitors. These compounds reproduced the aneuploidy-inducing phenotype of MCAK loss, reduced clonogenic survival of TNBC cells regardless of taxane-resistance, and the most potent of the three, C4, sensitized TNBC cells to paclitaxel. Collectively, our work shows promise that MCAK may serve as both a biomarker of prognosis and as a therapeutic target.
Pharmacological Potential of Small Molecules for Treating Corneal Neovascularization
(MDPI, 2020-07-08) Barry, Zachary; Park, Bomina; Corson, Timothy W.; Ophthalmology, School of Medicine
Under healthy conditions, the cornea is an avascular structure which allows for transparency and optimal visual acuity. Its avascular nature is maintained by a balance of proangiogenic and antiangiogenic factors. An imbalance of these factors can result in abnormal blood vessel proliferation into the cornea. This corneal neovascularization (CoNV) can stem from a variety of insults including hypoxia and ocular surface inflammation caused by trauma, infection, chemical burns, and immunological diseases. CoNV threatens corneal transparency, resulting in permanent vision loss. Mainstay treatments of CoNV have partial efficacy and associated side effects, revealing the need for novel treatments. Numerous natural products and synthetic small molecules have shown potential in preclinical studies in vivo as antiangiogenic therapies for CoNV. Such small molecules include synthetic inhibitors of the vascular endothelial growth factor (VEGF) receptor and other tyrosine kinases, plus repurposed antimicrobials, as well as natural source-derived flavonoid and non-flavonoid phytochemicals, immunosuppressants, vitamins, and histone deacetylase inhibitors. They induce antiangiogenic and anti-inflammatory effects through inhibition of VEGF, NF-κB, and other growth factor receptor pathways. Here, we review the potential of small molecules, both synthetics and natural products, targeting these and other molecular mechanisms, as antiangiogenic agents in the treatment of CoNV.
Radioligands targeting purinergic P2X7 receptor
(Elsevier, 2020-06) Zheng, Qi-Huang; Radiology and Imaging Sciences, School of Medicine
The purinergic P2X7 receptor (P2X7R) is an adenosine triphosphate (ATP) ligand-gated cationic channel receptor. P2X7R is closely associated with various inflammatory, immune, cancer, neurological, musculoskeletal and cardiovascular disorders. P2X7R is an interesting therapeutic target as well as molecular imaging target. This brief digest highlights the radioligands targeting P2X7R recently developed in drug discovery and molecular imaging agent development.
Systems and Network-Based Approaches for Personalized Medicine
(2014-11) Janga, Sarath Chandra; Edupuganti, Mohan Mallikarjuna Rao
Most biological outcomes in a cell arise from a complex interplay between different cellular entities such as proteins, DNA, RNA and metabolites. Therefore, a key challenge for biology in the twenty-first century is to understand the structure and dynamics of the complex web of interactions in a cell that contribute to its proper functioning. Recent years have seen a surge in the amount of “omics” data and an integration of several disciplines which has influenced all areas of life sciences, from molecular biology to medicine. With the emergence of a number of sophisticated tools and technologies as a result of genomics revolution, we are now in a position to view the molecular aspects of diseases at a systems level by incorporating various cellular entities into a network framework. Such systems/network-based approaches are not only enabling us to develop models of disease and wellness in a population but also contributing to our efforts to reverse engineer the molecular networks corresponding to disease states by perturbing using drug cocktails. These multi-scale personalized medicine approaches are likely to significantly re-shape the health care industry in the coming decades and decrease the division that we currently see between medicine and other biotechnology disciplines.
Two decades of research in discovery of anticancer drugs targeting STAT3, how close are we?
(Elsevier, 2018) Beebe, Jenny; Liu, Jing-Yuan; Zhang, Jian-Ting; Pharmacology and Toxicology, School of Medicine
Signal transducer and activator of transcription 3 (STAT3) controls many biological processes including differentiation, survival, proliferation, and angiogenesis. In normal healthy cells, STAT3 is tightly regulated to maintain a momentary active state. However, aberrant or constitutively activated STAT3 has been observed in many different cancers and constitutively activated STAT3 has been shown to associate with poor prognosis and tumor progression. For this reason, STAT3 has been studied as a possible target in the treatment of many different types of cancers. However, despite decades of research, a FDA-approved STAT3 inhibitor has yet to emerge. In this review, we will analyze past studies targeting STAT3 for drug discovery, understand possible causes of failure in these studies, and provide potential insights for future efforts to overcome these roadblocks.

Browsing by Subject "drug discovery"

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