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Mondello A, Dal Bo M, Toffoli G, Polano M. Machine learning in onco-pharmacogenomics: a path to precision medicine with many challenges. Front Pharmacol 2024; 14:1260276. [PMID: 38264526 PMCID: PMC10803549 DOI: 10.3389/fphar.2023.1260276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 12/26/2023] [Indexed: 01/25/2024] Open
Abstract
Over the past two decades, Next-Generation Sequencing (NGS) has revolutionized the approach to cancer research. Applications of NGS include the identification of tumor specific alterations that can influence tumor pathobiology and also impact diagnosis, prognosis and therapeutic options. Pharmacogenomics (PGx) studies the role of inheritance of individual genetic patterns in drug response and has taken advantage of NGS technology as it provides access to high-throughput data that can, however, be difficult to manage. Machine learning (ML) has recently been used in the life sciences to discover hidden patterns from complex NGS data and to solve various PGx problems. In this review, we provide a comprehensive overview of the NGS approaches that can be employed and the different PGx studies implicating the use of NGS data. We also provide an excursus of the ML algorithms that can exert a role as fundamental strategies in the PGx field to improve personalized medicine in cancer.
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Affiliation(s)
| | | | | | - Maurizio Polano
- Experimental and Clinical Pharmacology Unit, Centro di Riferimento Oncologico di Aviano (CRO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Aviano, Italy
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Paul SK, Guendouzi A, Banerjee A, Guendouzi A, Haldar R. Identification of approved drugs with ALDH1A1 inhibitory potential aimed at enhancing chemotherapy sensitivity in cancer cells: an in-silico drug repurposing approach. J Biomol Struct Dyn 2024:1-15. [PMID: 38189344 DOI: 10.1080/07391102.2023.2300127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 12/21/2023] [Indexed: 01/09/2024]
Abstract
The aldehyde dehydrogenase 1A1 (ALDH1A1) also known as retinal dehydrogenase, is an enzyme normally involved in the cellular metabolism, development and detoxification processes in healthy cells. However, it's also considered a cancer stem cell marker and its high levels of expression in several cancers, including breast, lung, ovarian, and colon cancer have been associated with poor prognosis and resistance to chemotherapy. Given its crucial role in chemotherapy resistance by detoxification of chemotherapeutic drugs, ALDH1A1 has attracted significant research interest as a potential therapeutic target for cancer. Though a few synthetic inhibitors of ALDH1A1 have been synthesized and their efficacy has been proved in-vitro and in-vivo studies, none of them have passed clinical trials so far. In this scenario, we have performed an in-silico study to verify whether any of the already approved drugs used for various purposes has the ability to inhibit catalytic activity of ALDH1A1, so that they can be repurposed for cancer therapy. Keeping in mind the feasibility of repurposing in a larger population we have selected the approved drugs from five widely used drug categories such as antibiotic, antiviral, antifungal, anti diabetic and antihypertensive for screening. Computational techniques like molecular docking, molecular dynamics simulations and MM-PBSA binding energy calculation have been used in this study to screen the approved drugs. Based on the logical analysis of results, we propose that three drugs - telmisartan, irbesartan and maraviroc can inhibit the catalytic activity of ALDH1A1 and thus can be repurposed to increase chemotherapy sensitivity in cancer cells.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sanjay Kumar Paul
- Department of Physiology, University of Calcutta, Kolkata, India
- Department of Zoology, Rammohan College, Kolkata, West Bengal, India
| | - Abdelmadjid Guendouzi
- Center for Research in Pharmaceutical Sciences (CRSP), Constantine, Algeria
- Ecole Normale Supérieure ENS Constantine, Constantine, Algeria
| | | | | | - Rajen Haldar
- Department of Physiology, University of Calcutta, Kolkata, India
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103
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Fatemi N, Karimpour M, Bahrami H, Zali MR, Chaleshi V, Riccio A, Nazemalhosseini-Mojarad E, Totonchi M. Current trends and future prospects of drug repositioning in gastrointestinal oncology. Front Pharmacol 2024; 14:1329244. [PMID: 38239190 PMCID: PMC10794567 DOI: 10.3389/fphar.2023.1329244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Accepted: 12/11/2023] [Indexed: 01/22/2024] Open
Abstract
Gastrointestinal (GI) cancers comprise a significant number of cancer cases worldwide and contribute to a high percentage of cancer-related deaths. To improve survival rates of GI cancer patients, it is important to find and implement more effective therapeutic strategies with better prognoses and fewer side effects. The development of new drugs can be a lengthy and expensive process, often involving clinical trials that may fail in the early stages. One strategy to address these challenges is drug repurposing (DR). Drug repurposing is a developmental strategy that involves using existing drugs approved for other diseases and leveraging their safety and pharmacological data to explore their potential use in treating different diseases. In this paper, we outline the existing therapeutic strategies and challenges associated with GI cancers and explore DR as a promising alternative approach. We have presented an extensive review of different DR methodologies, research efforts and examples of repurposed drugs within various GI cancer types, such as colorectal, pancreatic and liver cancers. Our aim is to provide a comprehensive overview of employing the DR approach in GI cancers to inform future research endeavors and clinical trials in this field.
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Affiliation(s)
- Nayeralsadat Fatemi
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mina Karimpour
- Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Hoda Bahrami
- Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Mohammad Reza Zali
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Vahid Chaleshi
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Andrea Riccio
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università degli Studi della Campania “Luigi Vanvitelli”, Caserta, Italy
- Institute of Genetics and Biophysics (IGB) “Adriano Buzzati-Traverso”, Consiglio Nazionale delle Ricerche (CNR), Naples, Italy
| | - Ehsan Nazemalhosseini-Mojarad
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mehdi Totonchi
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università degli Studi della Campania “Luigi Vanvitelli”, Caserta, Italy
- Department of Genetics, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran
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104
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Xiang S, Lawrence PJ, Peng B, Chiang C, Kim D, Shen L, Ning X. Modeling Path Importance for Effective Alzheimer's Disease Drug Repurposing. Pac Symp Biocomput 2024; 29:306-321. [PMID: 38160288 PMCID: PMC11056095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
Recently, drug repurposing has emerged as an effective and resource-efficient paradigm for AD drug discovery. Among various methods for drug repurposing, network-based methods have shown promising results as they are capable of leveraging complex networks that integrate multiple interaction types, such as protein-protein interactions, to more effectively identify candidate drugs. However, existing approaches typically assume paths of the same length in the network have equal importance in identifying the therapeutic effect of drugs. Other domains have found that same length paths do not necessarily have the same importance. Thus, relying on this assumption may be deleterious to drug repurposing attempts. In this work, we propose MPI (Modeling Path Importance), a novel network-based method for AD drug repurposing. MPI is unique in that it prioritizes important paths via learned node embeddings, which can effectively capture a network's rich structural information. Thus, leveraging learned embeddings allows MPI to effectively differentiate the importance among paths. We evaluate MPI against a commonly used baseline method that identifies anti-AD drug candidates primarily based on the shortest paths between drugs and AD in the network. We observe that among the top-50 ranked drugs, MPI prioritizes 20.0% more drugs with anti-AD evidence compared to the baseline. Finally, Cox proportional-hazard models produced from insurance claims data aid us in identifying the use of etodolac, nicotine, and BBB-crossing ACE-INHs as having a reduced risk of AD, suggesting such drugs may be viable candidates for repurposing and should be explored further in future studies.
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Affiliation(s)
- Shunian Xiang
- Biomedical Informatics Department, The Ohio State University, Columbus, OH 43210, USA
| | - Patrick J. Lawrence
- Biomedical Informatics Department, The Ohio State University, Columbus, OH 43210, USA
| | - Bo Peng
- Computer Science and Engineering Department, The Ohio State University, Columbus, OH 43210, USA
| | - ChienWei Chiang
- Biomedical Informatics Department, The Ohio State University, Columbus, OH 43210, USA
| | - Dokyoon Kim
- Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Li Shen
- Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Xia Ning
- Biomedical Informatics Department, The Ohio State University, Columbus, OH 43210, USA
- Computer Science and Engineering Department, The Ohio State University, Columbus, OH 43210, USA
- Translational Data Analytics Institute, The Ohio State University, Columbus, OH 43210, USA
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105
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Luciani A, Devuyst O. The CTNS-MTORC1 axis couples lysosomal cystine to epithelial cell fate decisions and is a targetable pathway in cystinosis. Autophagy 2024; 20:202-204. [PMID: 37621073 PMCID: PMC10761040 DOI: 10.1080/15548627.2023.2250165] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 08/09/2023] [Accepted: 08/11/2023] [Indexed: 08/26/2023] Open
Abstract
Differentiation and fate decisions are critical for the epithelial cells lining the proximal tubule (PT) of the kidney, but the signals involved remain unknown. Defective cystine mobilization from lysosomes through CTNS (cystinosin, lysosomal cystine transporter), which is mutated in cystinosis, triggers the dedifferentiation and dysfunction of the PT cells, causing kidney disease and severe metabolic complications. Using preclinical models and physiologically relevant cellular systems, along with functional assays and a generative artificial intelligence (AI)-powered engine, we found that cystine storage imparted by CTNS deficiency stimulates Ragulator-RRAG GTPase-dependent recruitment of MTORC1 and its constitutive activation. In turn, this diverts the catabolic trajectories and differentiating states of PT cells toward growth and proliferation, disrupting homeostasis and their specialized functions. Therapeutic MTORC1 inhibition by using low doses of rapamycin corrects lysosome function and differentiation downstream of cystine storage and ameliorates PT dysfunction in preclinical models of cystinosis. These discoveries suggest that cystine may act as a lysosomal fasting signal that tailors MTORC1 signaling to direct fate decisions in the kidney PT epithelium, highlighting novel therapeutic paradigms for cystinosis and other lysosome-related disorders.
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Affiliation(s)
| | - Olivier Devuyst
- Institute of Physiology, University of Zurich, Zurich, Switzerland
- Institute for Rare Diseases, UCLouvain Medical School, Brussels, Belgium
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106
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Tüylü Küçükkılınç T, Ercan A. Phenelzine protects against acetaminophen induced apoptosis in HepG2 cells. Drug Chem Toxicol 2024; 47:81-89. [PMID: 37246945 DOI: 10.1080/01480545.2023.2217696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 04/04/2023] [Accepted: 04/08/2023] [Indexed: 05/30/2023]
Abstract
Acetaminophen (APAP) overdosing is the most common cause of drug-induced liver failure. Despite extensive study, N-acetylcysteine is currently the only antidote utilized for treatment. The purpose of this study was to evaluate the effect and mechanisms of phenelzine, an FDA-approved antidepressant, on APAP-induced toxicity in HepG2 cells. The human liver hepatocellular cell line HepG2 was used to investigate APAP-induced cytotoxicity. The protective effects of phenelzine were determined by examining the cell viability, combination index calculation, Caspase 3/7 activation, Cytochrome c release, H2O2 levels, NO levels, GSH activity, PERK protein levels, and pathway enrichment analysis. Elevated H2O2 production and decreased glutathione (GSH) levels were indicators of APAP-induced oxidative stress. The combination index of 2.04 indicated that phenelzine had an antagonistic effect on APAP-induced toxicity. When compared to APAP alone, phenelzine treatment considerably reduced caspase 3/7 activation, cytochrome c release, and H2O2 generation. However, phenelzine had minimal effect on NO and GSH levels and did not alleviate ER stress. Pathway enrichment analysis revealed a potential connection between APAP toxicity and phenelzine metabolism. These findings suggested that phenelzine's protective effect against APAP-induced cytotoxicity could be attributed to the drug's capacity to reduce APAP-mediated apoptotic signaling.
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Affiliation(s)
| | - Ayşe Ercan
- Department of Biochemistry, Hacettepe University Faculty of Pharmacy, Ankara, Turkey
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107
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Shah BM, Modi P. Breaking Barriers: Current Advances and Future Directions in Mpox Therapy. Curr Drug Targets 2024; 25:62-76. [PMID: 38151842 DOI: 10.2174/0113894501281263231218070841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 11/21/2023] [Accepted: 11/28/2023] [Indexed: 12/29/2023]
Abstract
BACKGROUND Mpox, a newly discovered zoonotic infection, can be transmitted from animal to human and between humans. Serological and genomic studies are used to identify the virus. OBJECTIVE Currently, there are no proven effective treatments for Mpox. Also, the safety and efficacy of intravenous vaccinia immune globulin, oral Tecovirimat (an inhibitor of intracellular viral release), and oral Brincidofovir (a DNA polymerase inhibitor) against the Mpox virus are uncertain, highlighting the need for more effective and safe treatments. As a result, drug repurposing has emerged as a promising strategy to identify previously licensed drugs that can be repurposed to treat Mpox. RESULTS Various approaches have been employed to identify previously approved drugs that can target specific Mpox virus proteins, including thymidylate kinase, D9 decapping enzyme, E8 protein, Topoisomerase1, p37, envelope proteins (D13, A26, and H3), F13 protein, virus's main cysteine proteases, and DNA polymerase. CONCLUSION In this summary, we provide an overview of potential drugs that could be used to treat Mpox and discuss the underlying biological processes of their actions.
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Affiliation(s)
- Bhumi M Shah
- Department of Pharmaceutical Chemistry, L.J. Institute of Pharmacy, L.J. University, Ahmedabad, Gujarat 382210, India
| | - Palmi Modi
- Department of Pharmaceutical Chemistry, L.J. Institute of Pharmacy, L.J. University, Ahmedabad, Gujarat 382210, India
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108
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Spottiswoode N, Haston JC, Hanners NW, Gruenberg K, Kim A, DeRisi JL, Wilson MR. Challenges and advances in the medical treatment of granulomatous amebic encephalitis. Ther Adv Infect Dis 2024; 11:20499361241228340. [PMID: 38312848 PMCID: PMC10838035 DOI: 10.1177/20499361241228340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Accepted: 01/09/2024] [Indexed: 02/06/2024] Open
Abstract
Granulomatous amebic encephalitis, caused by the free-living amebae Balamuthia mandrillaris or Acanthamoeba species, is a rare and deadly infectious syndrome with a current mortality rate of >90%. Much work remains to define the optimal treatment for these infections. Here, we provide a comprehensive overview of the supporting evidence behind antimicrobials currently recommended by the Centers for Disease Control and Prevention (CDC) with updated statistics on survival rates and medication usage from the CDC Free-Living Ameba Database. We also discuss promising treatments, especially the emerging therapeutic agent nitroxoline, and provide recommendations for the next steps in this area.
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Affiliation(s)
- Natasha Spottiswoode
- Division of Infectious Diseases, University of California San Francisco, San Francisco, CA, USA
| | - Julia C. Haston
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Natasha W. Hanners
- Division of Pediatric Infectious Diseases, University of Texas Southwestern, Dallas, TX, USA
| | - Katherine Gruenberg
- Department of Clinical Pharmacy, University of California San Francisco School of Pharmacy, San Francisco, CA, USA
| | - Annie Kim
- Department of Clinical Pharmacy, Zuckerberg San Francisco General, San Francisco, CA, USA
| | - Joseph L. DeRisi
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
- Chan Zuckerberg Biohub SF, San Francisco, CA, USA
| | - Michael R. Wilson
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA 94143, USA
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Guo Y, Liu H, Yang M, Ding R, Gao Y, Niu X, Deng X, Wang J, Feng H, Qiu J. Novel metallo-β-lactamases inhibitors restore the susceptibility of carbapenems to New Delhi metallo-lactamase-1 (NDM-1)-harbouring bacteria. Br J Pharmacol 2024; 181:54-69. [PMID: 37539785 DOI: 10.1111/bph.16210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 06/24/2023] [Accepted: 07/20/2023] [Indexed: 08/05/2023] Open
Abstract
BACKGROUND AND PURPOSE The production of metallo-β-lactamases is a major mechanisms adopted by bacterial pathogens to resist carbapenems. Repurposing approved drugs to restore the efficacy of carbapenems represents an efficient and cost-effective approach to fight infections caused by carbapenem resistant pathogens. EXPERIMENTAL APPROACH The nitrocefin hydrolysis assay was employed to screen potential New Delhi metallo-lactamase-1 (NDM-1) inhibitors from a commercially available U.S. Food and Drug Administration (FDA) approved drug library. The mechanism of inhibition was clarified by metal restoration, inductively coupled plasma mass spectrometry (ICP-MS) and molecular dynamics simulation. The in vitro synergistic antibacterial effect of the identified inhibitors with meropenem was determined by the checkerboard minimum inhibitory concentration (MIC) assay, time-dependent killing assay and combined disc test. Three mouse infection models were used to further evaluate the in vivo therapeutic efficacy of combined therapy. KEY RESULTS Twelve FDA-approved compounds were initially screened to inhibit the ability of NDM-1 to hydrolyse nitrocefin. Among these compounds, dexrazoxane, embelin, candesartan cilexetil and nordihydroguaiaretic acid were demonstrated to inhibit all tested metallo-β-lactamases and showed an in vitro synergistic bactericidal effect with meropenem against metallo-β-lactamases-producing bacteria. Dexrazoxane, embelin and candesartan cilexetil are metal ion chelating agents, while the inhibition of NDM-1 by nordihydroguaiaretic acid involves its direct binding to the active region of NDM-1. Furthermore, these four drugs dramatically rescued the treatment efficacy of meropenem in three infection models. CONCLUSIONS AND IMPLICATIONS Our observations indicated that dexrazoxane, embelin, candesartan cilexetil and nordihydroguaiaretic acid are promising carbapenem adjuvants against metallo-β-lactamases-positive carbapenem resistant bacterial pathogens.
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Affiliation(s)
- Yan Guo
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Hongtao Liu
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Mengge Yang
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Rui Ding
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Yawen Gao
- College of Food Science and Engineering, Jilin University, Changchun, Jilin, China
| | - Xiaodi Niu
- College of Food Science and Engineering, Jilin University, Changchun, Jilin, China
| | - Xuming Deng
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Jianfeng Wang
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Haihua Feng
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
| | - Jiazhang Qiu
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China
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110
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Silva JD, Jupiter DC, Taglialatela G. Reduced Prevalence of Parkinson's Disease in Patients Prescribed Calcineurin Inhibitors. J Parkinsons Dis 2024; 14:533-543. [PMID: 38427501 DOI: 10.3233/jpd-230313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/03/2024]
Abstract
Background Preclinical evidence suggests calcineurin inhibitors (CNIs) combat α-synuclein-induced neuronal dysfunction and motor impairments. However, whether CNIs prevent or treat Parkinson's disease (PD) in humans has never been investigated. Objective We seek to ascertain if prescription of CNIs is linked to a decreased prevalence of PD in a varied patient population and to glimpse into the mechanism(s) and target site through which CNIs might decrease PD prevalence. Methods We analyzed electronic health records (EHRs) from patients prescribed the brain penetrant CNI tacrolimus (TAC), the peripherally restricted CNI cyclosporine (CySp), or the non-CNI sirolimus (SIR). For comparison, EHRs from a diverse population from the same network served as a general population-like control. After propensity-score matching, prevalence, odds, and hazards of PD diagnoses among these cohorts were compared. Results Patients prescribed CNIs have decreased odds of PD diagnosis compared to the general population-like control, while patients prescribed SIR do not. Notably, patients prescribed TAC have a decreased prevalence of PD compared to patients prescribed SIR or CySp. Conclusions Our results suggest CNIs, especially those acting within the brain, may prevent PD. The reduced prevalence of PD in patients prescribed TAC, compared to patients prescribed SIR, suggests that mechanisms of calcineurin inhibition- other than immunosuppression, which is common to both drugs- are driving the reduction. Therefore, CNIs may provide a promising therapeutic approach for PD.
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Affiliation(s)
- Jacqueline D Silva
- Department of Neurology, Mitchell Center for Neurodegenerative Disorders, University of Texas Medical Branch, Galveston, TX, USA
- Pharmacology and Toxicology Graduate Program, University of Texas Medical Branch, Galveston, TX, USA
| | - Daniel C Jupiter
- Department of Biostatistics and Data Science, University of Texas Medical Branch, Galveston, TX, USA
- Department of Orthopaedics and Rehabilitation, University of Texas Medical Branch, Galveston, TX, USA
| | - Giulio Taglialatela
- Department of Neurology, Mitchell Center for Neurodegenerative Disorders, University of Texas Medical Branch, Galveston, TX, USA
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111
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Chang J, Zou S, Xu S, Xiao Y, Zhu D. Screening of Inhibitors against Idiopathic Pulmonary Fibrosis: Few-shot Machine Learning and Molecule Docking based Drug Repurposing. Curr Comput Aided Drug Des 2024; 20:134-144. [PMID: 37066777 DOI: 10.2174/1573409919666230417080832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 02/12/2023] [Accepted: 02/16/2023] [Indexed: 04/18/2023]
Abstract
INTRODUCTION Idiopathic pulmonary fibrosis is a chronic progressive disorder and is diagnosed as post-COVID fibrosis. Idiopathic pulmonary fibrosis has no effective treatment because of the low therapeutic effects and side effects of currently available drugs. AIM The aim is to screen new inhibitors against idiopathic pulmonary fibrosis from traditional Chinese medicines. METHODS Few-shot-based machine learning and molecule docking were used to predict the potential activities of candidates and calculate the ligand-receptor interactions. In vitro A549 cell model was taken to verify the effects of the selected leads on idiopathic pulmonary fibrosis. RESULTS A logistic regression classifier model with an accuracy of 0.82 was built and, combined with molecule docking, used to predict the activities of candidates. 6 leads were finally screened out and 5 of them were in vitro experimentally verified as effective inhibitors against idiopathic pulmonary fibrosis. CONCLUSION Herbacetin, morusin, swertiamarin, vicenin-2, and vitexin were active inhibitors against idiopathic pulmonary fibrosis. Swertiamarin exhibited the highest anti-idiopathic pulmonary fibrosis effect and should be further in vivo investigated for its activity.
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Affiliation(s)
- Jun Chang
- College of Life Science, Jiangxi Science & Technology Normal University, Nanchang, Jiangxi, China
| | - Shaoqing Zou
- College of Life Science, Jiangxi Science & Technology Normal University, Nanchang, Jiangxi, China
| | - Subo Xu
- College of Life Science, Jiangxi Science & Technology Normal University, Nanchang, Jiangxi, China
| | - Yiwen Xiao
- College of Life Science, Jiangxi Science & Technology Normal University, Nanchang, Jiangxi, China
| | - Du Zhu
- College of Life Science, Jiangxi Science & Technology Normal University, Nanchang, Jiangxi, China
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112
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Driscoll RK, Lyne SB, Voce DJ, Maraka S, Gondi V, Chmura SJ, Dixit KS, Kumthekar PU, Karrison TG, Pytel P, Collins JM, Stupp R, Merrell RT, Lukas RV, Yamini B. A multi-institutional phase I study of acetazolamide with temozolomide in adults with newly diagnosed MGMT-methylated malignant glioma. Neurooncol Adv 2024; 6:vdae014. [PMID: 38420615 PMCID: PMC10901541 DOI: 10.1093/noajnl/vdae014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2024] Open
Abstract
Background A significant unmet need exists for the treatment of glioblastoma, IDH-wildtype (GBM). Preclinical work shows that acetazolamide sensitizes GBM to temozolomide (TMZ) by overcoming TMZ resistance due to BCL-3-dependent upregulation of carbonic anhydrase. Acetazolamide is Food and Drug Administration-approved for the treatment of altitude sickness. Drug repurposing enables the application of drugs to diseases beyond initial indications. This multi-institutional, open-label, phase I trial examined a combination of acetazolamide and TMZ in patients with MGMT promoter-methylated high-grade glioma. Methods A total of 24 patients (GBM, IDH-wildtype = 22; Grade 4 astrocytoma, IDH-mutant = 1; Grade 3 astrocytoma, IDH-mutant = 1) were accrued over 17 months. All patients received oral acetazolamide (250 mg BID for 7 days increased to 500 mg BID for Days 8-21 of each 28-day cycle) during the adjuvant phase of TMZ for up to 6 cycles. Results No patient had a dose-limiting toxicity. Adverse events were consistent with known sequelae of acetazolamide and TMZ. In the 23 WHO Grade 4 patients, the median overall survival (OS) was 30.1 months and the median progression-free survival was 16.0 months. The 2-year OS was 60.9%. In total 37% of the study population had high BCL-3 staining and trended toward shorter OS (17.2 months vs N.R., P = .06). Conclusions The addition of acetazolamide is safe and tolerable in GBM patients receiving standard TMZ. Survival results compare favorably to historical data from randomized trials in patients with MGMT promoter-methylated GBM and support examination of acetazolamide in a randomized trial. BCL-3 expression is a potential biomarker for prognosis in GBM or for patients more likely to benefit from TMZ.
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Affiliation(s)
- Riley K Driscoll
- Department of Neurological Surgery, University of Chicago Medicine, Chicago, Illinois, USA
| | - Sean B Lyne
- Department of Neurological Surgery, University of Chicago Medicine, Chicago, Illinois, USA
| | - David J Voce
- Department of Neurological Surgery, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Stefania Maraka
- Department of Neurology and Rehabilitation, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Vinai Gondi
- Proton Therapy Center and Northwestern Medicine Cancer Center, Warrensville, Illinois, USA
| | - Steven J Chmura
- Department of Radiation and Cellular Oncology, University of Chicago Medicine, Chicago, Illinois, USA
| | - Karan S Dixit
- Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
- Lou & Jean Malnati Brain Tumor Institute, Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, Illinois, USA
| | - Priya U Kumthekar
- Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
- Lou & Jean Malnati Brain Tumor Institute, Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, Illinois, USA
| | - Theodore G Karrison
- Department of Public Health Sciences, University of Chicago, Chicago, Illinois, USA
| | - Peter Pytel
- Department of Pathology, University of Chicago Medicine, Chicago, Illinois, USA
| | - John M Collins
- Department of Radiology, University of Chicago Medicine, Chicago, Illinois, USA
| | - Roger Stupp
- Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
- Lou & Jean Malnati Brain Tumor Institute, Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, Illinois, USA
- Division of Hematology/Oncology, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Ryan T Merrell
- NorthShore University Health System, Evanston, Illinois, USA
| | - Rimas V Lukas
- Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
- Lou & Jean Malnati Brain Tumor Institute, Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, Illinois, USA
| | - Bakhtiar Yamini
- Department of Neurological Surgery, University of Chicago Medicine, Chicago, Illinois, USA
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Yesharim L, Teimourian S. Drug repurposing based on differentially expressed genes suggests drug combinations with possible synergistic effects in treatment of lung adenocarcinoma. Cancer Biol Ther 2023; 24:2253586. [PMID: 37710391 PMCID: PMC10506443 DOI: 10.1080/15384047.2023.2253586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 06/10/2023] [Accepted: 08/25/2023] [Indexed: 09/16/2023] Open
Abstract
Lung adenocarcinoma is one of the leading causes of cancer-related mortality globally. Various treatment approaches and drugs had little influence on overall survival; thus, new drugs and treatment strategies are needed. Drug repositioning (repurposing) seems a favorable approach considering that developing new drugs needs much more time and costs. We performed a meta-analysis on 6 microarray datasets to obtain the main genes with significantly altered expression in lung adenocarcinoma. Following that, we found major gene clusters and hub genes. We assessed their enrichment in biological pathways to get insight into the underlying biological process involved in lung adenocarcinoma pathogenesis. The L1000 database was explored for drug perturbations that might reverse the expression of differentially expressed genes in lung adenocarcinoma. We evaluated the potential drug combinations that interact the most with hub genes and hence have the most potential to reverse the disease process. A total of 2148 differentially expressed genes were identified. Six main gene clusters and 27 significant hub genes mainly involved in cell cycle regulation have been identified. By assessing the interaction between 3 drugs and hub genes and information gained from previous clinical investigations, we suggested the three possible repurposed drug combinations, Vorinostat - Dorsomorphin, PP-110 - Dorsomorphin, and Puromycin - Vorinostat with a high chance of success in clinical trials.
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Affiliation(s)
- Liora Yesharim
- Department of Medical Genetics, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Shahram Teimourian
- Department of Medical Genetics, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
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114
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Ren P, Li S, Wang S, Zhang X, Bai F. Computer-Aided Prediction of the Interactions of Viral Proteases with Antiviral Drugs: Antiviral Potential of Broad-Spectrum Drugs. Molecules 2023; 29:225. [PMID: 38202808 PMCID: PMC10780089 DOI: 10.3390/molecules29010225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 12/27/2023] [Accepted: 12/29/2023] [Indexed: 01/12/2024] Open
Abstract
Human society is facing the threat of various viruses. Proteases are promising targets for the treatment of viral infections. In this study, we collected and profiled 170 protease sequences from 125 viruses that infect humans. Approximately 73 of them are viral 3-chymotrypsin-like proteases (3CLpro), and 11 are pepsin-like aspartic proteases (PAPs). Their sequences, structures, and substrate characteristics were carefully analyzed to identify their conserved nature for proposing a pan-3CLpro or pan-PAPs inhibitor design strategy. To achieve this, we used computational prediction and modeling methods to predict the binding complex structures for those 73 3CLpro with 4 protease inhibitors of SARS-CoV-2 and 11 protease inhibitors of HCV. Similarly, the complex structures for the 11 viral PAPs with 9 protease inhibitors of HIV were also obtained. The binding affinities between these compounds and proteins were also evaluated to assess their pan-protease inhibition via MM-GBSA. Based on the drugs targeting viral 3CLpro and PAPs, repositioning of the active compounds identified several potential uses for these drug molecules. As a result, Compounds 1-2, modified based on the structures of Ray1216 and Asunaprevir, indicate potential inhibition of DENV protease according to our computational simulation results. These studies offer ideas and insights for future research in the design of broad-spectrum antiviral drugs.
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Affiliation(s)
- Pengxuan Ren
- School of Life Science and Technology, Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China; (P.R.); (S.L.); (S.W.)
| | - Shiwei Li
- School of Life Science and Technology, Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China; (P.R.); (S.L.); (S.W.)
| | - Shihang Wang
- School of Life Science and Technology, Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China; (P.R.); (S.L.); (S.W.)
| | - Xianglei Zhang
- School of Life Science and Technology, Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China; (P.R.); (S.L.); (S.W.)
| | - Fang Bai
- School of Life Science and Technology, Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China; (P.R.); (S.L.); (S.W.)
- School of Information Science and Technology, ShanghaiTech University, Shanghai 201210, China
- Shanghai Clinical Research and Trial Center, Shanghai 201210, China
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115
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Zhou Y, Wong MW. In Silico Screening of Multi-Domain Targeted Inhibitors for PTK6: A Strategy Integrating Drug Repurposing and Consensus Docking. Pharmaceuticals (Basel) 2023; 17:60. [PMID: 38256893 PMCID: PMC10818313 DOI: 10.3390/ph17010060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 12/28/2023] [Accepted: 12/28/2023] [Indexed: 01/24/2024] Open
Abstract
Protein tyrosine kinase 6 (PTK6), also known as breast tumor kinase (BRK), serves as a non-receptor intracellular tyrosine kinase within the Src kinases family. Structurally resembling other Src kinases, PTK6 possesses an Src homology 3 (SH3) domain, an Src homology 2 (SH2) domain, and a tyrosine kinase domain (SH1). While considerable efforts have been dedicated to designing PTK6 inhibitors targeting the SH1 domain, which is responsible for kinase activity in various pathways, it has been observed that solely inhibiting the SH1 domain does not effectively suppress PTK6 activity. Subsequent investigations have revealed the involvement of SH2 and SH3 domains in intramolecular and substrate binding interactions, which are crucial for PTK6 function. Consequently, the identification of PTK6 inhibitors targeting not only the SH1 domain but also the SH2 and SH3 domains becomes imperative. Through an in silico structural-based virtual screening approach, incorporating drug repurposing and a consensus docking approach, we have successfully identified four potential ligands capable of concurrently inhibiting the tyrosine kinase domain and SH2/SH3 domains of PT6K simultaneously. This finding suggests potential pathways for therapeutic interventions in PTK6 inhibition.
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Affiliation(s)
| | - Ming Wah Wong
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore;
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Harrer DC, Lüke F, Pukrop T, Ghibelli L, Reichle A, Heudobler D. Addressing Genetic Tumor Heterogeneity, Post-Therapy Metastatic Spread, Cancer Repopulation, and Development of Acquired Tumor Cell Resistance. Cancers (Basel) 2023; 16:180. [PMID: 38201607 PMCID: PMC10778239 DOI: 10.3390/cancers16010180] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 12/08/2023] [Accepted: 12/12/2023] [Indexed: 01/12/2024] Open
Abstract
The concept of post-therapy metastatic spread, cancer repopulation and acquired tumor cell resistance (M-CRAC) rationalizes tumor progression because of tumor cell heterogeneity arising from post-therapy genetic damage and subsequent tissue repair mechanisms. Therapeutic strategies designed to specifically address M-CRAC involve tissue editing approaches, such as low-dose metronomic chemotherapy and the use of transcriptional modulators with or without targeted therapies. Notably, tumor tissue editing holds the potential to treat patients, who are refractory to or relapsing (r/r) after conventional chemotherapy, which is usually based on administering a maximum tolerable dose of a cytostatic drugs. Clinical trials enrolling patients with r/r malignancies, e.g., non-small cell lung cancer, Hodgkin's lymphoma, Langerhans cell histiocytosis and acute myelocytic leukemia, indicate that tissue editing approaches could yield tangible clinical benefit. In contrast to conventional chemotherapy or state-of-the-art precision medicine, tissue editing employs a multi-pronged approach targeting important drivers of M-CRAC across various tumor entities, thereby, simultaneously engaging tumor cell differentiation, immunomodulation, and inflammation control. In this review, we highlight the M-CRAC concept as a major factor in resistance to conventional cancer therapies and discusses tissue editing as a potential treatment.
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Affiliation(s)
- Dennis Christoph Harrer
- Department of Internal Medicine III, Hematology and Oncology, University Hospital Regensburg, Franz-Josef-Strauß-Allee 11, 93053 Regensburg, Germany; (D.C.H.); (F.L.); (T.P.); (D.H.)
| | - Florian Lüke
- Department of Internal Medicine III, Hematology and Oncology, University Hospital Regensburg, Franz-Josef-Strauß-Allee 11, 93053 Regensburg, Germany; (D.C.H.); (F.L.); (T.P.); (D.H.)
- Division of Personalized Tumor Therapy, Fraunhofer Institute for Toxicology and Experimental Medicine, 30625 Regensburg, Germany
| | - Tobias Pukrop
- Department of Internal Medicine III, Hematology and Oncology, University Hospital Regensburg, Franz-Josef-Strauß-Allee 11, 93053 Regensburg, Germany; (D.C.H.); (F.L.); (T.P.); (D.H.)
- Bavarian Cancer Research Center (BZKF), University Hospital Regensburg, 93053 Regensburg, Germany
| | - Lina Ghibelli
- Department of Biology, University of Rome “Tor Vergata”, 00133 Rome, Italy;
| | - Albrecht Reichle
- Department of Internal Medicine III, Hematology and Oncology, University Hospital Regensburg, Franz-Josef-Strauß-Allee 11, 93053 Regensburg, Germany; (D.C.H.); (F.L.); (T.P.); (D.H.)
| | - Daniel Heudobler
- Department of Internal Medicine III, Hematology and Oncology, University Hospital Regensburg, Franz-Josef-Strauß-Allee 11, 93053 Regensburg, Germany; (D.C.H.); (F.L.); (T.P.); (D.H.)
- Bavarian Cancer Research Center (BZKF), University Hospital Regensburg, 93053 Regensburg, Germany
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Almeida-Nunes DL, Silvestre R, Dinis-Oliveira RJ, Ricardo S. Enhancing Immunotherapy in Ovarian Cancer: The Emerging Role of Metformin and Statins. Int J Mol Sci 2023; 25:323. [PMID: 38203494 PMCID: PMC10779012 DOI: 10.3390/ijms25010323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Revised: 12/21/2023] [Accepted: 12/22/2023] [Indexed: 01/12/2024] Open
Abstract
Ovarian cancer metastization is accompanied by the development of malignant ascites, which are associated with poor prognosis. The acellular fraction of this ascitic fluid contains tumor-promoting soluble factors, bioactive lipids, cytokines, and extracellular vesicles, all of which communicate with the tumor cells within this peritoneal fluid. Metabolomic profiling of ovarian cancer ascites has revealed significant differences in the pathways of fatty acids, cholesterol, glucose, and insulin. The proteins involved in these pathways promote tumor growth, resistance to chemotherapy, and immune evasion. Unveiling the key role of this liquid tumor microenvironment is crucial for discovering more efficient treatment options. This review focuses on the cholesterol and insulin pathways in ovarian cancer, identifying statins and metformin as viable treatment options when combined with standard chemotherapy. These findings are supported by clinical trials showing improved overall survival with these combinations. Additionally, statins and metformin are associated with the reversal of T-cell exhaustion, positioning these drugs as potential combinatory strategies to improve immunotherapy outcomes in ovarian cancer patients.
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Affiliation(s)
- Diana Luísa Almeida-Nunes
- Differentiation and Cancer Group, Institute for Research and Innovation in Health (i3S) of the University of Porto, 4200-135 Porto, Portugal;
- 1H-TOXRUN—One Health Toxicology Research Unit, University Institute of Health Sciences, CESPU, CRL, 4585-116 Gandra, Portugal;
| | - Ricardo Silvestre
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, 4710-057 Braga, Portugal;
- ICVS/3B’s—PT Government Associate Laboratory, 4710-057 Braga, Portugal
| | - Ricardo Jorge Dinis-Oliveira
- 1H-TOXRUN—One Health Toxicology Research Unit, University Institute of Health Sciences, CESPU, CRL, 4585-116 Gandra, Portugal;
- UCIBIO-REQUIMTE, Laboratory of Toxicology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4169-007 Porto, Portugal
- Department of Public Health and Forensic Sciences, and Medical Education, Faculty of Medicine, University of Porto, 4169-007 Porto, Portugal
- FOREN—Forensic Science Experts, 1400-136 Lisboa, Portugal
| | - Sara Ricardo
- Differentiation and Cancer Group, Institute for Research and Innovation in Health (i3S) of the University of Porto, 4200-135 Porto, Portugal;
- 1H-TOXRUN—One Health Toxicology Research Unit, University Institute of Health Sciences, CESPU, CRL, 4585-116 Gandra, Portugal;
- Faculty of Medicine, University of Porto, 4169-007 Porto, Portugal
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Sanjak J, Binder J, Yadaw AS, Zhu Q, Mathé EA. Clustering rare diseases within an ontology-enriched knowledge graph. J Am Med Inform Assoc 2023; 31:154-164. [PMID: 37759342 PMCID: PMC10746319 DOI: 10.1093/jamia/ocad186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 08/01/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023] Open
Abstract
OBJECTIVE Identifying sets of rare diseases with shared aspects of etiology and pathophysiology may enable drug repurposing. Toward that aim, we utilized an integrative knowledge graph to construct clusters of rare diseases. MATERIALS AND METHODS Data on 3242 rare diseases were extracted from the National Center for Advancing Translational Science Genetic and Rare Diseases Information center internal data resources. The rare disease data enriched with additional biomedical data, including gene and phenotype ontologies, biological pathway data, and small molecule-target activity data, to create a knowledge graph (KG). Node embeddings were trained and clustered. We validated the disease clusters through semantic similarity and feature enrichment analysis. RESULTS Thirty-seven disease clusters were created with a mean size of 87 diseases. We validate the clusters quantitatively via semantic similarity based on the Orphanet Rare Disease Ontology. In addition, the clusters were analyzed for enrichment of associated genes, revealing that the enriched genes within clusters are highly related. DISCUSSION We demonstrate that node embeddings are an effective method for clustering diseases within a heterogenous KG. Semantically similar diseases and relevant enriched genes have been uncovered within the clusters. Connections between disease clusters and drugs are enumerated for follow-up efforts. CONCLUSION We lay out a method for clustering rare diseases using graph node embeddings. We develop an easy-to-maintain pipeline that can be updated when new data on rare diseases emerges. The embeddings themselves can be paired with other representation learning methods for other data types, such as drugs, to address other predictive modeling problems.
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Affiliation(s)
- Jaleal Sanjak
- Division of Pre-Clinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD, United States
- Chief Technology Office, Booz Allen Hamilton, Bethesda, MD, United States
| | - Jessica Binder
- Division of Pre-Clinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD, United States
| | - Arjun Singh Yadaw
- Division of Pre-Clinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD, United States
| | - Qian Zhu
- Division of Pre-Clinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD, United States
| | - Ewy A Mathé
- Division of Pre-Clinical Innovation, National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Rockville, MD, United States
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Spadella MA, Silva EJR, Chies AB, Almeida LAD. Insights Into Antioxidant Strategies to Counteract Radiation-Induced Male Infertility. Antioxid Redox Signal 2023. [PMID: 37917108 DOI: 10.1089/ars.2023.0282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/03/2023]
Abstract
Significance: Radiotherapy, which employs ionizing radiation to destroy or prevent the multiplication of tumor cells, has been increasingly used in the treatment of neoplastic diseases, especially cancers. However, radiation collaterally leads to prolonged periods of sperm count suppression, presumably due to impaired spermatogenesis by depleting the germ cell pool, which has long-term side effects for male reproduction. Recent Advances: Studies of antioxidant compounds as a potential strategy for male fertility preservation have been performed mainly from animal models, aiming to prevent and restore the male germinal tissue and its function, particularly against the oxidative stress effects of radiation. Evidence in preclinical and clinical trials has shown that inhibitors of the renin-angiotensin system and other drugs, such as statins and metformin, are candidates for ameliorating radiation-induced damage to several tissues, including the testis and prostate. Critical Issues: Research for developing an ideal radioprotective agent is challenging due to toxicity in the normal tissue, tumor radioresistance, cellular response to radiation, costs, regulation, and timeline development. Moreover, male radioprotection experiments in humans, mainly clinical trials, are scarce and use few individuals. This scenario is reflected in the slow progress of innovation in the radioprotection field. Future Directions: Expanding human studies to provide clues on the efficacy and safety of radioprotective compounds in the human reproductive system is necessary. Drug repurposing, frequently used in clinical practice, can be a way to shorten the development pipeline for innovative approaches for radioprotection or radiomitigation of the repercussions of radiotherapy in the male reproductive system.
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Affiliation(s)
| | - Erick J R Silva
- Department of Biophysics and Pharmacology, Institute of Biosciences of Botucatu, São Paulo State University, Botucatu, São Paulo, Brazil
| | - Agnaldo Bruno Chies
- Laboratory of Pharmacology; Marília Medical School-Famema, Marília, São Paulo, Brazil
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Osmanoglu Ö, Gupta SK, Almasi A, Yagci S, Srivastava M, Araujo GHM, Nagy Z, Balkenhol J, Dandekar T. Signaling network analysis reveals fostamatinib as a potential drug to control platelet hyperactivation during SARS-CoV-2 infection. Front Immunol 2023; 14:1285345. [PMID: 38187394 PMCID: PMC10768010 DOI: 10.3389/fimmu.2023.1285345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 12/06/2023] [Indexed: 01/09/2024] Open
Abstract
Introduction Pro-thrombotic events are one of the prevalent causes of intensive care unit (ICU) admissions among COVID-19 patients, although the signaling events in the stimulated platelets are still unclear. Methods We conducted a comparative analysis of platelet transcriptome data from healthy donors, ICU, and non-ICU COVID-19 patients to elucidate these mechanisms. To surpass previous analyses, we constructed models of involved networks and control cascades by integrating a global human signaling network with transcriptome data. We investigated the control of platelet hyperactivation and the specific proteins involved. Results Our study revealed that control of the platelet network in ICU patients is significantly higher than in non-ICU patients. Non-ICU patients require control over fewer proteins for managing platelet hyperactivity compared to ICU patients. Identification of indispensable proteins highlighted key subnetworks, that are targetable for system control in COVID-19-related platelet hyperactivity. We scrutinized FDA-approved drugs targeting indispensable proteins and identified fostamatinib as a potent candidate for preventing thrombosis in COVID-19 patients. Discussion Our findings shed light on how SARS-CoV-2 efficiently affects host platelets by targeting indispensable and critical proteins involved in the control of platelet activity. We evaluated several drugs for specific control of platelet hyperactivity in ICU patients suffering from platelet hyperactivation. The focus of our approach is repurposing existing drugs for optimal control over the signaling network responsible for platelet hyperactivity in COVID-19 patients. Our study offers specific pharmacological recommendations, with drug prioritization tailored to the distinct network states observed in each patient condition. Interactive networks and detailed results can be accessed at https://fostamatinib.bioinfo-wuerz.eu/.
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Affiliation(s)
- Özge Osmanoglu
- Functional Genomics & Systems Biology Group, Department of Bioinformatics, Biocenter, University of Wuerzburg, Wuerzburg, Germany
| | - Shishir K. Gupta
- Evolutionary Genomics Group, Center for Computational and Theoretical Biology, University of Würzburg, Würzburg, Germany
- Institute of Botany, Heinrich Heine University, Düsseldorf, Germany
| | - Anna Almasi
- Functional Genomics & Systems Biology Group, Department of Bioinformatics, Biocenter, University of Wuerzburg, Wuerzburg, Germany
| | - Seray Yagci
- Functional Genomics & Systems Biology Group, Department of Bioinformatics, Biocenter, University of Wuerzburg, Wuerzburg, Germany
| | - Mugdha Srivastava
- Core Unit Systems Medicine, University of Wuerzburg, Wuerzburg, Germany
- Algorithmic Bioinformatics, Department of Computer Science, Heinrich Heine University, Düsseldorf, Germany
| | - Gabriel H. M. Araujo
- University Hospital Würzburg, Institute of Experimental Biomedicine, Würzburg, Germany
| | - Zoltan Nagy
- University Hospital Würzburg, Institute of Experimental Biomedicine, Würzburg, Germany
| | - Johannes Balkenhol
- Functional Genomics & Systems Biology Group, Department of Bioinformatics, Biocenter, University of Wuerzburg, Wuerzburg, Germany
- Chair of Molecular Microscopy, Rudolf Virchow Center for Integrative and Translation Bioimaging, University of Würzburg, Würzburg, Germany
| | - Thomas Dandekar
- Functional Genomics & Systems Biology Group, Department of Bioinformatics, Biocenter, University of Wuerzburg, Wuerzburg, Germany
- European Molecular Biology Laboratory (EMBL) Heidelberg, BioComputing Unit, Heidelberg, Germany
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She P, Yang Y, Li L, Li Y, Liu S, Li Z, Zhou L, Wu Y. Repurposing of the antimalarial agent tafenoquine to combat MRSA. mSystems 2023; 8:e0102623. [PMID: 38047647 PMCID: PMC10734505 DOI: 10.1128/msystems.01026-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 10/25/2023] [Indexed: 12/05/2023] Open
Abstract
IMPORTANCE This study represents the first investigation into the antimicrobial effect of TAF against S. aureus and its potential mechanisms. Our data highlighted the effects of TAF against MRSA planktonic cells, biofilms, and persister cells, which is conducive to broadening the application of TAF. Through mechanistic studies, we revealed that TAF targets bacterial cell membranes. In addition, the in vivo experiments in mice demonstrated the safety and antimicrobial efficacy of TAF, suggesting that TAF could be a potential antibacterial drug candidate for the treatment of infections caused by multiple drug-resistant S. aureus.
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Affiliation(s)
- Pengfei She
- Department of Laboratory Medicine, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Yifan Yang
- Department of Laboratory Medicine, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Linhui Li
- Department of Laboratory Medicine, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Yimin Li
- Department of Laboratory Medicine, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Shasha Liu
- Department of Laboratory Medicine, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Zehao Li
- Department of Laboratory Medicine, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Linying Zhou
- Department of Laboratory Medicine, The Affiliated Changsha Hospital of Xiangya School of Medicine (The First Hospital of Changsha), Central South University, Changsha, China
| | - Yong Wu
- Department of Laboratory Medicine, The Affiliated Changsha Hospital of Xiangya School of Medicine (The First Hospital of Changsha), Central South University, Changsha, China
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De Sousa-Coelho AL, Fraqueza G, Aureliano M. Repurposing Therapeutic Drugs Complexed to Vanadium in Cancer. Pharmaceuticals (Basel) 2023; 17:12. [PMID: 38275998 PMCID: PMC10819319 DOI: 10.3390/ph17010012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 12/16/2023] [Accepted: 12/18/2023] [Indexed: 01/27/2024] Open
Abstract
Repurposing drugs by uncovering new indications for approved drugs accelerates the process of establishing new treatments and reduces the high costs of drug discovery and development. Metal complexes with clinically approved drugs allow further opportunities in cancer therapy-many vanadium compounds have previously shown antitumor effects, which makes vanadium a suitable metal to complex with therapeutic drugs, potentially improving their efficacy in cancer treatment. In this review, covering the last 25 years of research in the field, we identified non-oncology-approved drugs suitable as ligands to obtain different vanadium complexes. Metformin-decavanadate, vanadium-bisphosphonates, vanadyl(IV) complexes with non-steroidal anti-inflammatory drugs, and cetirizine and imidazole-based oxidovanadium(IV) complexes, each has a parent drug known to have different medicinal properties and therapeutic indications, and all showed potential as novel anticancer treatments. Nevertheless, the precise mechanisms of action for these vanadium compounds against cancer are still not fully understood.
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Affiliation(s)
- Ana Luísa De Sousa-Coelho
- Algarve Biomedical Center Research Institute (ABC-RI), Universidade do Algarve, 8005-139 Faro, Portugal
- Algarve Biomedical Center (ABC), Universidade do Algarve, 8005-139 Faro, Portugal
- Escola Superior de Saúde, Universidade do Algarve (ESSUAlg), 8005-139 Faro, Portugal
| | - Gil Fraqueza
- Instituto Superior de Engenharia (ISE), Universidade do Algarve, 8005-139 Faro, Portugal;
- Centro de Ciências do Mar (CCMar), Universidade do Algarve, 8005-139 Faro, Portugal
| | - Manuel Aureliano
- Centro de Ciências do Mar (CCMar), Universidade do Algarve, 8005-139 Faro, Portugal
- Faculdade de Ciências e Tecnologia (FCT), Universidade do Algarve, 8005-139 Faro, Portugal
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Chiariello M, Inzalaco G, Barone V, Gherardini L. Overcoming challenges in glioblastoma treatment: targeting infiltrating cancer cells and harnessing the tumor microenvironment. Front Cell Neurosci 2023; 17:1327621. [PMID: 38188666 PMCID: PMC10767996 DOI: 10.3389/fncel.2023.1327621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 12/05/2023] [Indexed: 01/09/2024] Open
Abstract
Glioblastoma (GB) is a highly malignant primary brain tumor with limited treatment options and poor prognosis. Despite current treatment approaches, including surgical resection, radiation therapy, and chemotherapy with temozolomide (TMZ), GB remains mostly incurable due to its invasive growth pattern, limited drug penetration beyond the blood-brain barrier (BBB), and resistance to conventional therapies. One of the main challenges in GB treatment is effectively eliminating infiltrating cancer cells that remain in the brain parenchyma after primary tumor resection. We've reviewed the most recent challenges and surveyed the potential strategies aimed at enhancing local treatment outcomes.
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Affiliation(s)
- Mario Chiariello
- Institute of Clinical Physiology, Consiglio Nazionale delle Ricerche, Via Fiorentina, Siena, Italy
- Core Research Laboratory (CRL), Istituto per lo Studio, la Prevenzione e la Rete Oncologica (ISPRO), Via Fiorentina, Siena, Italy
| | - Giovanni Inzalaco
- Institute of Clinical Physiology, Consiglio Nazionale delle Ricerche, Via Fiorentina, Siena, Italy
- Core Research Laboratory (CRL), Istituto per lo Studio, la Prevenzione e la Rete Oncologica (ISPRO), Via Fiorentina, Siena, Italy
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Virginia Barone
- Department of Molecular and Developmental Medicine, University of Siena, Siena, Italy
| | - Lisa Gherardini
- Institute of Clinical Physiology, Consiglio Nazionale delle Ricerche, Via Fiorentina, Siena, Italy
- Core Research Laboratory (CRL), Istituto per lo Studio, la Prevenzione e la Rete Oncologica (ISPRO), Via Fiorentina, Siena, Italy
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Anderson C, Bucholc M, McClean PL, Zhang SD. The Potential of a Stratified Approach to Drug Repurposing in Alzheimer's Disease. Biomolecules 2023; 14:11. [PMID: 38275752 PMCID: PMC10813465 DOI: 10.3390/biom14010011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 12/13/2023] [Accepted: 12/15/2023] [Indexed: 01/27/2024] Open
Abstract
Alzheimer's disease (AD) is a complex neurodegenerative condition that is characterized by the build-up of amyloid-beta plaques and neurofibrillary tangles. While multiple theories explaining the aetiology of the disease have been suggested, the underlying cause of the disease is still unknown. Despite this, several modifiable and non-modifiable factors that increase the risk of developing AD have been identified. To date, only eight AD drugs have ever gained regulatory approval, including six symptomatic and two disease-modifying drugs. However, not all are available in all countries and high costs associated with new disease-modifying biologics prevent large proportions of the patient population from accessing them. With the current patient population expected to triple by 2050, it is imperative that new, effective, and affordable drugs become available to patients. Traditional drug development strategies have a 99% failure rate in AD, which is far higher than in other disease areas. Even when a drug does reach the market, additional barriers such as high cost and lack of accessibility prevent patients from benefiting from them. In this review, we discuss how a stratified medicine drug repurposing approach may address some of the limitations and barriers that traditional strategies face in relation to drug development in AD. We believe that novel, stratified drug repurposing studies may expedite the discovery of alternative, effective, and more affordable treatment options for a rapidly expanding patient population in comparison with traditional drug development methods.
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Affiliation(s)
- Chloe Anderson
- Personalised Medicine Centre, School of Medicine, Altnagelvin Hospital Campus, Ulster University, Glenshane Road, Derry/Londonderry BT47 6SB, UK;
| | - Magda Bucholc
- School of Computing, Engineering and Intelligent Systems, Magee Campus, Ulster University, Northland Road, Derry/Londonderry BT48 7JL, UK
| | - Paula L. McClean
- Personalised Medicine Centre, School of Medicine, Altnagelvin Hospital Campus, Ulster University, Glenshane Road, Derry/Londonderry BT47 6SB, UK;
| | - Shu-Dong Zhang
- Personalised Medicine Centre, School of Medicine, Altnagelvin Hospital Campus, Ulster University, Glenshane Road, Derry/Londonderry BT47 6SB, UK;
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Zhang L, Wang F, Xia K, Yu Z, Fu Y, Huang T, Fan D. Unlocking the Medicinal Mysteries: Preventing Lacunar Stroke with Drug Repurposing. Biomedicines 2023; 12:17. [PMID: 38275377 PMCID: PMC10813761 DOI: 10.3390/biomedicines12010017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 12/10/2023] [Accepted: 12/11/2023] [Indexed: 01/27/2024] Open
Abstract
Currently, only the general control of the risk factors is known to prevent lacunar cerebral infarction, but it is unknown which type of medication for controlling the risk factors has a causal relationship with reducing the risk of lacunar infarction. To unlock this medical mystery, drug-target Mendelian randomization analysis was applied to estimate the effect of common antihypertensive agents, hypolipidemic agents, and hypoglycemic agents on lacunar stroke. Lacunar stroke data for the transethnic analysis were derived from meta-analyses comprising 7338 cases and 254,798 controls. We have confirmed that genetic variants mimicking calcium channel blockers were found to most stably prevent lacunar stroke. The genetic variants at or near HMGCR, NPC1L1, and APOC3 were predicted to decrease lacunar stroke incidence in drug-target MR analysis. These variants mimic the effects of statins, ezetimibe, and antisense anti-apoC3 agents, respectively. Genetically proxied GLP1R agonism had a marginal effect on lacunar stroke, while a genetically proxied improvement in overall glycemic control was associated with reduced lacunar stroke risk. Here, we show that certain categories of drugs currently used in clinical practice can more effectively reduce the risk of stroke. Repurposing several drugs with well-established safety and low costs for lacunar stroke prevention should be given high priority when doctors are making decisions in clinical practice. This may contribute to healthier brain aging.
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Affiliation(s)
- Linjing Zhang
- Department of Neurology, Peking University Third Hospital, Beijing 100191, China; (L.Z.); (F.W.); (K.X.); (Z.Y.); (Y.F.)
| | - Fan Wang
- Department of Neurology, Peking University Third Hospital, Beijing 100191, China; (L.Z.); (F.W.); (K.X.); (Z.Y.); (Y.F.)
| | - Kailin Xia
- Department of Neurology, Peking University Third Hospital, Beijing 100191, China; (L.Z.); (F.W.); (K.X.); (Z.Y.); (Y.F.)
| | - Zhou Yu
- Department of Neurology, Peking University Third Hospital, Beijing 100191, China; (L.Z.); (F.W.); (K.X.); (Z.Y.); (Y.F.)
| | - Yu Fu
- Department of Neurology, Peking University Third Hospital, Beijing 100191, China; (L.Z.); (F.W.); (K.X.); (Z.Y.); (Y.F.)
| | - Tao Huang
- Department of Neurology, Peking University Third Hospital, Beijing 100191, China; (L.Z.); (F.W.); (K.X.); (Z.Y.); (Y.F.)
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing 100871, China
- Center for Intelligent Public Health, Institute for Artificial Intelligence, Peking University, Beijing 100871, China
| | - Dongsheng Fan
- Department of Neurology, Peking University Third Hospital, Beijing 100191, China; (L.Z.); (F.W.); (K.X.); (Z.Y.); (Y.F.)
- Beijing Key Laboratory of Biomarker and Translational Research in Neurodegenerative Diseases, Beijing 100191, China
- Key Laboratory for Neuroscience, National Health Commission/Ministry of Education, Peking University, Beijing 100871, China
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Pușcașu C, Zanfirescu A, Negreș S, Șeremet OC. Exploring the Multifaceted Potential of Sildenafil in Medicine. Medicina (Kaunas) 2023; 59:2190. [PMID: 38138293 PMCID: PMC10744870 DOI: 10.3390/medicina59122190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 12/11/2023] [Accepted: 12/14/2023] [Indexed: 12/24/2023]
Abstract
Phosphodiesterase type 5 (PDE5) is pivotal in cellular signalling, regulating cyclic guanosine monophosphate (cGMP) levels crucial for smooth muscle relaxation and vasodilation. By targeting cGMP for degradation, PDE5 inhibits sustained vasodilation. PDE5 operates in diverse anatomical regions, with its upregulation linked to various pathologies, including cancer and neurodegenerative diseases. Sildenafil, a selective PDE5 inhibitor, is prescribed for erectile dysfunction and pulmonary arterial hypertension. However, considering the extensive roles of PDE5, sildenafil might be useful in other pathologies. This review aims to comprehensively explore sildenafil's therapeutic potential across medicine, addressing a gap in the current literature. Recognising sildenafil's broader potential may unveil new treatment avenues, optimising existing approaches and broadening its clinical application.
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Affiliation(s)
| | - Anca Zanfirescu
- Faculty of Pharmacy, “Carol Davila” University of Medicine and Pharmacy, Traian Vuia 6, 020956 Bucharest, Romania; (C.P.); (S.N.); (O.C.Ș.)
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Chen D, Chen S, Zhou F, Bo Chen L, Chen MW. Synergistic Effects of Tranylcypromine and NRF2 Inhibitor: A Repurposing Strategy for Effective Cancer Therapy. ChemMedChem 2023; 18:e202300282. [PMID: 37871186 DOI: 10.1002/cmdc.202300282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 10/19/2023] [Accepted: 10/23/2023] [Indexed: 10/25/2023]
Abstract
Drug repurposing has emerged as an attractive strategy for accelerating drug discovery for cancer treatment. In this study, we investigated combining Tranylcypromine (TCP) with a number of well-characterized drugs. Among these combinations, NRF2 inhibitor (ML385) exhibited synergistic effects in combination with TCP. Specifically, our results showed that the combination of TCP and ML385 resulted in a significant reduction in tumor proliferation while neither drug affected cancer cell growth meaningfully on its own. While further studies are needed to understand fully the extent of the synergistic efficacy, the underlying respective mechanisms and the potential side effects of this approach, our study has yielded a promising start for the development of an effective combination cancer therapy.
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Affiliation(s)
- Delos Chen
- Curamir Therapeutics, Inc., 3 Gill Street, Unit G, 01801, Woburn, MA, USA
- Mustians House, Eton College, Eton Wick Road, SL4 6EX, Eton, Berkshire, UK
| | - Skye Chen
- Curamir Therapeutics, Inc., 3 Gill Street, Unit G, 01801, Woburn, MA, USA
- Mustians House, Eton College, Eton Wick Road, SL4 6EX, Eton, Berkshire, UK
| | - Fangheng Zhou
- Curamir Therapeutics, Inc., 3 Gill Street, Unit G, 01801, Woburn, MA, USA
| | - Lan Bo Chen
- Curamir Therapeutics, Inc., 3 Gill Street, Unit G, 01801, Woburn, MA, USA
- Department of Pathology, Harvard Medical School, 25 Shattuck Street, 02115, Boston, MA, USA
| | - Ming-Wei Chen
- Curamir Therapeutics, Inc., 3 Gill Street, Unit G, 01801, Woburn, MA, USA
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Ramos S, Vicente-Blázquez A, López-Rubio M, Gallego-Yerga L, Álvarez R, Peláez R. Frentizole, a Nontoxic Immunosuppressive Drug, and Its Analogs Display Antitumor Activity via Tubulin Inhibition. Int J Mol Sci 2023; 24:17474. [PMID: 38139302 PMCID: PMC10744269 DOI: 10.3390/ijms242417474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/04/2023] [Accepted: 12/09/2023] [Indexed: 12/24/2023] Open
Abstract
Antimitotic agents are one of the more successful types of anticancer drugs, but they suffer from toxicity and resistance. The application of approved drugs to new indications (i.e., drug repurposing) is a promising strategy for the development of new drugs. It relies on finding pattern similarities: drug effects to other drugs or conditions, similar toxicities, or structural similarity. Here, we recursively searched a database of approved drugs for structural similarity to several antimitotic agents binding to a specific site of tubulin, with the expectation of finding structures that could fit in it. These searches repeatedly retrieved frentizole, an approved nontoxic anti-inflammatory drug, thus indicating that it might behave as an antimitotic drug devoid of the undesired toxic effects. We also show that the usual repurposing approach to searching for targets of frentizole failed in most cases to find such a relationship. We synthesized frentizole and a series of analogs to assay them as antimitotic agents and found antiproliferative activity against HeLa tumor cells, inhibition of microtubule formation within cells, and arrest at the G2/M phases of the cell cycle, phenotypes that agree with binding to tubulin as the mechanism of action. The docking studies suggest binding at the colchicine site in different modes. These results support the repurposing of frentizole for cancer treatment, especially for glioblastoma.
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Affiliation(s)
- Sergio Ramos
- Laboratorio de Química Orgánica y Farmacéutica, Departamento de Ciencias Farmacéuticas, Campus Miguel de Unamuno, Universidad de Salamanca, 37008 Salamanca, Spain; (S.R.); (M.L.-R.); (L.G.-Y.); (R.Á.)
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Facultad de Farmacia, Campus Miguel de Unamuno, Universidad de Salamanca, 37008 Salamanca, Spain
- Centro de Investigación de Enfermedades Tropicales de la Universidad de Salamanca (CIETUS), Facultad de Farmacia, Campus Miguel de Unamuno, Universidad de Salamanca, 37008 Salamanca, Spain
| | - Alba Vicente-Blázquez
- Laboratorio de Química Orgánica y Farmacéutica, Departamento de Ciencias Farmacéuticas, Campus Miguel de Unamuno, Universidad de Salamanca, 37008 Salamanca, Spain; (S.R.); (M.L.-R.); (L.G.-Y.); (R.Á.)
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Facultad de Farmacia, Campus Miguel de Unamuno, Universidad de Salamanca, 37008 Salamanca, Spain
- Centro de Investigación de Enfermedades Tropicales de la Universidad de Salamanca (CIETUS), Facultad de Farmacia, Campus Miguel de Unamuno, Universidad de Salamanca, 37008 Salamanca, Spain
| | - Marta López-Rubio
- Laboratorio de Química Orgánica y Farmacéutica, Departamento de Ciencias Farmacéuticas, Campus Miguel de Unamuno, Universidad de Salamanca, 37008 Salamanca, Spain; (S.R.); (M.L.-R.); (L.G.-Y.); (R.Á.)
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Facultad de Farmacia, Campus Miguel de Unamuno, Universidad de Salamanca, 37008 Salamanca, Spain
- Centro de Investigación de Enfermedades Tropicales de la Universidad de Salamanca (CIETUS), Facultad de Farmacia, Campus Miguel de Unamuno, Universidad de Salamanca, 37008 Salamanca, Spain
| | - Laura Gallego-Yerga
- Laboratorio de Química Orgánica y Farmacéutica, Departamento de Ciencias Farmacéuticas, Campus Miguel de Unamuno, Universidad de Salamanca, 37008 Salamanca, Spain; (S.R.); (M.L.-R.); (L.G.-Y.); (R.Á.)
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Facultad de Farmacia, Campus Miguel de Unamuno, Universidad de Salamanca, 37008 Salamanca, Spain
- Centro de Investigación de Enfermedades Tropicales de la Universidad de Salamanca (CIETUS), Facultad de Farmacia, Campus Miguel de Unamuno, Universidad de Salamanca, 37008 Salamanca, Spain
| | - Raquel Álvarez
- Laboratorio de Química Orgánica y Farmacéutica, Departamento de Ciencias Farmacéuticas, Campus Miguel de Unamuno, Universidad de Salamanca, 37008 Salamanca, Spain; (S.R.); (M.L.-R.); (L.G.-Y.); (R.Á.)
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Facultad de Farmacia, Campus Miguel de Unamuno, Universidad de Salamanca, 37008 Salamanca, Spain
- Centro de Investigación de Enfermedades Tropicales de la Universidad de Salamanca (CIETUS), Facultad de Farmacia, Campus Miguel de Unamuno, Universidad de Salamanca, 37008 Salamanca, Spain
| | - Rafael Peláez
- Laboratorio de Química Orgánica y Farmacéutica, Departamento de Ciencias Farmacéuticas, Campus Miguel de Unamuno, Universidad de Salamanca, 37008 Salamanca, Spain; (S.R.); (M.L.-R.); (L.G.-Y.); (R.Á.)
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Facultad de Farmacia, Campus Miguel de Unamuno, Universidad de Salamanca, 37008 Salamanca, Spain
- Centro de Investigación de Enfermedades Tropicales de la Universidad de Salamanca (CIETUS), Facultad de Farmacia, Campus Miguel de Unamuno, Universidad de Salamanca, 37008 Salamanca, Spain
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Pace A, Lombardi G, Villani V, Benincasa D, Abbruzzese C, Cestonaro I, Corrà M, Padovan M, Cerretti G, Caccese M, Silvani A, Gaviani P, Giannarelli D, Ciliberto G, Paggi MG. Efficacy and safety of chlorpromazine as an adjuvant therapy for glioblastoma in patients with unmethylated MGMT gene promoter: RACTAC, a phase II multicenter trial. Front Oncol 2023; 13:1320710. [PMID: 38162492 PMCID: PMC10755935 DOI: 10.3389/fonc.2023.1320710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 11/20/2023] [Indexed: 01/03/2024] Open
Abstract
Introduction Drug repurposing is a promising strategy to develop new treatments for glioblastoma. In this phase II clinical trial, we evaluated the addition of chlorpromazine to temozolomide in the adjuvant phase of the standard first-line therapeutic protocol in patients with unmethylated MGMT gene promoter. Methods This was a multicenter phase II single-arm clinical trial. The experimental procedure involved the combination of CPZ with standard treatment with TMZ in the adjuvant phase of the Stupp protocol in newly-diagnosed GBM patients carrying an unmethylated MGMT gene promoter. Progression-free survival was the primary endpoint. Secondary endpoints were overall survival and toxicity. Results Forty-one patients were evaluated. Twenty patients (48.7%) completed 6 cycles of treatment with TMZ+CPZ. At 6 months, 27 patients (65.8%) were without progression, achieving the primary endpoint. Median PFS was 8.0 months (95% CI: 7.0-9.0). Median OS was 15.0 months (95% CI: 13.1-16.9). Adverse events led to reduction or interruption of CPZ dosage in 4 patients (9.7%). Discussion The addition of CPZ to standard TMZ in the first-line treatment of GBM patients with unmethylated MGMT gene promoter was safe and led to a longer PFS than expected in this population of patients. These findings provide proof-of-concept for the potential of adding CPZ to standard TMZ treatment in GBM patients with unmethylated MGMT gene promoter. Clinical trial registration https://clinicaltrials.gov/study/NCT04224441, identifier NCT04224441.
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Affiliation(s)
- Andrea Pace
- IRCCS - Regina Elena National Cancer Institute, Rome, Italy
| | | | | | | | | | | | - Martina Corrà
- Veneto Institute of Oncology IOV-IRCCS, Padua, Italy
| | - Marta Padovan
- Veneto Institute of Oncology IOV-IRCCS, Padua, Italy
| | | | - Mario Caccese
- Veneto Institute of Oncology IOV-IRCCS, Padua, Italy
| | | | | | | | | | - Marco G. Paggi
- IRCCS - Regina Elena National Cancer Institute, Rome, Italy
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Sotorilli GE, Gravina HD, de Carvalho AC, Shimizu JF, Fontoura MA, Melo-Hanchuk TD, Cordeiro AT, Marques RE. Phenotypical Screening of an MMV Open Box Library and Identification of Compounds with Antiviral Activity against St. Louis Encephalitis Virus. Viruses 2023; 15:2416. [PMID: 38140657 PMCID: PMC10747599 DOI: 10.3390/v15122416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 12/02/2023] [Accepted: 12/09/2023] [Indexed: 12/24/2023] Open
Abstract
St. Louis encephalitis virus (SLEV) is a neglected mosquito-borne Flavivirus that may cause severe neurological disease in humans and other animals. There are no specific treatments against SLEV infection or disease approved for human use, and drug repurposing may represent an opportunity to accelerate the development of treatments against SLEV. Here we present a scalable, medium-throughput phenotypic cell culture-based screening assay on Vero CCL81 cells to identify bioactive compounds that could be repurposed against SLEV infection. We screened eighty compounds from the Medicines for Malaria Venture (MMV) COVID Box library to identify nine (11%) compounds that protected cell cultures from SLEV-induced cytopathic effects, with low- to mid-micromolar potencies. We validated six hit compounds using viral plaque-forming assays to find that the compounds ABT-239, Amiodarone, Fluphenazine, Posaconazole, Triparanol, and Vidofludimus presented varied levels of antiviral activity and selectivity depending on the mammalian cell type used for testing. Importantly, we identified and validated the antiviral activity of the anti-flavivirus nucleoside analog 7DMA against SLEV. Triparanol and Fluphenazine reduced infectious viral loads in both Vero CCL81 and HBEC-5i cell cultures and, similar to the other validated compounds, are likely to exert antiviral activity through a molecular target in the host.
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Affiliation(s)
- Giuliana Eboli Sotorilli
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas 13083-100, Brazil; (G.E.S.); (H.D.G.); (A.C.d.C.); (J.F.S.); (M.A.F.); (T.D.M.-H.); (A.T.C.)
- Department of Genetics, Microbiology and Immunology, Institute of Biology, State University of Campinas (UNICAMP), Campinas 13083-100, Brazil
| | - Humberto Doriguetto Gravina
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas 13083-100, Brazil; (G.E.S.); (H.D.G.); (A.C.d.C.); (J.F.S.); (M.A.F.); (T.D.M.-H.); (A.T.C.)
| | - Ana Carolina de Carvalho
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas 13083-100, Brazil; (G.E.S.); (H.D.G.); (A.C.d.C.); (J.F.S.); (M.A.F.); (T.D.M.-H.); (A.T.C.)
- Department of Genetics, Microbiology and Immunology, Institute of Biology, State University of Campinas (UNICAMP), Campinas 13083-100, Brazil
| | - Jacqueline Farinha Shimizu
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas 13083-100, Brazil; (G.E.S.); (H.D.G.); (A.C.d.C.); (J.F.S.); (M.A.F.); (T.D.M.-H.); (A.T.C.)
| | - Marina Alves Fontoura
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas 13083-100, Brazil; (G.E.S.); (H.D.G.); (A.C.d.C.); (J.F.S.); (M.A.F.); (T.D.M.-H.); (A.T.C.)
- Department of Cellular and Structural Biology, Institute of Biology, State University of Campinas (UNICAMP), Campinas 13083-100, Brazil
| | - Talita Diniz Melo-Hanchuk
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas 13083-100, Brazil; (G.E.S.); (H.D.G.); (A.C.d.C.); (J.F.S.); (M.A.F.); (T.D.M.-H.); (A.T.C.)
| | - Artur Torres Cordeiro
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas 13083-100, Brazil; (G.E.S.); (H.D.G.); (A.C.d.C.); (J.F.S.); (M.A.F.); (T.D.M.-H.); (A.T.C.)
| | - Rafael Elias Marques
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas 13083-100, Brazil; (G.E.S.); (H.D.G.); (A.C.d.C.); (J.F.S.); (M.A.F.); (T.D.M.-H.); (A.T.C.)
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Rakshit G, Biswas A, Jayaprakash V. In Silico Drug Repurposing Studies for the Discovery of Novel Salicyl-AMP Ligase (MbtA)Inhibitors. Pathogens 2023; 12:1433. [PMID: 38133316 PMCID: PMC10745912 DOI: 10.3390/pathogens12121433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 11/28/2023] [Accepted: 12/06/2023] [Indexed: 12/23/2023] Open
Abstract
Tuberculosis (TB) continues to pose a global health challenge, exacerbated by the rise of drug-resistant strains. The development of new TB therapies is an arduous and time-consuming process. To expedite the discovery of effective treatments, computational structure-based drug repurposing has emerged as a promising strategy. From this perspective, conditionally essential targets present a valuable opportunity, and the mycobactin biosynthesis pathway stands out as a prime example highlighting the intricate response of Mycobacterium tuberculosis (Mtb) to changes in iron availability. This study focuses on the repurposing and revival of FDA-approved drugs (library) as potential inhibitors of MbtA, a crucial enzyme in mycobactin biosynthesis in Mtb conserved among all species of mycobacteria. The literature suggests this pathway to be associated with drug efflux pumps, which potentially contribute to drug resistance. This makes it a potential target for antitubercular drug discovery. Herein, we utilized cheminformatics and structure-based drug repurposing approaches, viz., molecular docking, dynamics, and PCA analysis, to decode the intermolecular interactions and binding affinity of the FDA-reported molecules against MbtA. Virtual screening revealed ten molecules with significant binding affinities and interactions with MbtA. These drugs, originally designed for different therapeutic indications (four antiviral, three anticancer, one CYP450 inhibitor, one ACE inhibitor, and one leukotriene antagonist), were repurposed as potential MbtA inhibitors. Furthermore, our study explores the binding modes and interactions between these drugs and MbtA, shedding light on the structural basis of their inhibitory potential. Principal component analysis highlighted significant motions in MbtA-bound ligands, emphasizing the stability of the top protein-ligand complexes (PLCs). This computational approach provides a swift and cost-effective method for identifying new MbtA inhibitors, which can subsequently undergo validation through experimental assays. This streamlined process is facilitated by the fact that these compounds are already FDA-approved and have established safety and efficacy profiles. This study has the potential to lay the groundwork for addressing the urgent global health challenge at hand, specifically in the context of combating antimicrobial resistance (AMR) and tuberculosis (TB).
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Affiliation(s)
| | | | - Venkatesan Jayaprakash
- Department of Pharmaceutical Sciences & Technology, Birla Institute of Technology, Mesra, Ranchi 835215, Jharkhand, India; (G.R.); (A.B.)
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Pisoni LA, Semple SJ, Liu S, Sykes MJ, Venter H. Combined Structure- and Ligand-Based Approach for the Identification of Inhibitors of AcrAB-TolC in Escherichia coli. ACS Infect Dis 2023; 9:2504-2522. [PMID: 37888944 DOI: 10.1021/acsinfecdis.3c00350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
The inhibition of efflux pumps is a promising approach to combating multidrug-resistant bacteria. We have developed a combined structure- and ligand-based model, using OpenEye software, for the identification of inhibitors of AcrB, the inner membrane protein component of the AcrAB-TolC efflux pump in Escherichia coli. From a database of 1391 FDA-approved drugs, 23 compounds were selected to test for efflux inhibition in E. coli. Seven compounds, including ivacaftor (25), butenafine (19), naftifine (27), pimozide (30), thioridazine (35), trifluoperazine (37), and meloxicam (26), enhanced the activity of at least one antimicrobial substrate and inhibited the efflux pump-mediated removal of the substrate Nile Red from cells. Ivacaftor (25) inhibited efflux dose dependently, had no effect on an E. coli strain with genomic deletion of the gene encoding AcrB, and did not damage the bacterial outer membrane. In the presence of a sub-minimum inhibitory concentration (MIC) of the outer membrane permeabilizer colistin, ivacaftor at 1 μg/mL reduced the MICs of erythromycin and minocycline by 4- to 8-fold. The identification of seven potential AcrB inhibitors shows the merits of a combined structure- and ligand-based approach to virtual screening.
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Affiliation(s)
- Lily A Pisoni
- Health and Biomedical Innovation, Clinical and Health Sciences, University of South Australia, Adelaide, South Australia 5000, Australia
- Quality Use of Medicines and Pharmacy Research Centre, Clinical and Health Sciences, University of South Australia, Adelaide, South Australia 5000, Australia
| | - Susan J Semple
- Quality Use of Medicines and Pharmacy Research Centre, Clinical and Health Sciences, University of South Australia, Adelaide, South Australia 5000, Australia
| | - Sida Liu
- Health and Biomedical Innovation, Clinical and Health Sciences, University of South Australia, Adelaide, South Australia 5000, Australia
| | - Matthew J Sykes
- Health and Biomedical Innovation, Clinical and Health Sciences, University of South Australia, Adelaide, South Australia 5000, Australia
| | - Henrietta Venter
- Health and Biomedical Innovation, Clinical and Health Sciences, University of South Australia, Adelaide, South Australia 5000, Australia
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Xisto MIDDS, Rollin-Pinheiro R, Rochetti VP, de Castro-Almeida Y, Borba-Santos LP, dos Santos-Freitas GMP, Cypriano J, Abreu FDÁ, Rozental S, Barreto-Bergter E. Miltefosine: A Repurposing Drug against Mucorales Pathogens. J Fungi (Basel) 2023; 9:1166. [PMID: 38132767 PMCID: PMC10744482 DOI: 10.3390/jof9121166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 11/27/2023] [Accepted: 12/01/2023] [Indexed: 12/23/2023] Open
Abstract
Mucorales are a group of non-septated filamentous fungi widely distributed in nature, frequently associated with human infections, and are intrinsically resistant to many antifungal drugs. For these reasons, there is an urgent need to improve the clinical management of mucormycosis. Miltefosine, which is a phospholipid analogue of alkylphosphocholine, has been considered a promising repurposing drug to be used to treat fungal infections. In the present study, miltefosine displayed antifungal activity against a variety of Mucorales species, and it was also active against biofilms formed by these fungi. Treatment with miltefosine revealed modifications of cell wall components, neutral lipids, mitochondrial membrane potential, cell morphology, and the induction of oxidative stress. Treated Mucorales cells also presented an increased susceptibility to SDS. Purified ergosterol and glucosylceramide added to the culture medium increased miltefosine MIC, suggesting its interaction with fungal lipids. These data contribute to elucidating the effect of a promising drug repurposed to act against some relevant fungal pathogens that significantly impact public health.
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Affiliation(s)
- Mariana Ingrid Dutra da Silva Xisto
- Laboratório de Química Biológica de Microrganismos, Departamento de Microbiologia Geral, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil; (R.R.-P.); (V.P.R.); (Y.d.C.-A.); (G.M.P.d.S.-F.)
| | - Rodrigo Rollin-Pinheiro
- Laboratório de Química Biológica de Microrganismos, Departamento de Microbiologia Geral, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil; (R.R.-P.); (V.P.R.); (Y.d.C.-A.); (G.M.P.d.S.-F.)
| | - Victor Pereira Rochetti
- Laboratório de Química Biológica de Microrganismos, Departamento de Microbiologia Geral, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil; (R.R.-P.); (V.P.R.); (Y.d.C.-A.); (G.M.P.d.S.-F.)
| | - Yuri de Castro-Almeida
- Laboratório de Química Biológica de Microrganismos, Departamento de Microbiologia Geral, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil; (R.R.-P.); (V.P.R.); (Y.d.C.-A.); (G.M.P.d.S.-F.)
| | - Luana Pereira Borba-Santos
- Laboratório de Biologia Celular de Fungos, Programa de Biologia Celular e Parasitologia, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil; (L.P.B.-S.); (S.R.)
| | - Giulia Maria Pires dos Santos-Freitas
- Laboratório de Química Biológica de Microrganismos, Departamento de Microbiologia Geral, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil; (R.R.-P.); (V.P.R.); (Y.d.C.-A.); (G.M.P.d.S.-F.)
| | - Jefferson Cypriano
- Laboratório de Biologia Celular e Magnetotaxia & Unidade de Microscopia Multiusuário, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil; (J.C.); (F.d.Á.A.)
| | - Fernanda de Ávila Abreu
- Laboratório de Biologia Celular e Magnetotaxia & Unidade de Microscopia Multiusuário, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil; (J.C.); (F.d.Á.A.)
| | - Sonia Rozental
- Laboratório de Biologia Celular de Fungos, Programa de Biologia Celular e Parasitologia, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil; (L.P.B.-S.); (S.R.)
| | - Eliana Barreto-Bergter
- Laboratório de Química Biológica de Microrganismos, Departamento de Microbiologia Geral, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil; (R.R.-P.); (V.P.R.); (Y.d.C.-A.); (G.M.P.d.S.-F.)
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Criscuolo E, De Sciscio ML, De Cristofaro A, Nicoara C, Maccarrone M, Fezza F. Computational and Experimental Drug Repurposing of FDA-Approved Compounds Targeting the Cannabinoid Receptor CB1. Pharmaceuticals (Basel) 2023; 16:1678. [PMID: 38139805 PMCID: PMC10747202 DOI: 10.3390/ph16121678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 11/25/2023] [Accepted: 11/30/2023] [Indexed: 12/24/2023] Open
Abstract
The cannabinoid receptor 1 (CB1R) plays a pivotal role in regulating various physiopathological processes, thus positioning itself as a promising and sought-after therapeutic target. However, the search for specific and effective CB1R ligands has been challenging, prompting the exploration of drug repurposing (DR) strategies. In this study, we present an innovative DR approach that combines computational screening and experimental validation to identify potential Food and Drug Administration (FDA)-approved compounds that can interact with the CB1R. Initially, a large-scale virtual screening was conducted using molecular docking simulations, where a library of FDA-approved drugs was screened against the CB1R's three-dimensional structures. This in silico analysis allowed us to prioritize compounds based on their binding affinity through two different filters. Subsequently, the shortlisted compounds were subjected to in vitro assays using cellular and biochemical models to validate their interaction with the CB1R and determine their functional impact. Our results reveal FDA-approved compounds that exhibit promising interactions with the CB1R. These findings open up exciting opportunities for DR in various disorders where CB1R signaling is implicated. In conclusion, our integrated computational and experimental approach demonstrates the feasibility of DR for discovering CB1R modulators from existing FDA-approved compounds. By leveraging the wealth of existing pharmacological data, this strategy accelerates the identification of potential therapeutics while reducing development costs and timelines. The findings from this study hold the potential to advance novel treatments for a range of CB1R -associated diseases, presenting a significant step forward in drug discovery research.
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Affiliation(s)
- Emanuele Criscuolo
- Department of Experimental Medicine, Tor Vergata University of Rome, Via Montpellier 1, 00121 Rome, Italy; (E.C.); (C.N.)
| | - Maria Laura De Sciscio
- Department of Medicine, Campus Bio-Medico University of Rome, Via Alvaro del Portillo 21, 00128 Rome, Italy; (M.L.D.S.); (A.D.C.)
| | - Angela De Cristofaro
- Department of Medicine, Campus Bio-Medico University of Rome, Via Alvaro del Portillo 21, 00128 Rome, Italy; (M.L.D.S.); (A.D.C.)
| | - Catalin Nicoara
- Department of Experimental Medicine, Tor Vergata University of Rome, Via Montpellier 1, 00121 Rome, Italy; (E.C.); (C.N.)
| | - Mauro Maccarrone
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio, Coppito, 67100 L’Aquila, Italy
- European Center for Brain Research/Santa Lucia Foundation IRCCS, Via Del Fosso di Fiorano 64, 00143 Rome, Italy
| | - Filomena Fezza
- Department of Experimental Medicine, Tor Vergata University of Rome, Via Montpellier 1, 00121 Rome, Italy; (E.C.); (C.N.)
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135
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Kori M, Temiz K, Gov E. Network medicine approaches for identification of novel prognostic systems biomarkers and drug candidates for papillary thyroid carcinoma. J Cell Mol Med 2023; 27:4171-4180. [PMID: 37859510 PMCID: PMC10746936 DOI: 10.1111/jcmm.18002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 09/21/2023] [Accepted: 10/07/2023] [Indexed: 10/21/2023] Open
Abstract
Papillary thyroid carcinoma (PTC) is one of the most common endocrine carcinomas worldwide and the aetiology of this cancer is still not well understood. Therefore, it remains important to understand the disease mechanism and find prognostic biomarkers and/or drug candidates for PTC. Compared with approaches based on single-gene assessment, network medicine analysis offers great promise to address this need. Accordingly, in the present study, we performed differential co-expressed network analysis using five transcriptome datasets in patients with PTC and healthy controls. Following meta-analysis of the transcriptome datasets, we uncovered common differentially expressed genes (DEGs) for PTC and, using these genes as proxies, found a highly clustered differentially expressed co-expressed module: a 'PTC-module'. Using independent data, we demonstrated the high prognostic capacity of the PTC-module and designated this module as a prognostic systems biomarker. In addition, using the nodes of the PTC-module, we performed drug repurposing and text mining analyzes to identify novel drug candidates for the disease. We performed molecular docking simulations, and identified: 4-demethoxydaunorubicin hydrochloride, AS605240, BRD-A60245366, ER 27319 maleate, sinensetin, and TWS119 as novel drug candidates whose efficacy was also confirmed by in silico analyzes. Consequently, we have highlighted here the need for differential co-expression analysis to gain a systems-level understanding of a complex disease, and we provide candidate prognostic systems biomarker and novel drugs for PTC.
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Affiliation(s)
- Medi Kori
- Faculty of Health SciencesAcibadem Mehmet Ali Aydinlar UniversityİstanbulTürkiye
- Department of BioengineeringMarmara UniversityİstanbulTürkiye
| | - Kubra Temiz
- Department of BioengineeringAdana Alparslan Turkes Science and Technology UniversityAdanaTürkiye
| | - Esra Gov
- Department of BioengineeringAdana Alparslan Turkes Science and Technology UniversityAdanaTürkiye
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136
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Alagarsamy V, Shyam Sundar P, Raja Solomon V, Narendhar B, Sulthana MT, Rohitha K, Dhanwar S, Dharshini Aishwarya A, Murugesan S. Pharmacophore modelling-based drug repurposing approaches for monkeypox therapeutics. J Biomol Struct Dyn 2023; 41:10678-10689. [PMID: 36905675 DOI: 10.1080/07391102.2023.2188428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 12/05/2022] [Indexed: 03/13/2023]
Abstract
Monkeypox is a zoonotic viral disease that mainly affects tropical rainforest regions of central and west Africa, with sporadic exportations to other places. Since there is no cure, treating monkeypox with an antiviral drug developed for smallpox is currently acceptable. Our study mainly focused on finding new therapeutics to target monkeypox from existing compounds or medications. It is a successful method for discovering or developing medicinal compounds with novel pharmacological or therapeutic applications. In this study, homology modelling developed the Monkeypox VarTMPK (IMNR) structure. Ligand-based pharmacophore was generated using the best docking pose of standard ticovirimat. Further, molecular docking analysis showed compounds, tetrahydroxycurcumin, procyanidin, rutin, vicenin-2, kaempferol 3-(6''-malonylglucoside) were the top five binding energy compounds against VarTMPK (1MNR). Furthermore, we carried out MD simulations for 100 ns for the six compounds, including reference based on the binding energies and interactions. MD studies revealed that as ticovirimat interacted with residues Lys17, Ser18, and Arg45, all the above five compounds interacted with the same amino acids at the active site during docking and simulation studies. Among all the compounds, ZINC4649679 (Tetrahydroxycurcumin) was shown to have the highest binding energy -9.7 kcal/mol and also observed stable protein-ligand complex during MD studies. ADMET profile estimation showed that the docked phytochemicals were safe. However, further biological assessment through a wet lab is essential to measure the efficacy and safety of the compounds.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- V Alagarsamy
- Medicinal Chemistry Research Laboratory, MNR College of Pharmacy, Sangareddy, Hyderabad, India
| | - P Shyam Sundar
- Medicinal Chemistry Research Laboratory, MNR College of Pharmacy, Sangareddy, Hyderabad, India
| | - V Raja Solomon
- Medicinal Chemistry Research Laboratory, MNR College of Pharmacy, Sangareddy, Hyderabad, India
| | - B Narendhar
- Medicinal Chemistry Research Laboratory, MNR College of Pharmacy, Sangareddy, Hyderabad, India
| | - M T Sulthana
- Medicinal Chemistry Research Laboratory, MNR College of Pharmacy, Sangareddy, Hyderabad, India
| | - Kotha Rohitha
- Medicinal Chemistry Research Laboratory, MNR College of Pharmacy, Sangareddy, Hyderabad, India
| | - Sangeeta Dhanwar
- Medicinal Chemistry Research Laboratory, MNR College of Pharmacy, Sangareddy, Hyderabad, India
| | - A Dharshini Aishwarya
- Medicinal Chemistry Research Laboratory, MNR College of Pharmacy, Sangareddy, Hyderabad, India
| | - S Murugesan
- Department of Pharmacy, BITS, Pilani, Pilani, Rajasthan, India
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137
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Lee Y, Nam S. Network and Computational Drug Repurposing Analysis for c-Myc Inhibition in Burkitt Lymphoma. Cancer Genomics Proteomics 2023; 20:712-722. [PMID: 38035700 PMCID: PMC10687731 DOI: 10.21873/cgp.20418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 09/08/2023] [Accepted: 10/05/2023] [Indexed: 12/02/2023] Open
Abstract
BACKGROUND/AIM The treatment rate of Burkitt lymphoma (BL) is still low in low-income countries and among elderly patients. The c-Myc dysregulation induced by mutations is one of the characteristics of BL. However, studies on the downstream signaling pathways of c-Myc are still lacking. This study aimed to identify the signaling pathways regulated by c-Myc. MATERIALS AND METHODS Network and gene set analyses using c-Myc inhibition (i.e., c-Myc knock-down and c-Myc inhibitor treatment) transcriptome datasets for BL cell lines were performed to determine the pathways regulated by c-Myc. In addition, computational drug repurposing was used to identify drugs that can regulate c-Myc downstream signaling pathway. RESULTS Computational drug repurposing revealed that the ERK/MAPK signaling pathway is regulated by c-Myc in BL and that this pathway can be modulated by vorinostat. Furthermore, in the pharmacogenomics database, vorinostat showed a cell viability half-maximal inhibitory concentration of less than 2 μM in the BL cell lines. CONCLUSION The downstream signaling pathway regulated by c-Myc and the drug that can modulate this pathway is presented for the first time.
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Affiliation(s)
- Yongmin Lee
- Department of Health Sciences and Technology, Gachon Advanced Institute for Health Sciences and Technology (GAIHST), Gachon University, Incheon, Republic of Korea
| | - Seungyoon Nam
- Department of Health Sciences and Technology, Gachon Advanced Institute for Health Sciences and Technology (GAIHST), Gachon University, Incheon, Republic of Korea;
- Department of Genome Medicine and Science, AI Convergence Center for Medical Science, Gachon Institute of Genome Medicine and Science, Gachon University Gil Medical Center, Gachon University College of Medicine, Incheon, Republic of Korea
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Zhang N, Tan Z, Wei J, Zhang S, Liu Y, Miao Y, Ding Q, Yi W, Gan M, Li C, Liu B, Wang H, Zheng Z. Identification of novel anti-ZIKV drugs from viral-infection temporal gene expression profiles. Emerg Microbes Infect 2023; 12:2174777. [PMID: 36715162 PMCID: PMC9946313 DOI: 10.1080/22221751.2023.2174777] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Zika virus (ZIKV) infections are typically asymptomatic but cause severe neurological complications (e.g. Guillain-Barré syndrome in adults, and microcephaly in newborns). There are currently no specific therapy or vaccine options available to prevent ZIKV infections. Temporal gene expression profiles of ZIKV-infected human brain microvascular endothelial cells (HBMECs) were used in this study to identify genes essential for viral replication. These genes were then used to identify novel anti-ZIKV agents and validated in publicly available data and functional wet-lab experiments. Here, we found that ZIKV effectively evaded activation of immune response-related genes and completely reprogrammed cellular transcriptional architectures. Knockdown of genes, which gradually upregulated during viral infection but showed distinct expression patterns between ZIKV- and mock infection, discovered novel proviral and antiviral factors. One-third of the 74 drugs found through signature-based drug repositioning and cross-reference with the Drug Gene Interaction Database (DGIdb) were known anti-ZIKV agents. In cellular assays, two promising antiviral candidates (Luminespib/NVP-AUY922, L-161982) were found to reduce viral replication without causing cell toxicity. Overall, our time-series transcriptome-based methods offer a novel and feasible strategy for antiviral drug discovery. Our strategies, which combine conventional and data-driven analysis, can be extended for other pathogens causing pandemics in the future.
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Affiliation(s)
- Nailou Zhang
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, People’s Republic of China
| | - Zhongyuan Tan
- The Joint Laboratory for Translational Precision Medicine, a. Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, People's Republic of China and b. Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, People's Republic of China
| | - Jinbo Wei
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, People’s Republic of China
| | - Sai Zhang
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, People’s Republic of China
| | - Yan Liu
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, People’s Republic of China
| | - Yuanjiu Miao
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, People’s Republic of China
| | - Qingwen Ding
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, People’s Republic of China
| | - Wenfu Yi
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, People’s Republic of China
| | - Min Gan
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, People’s Republic of China
| | - Chunjie Li
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, People’s Republic of China
| | - Bin Liu
- Characteristic Medical Center of Chinese People’s Armed Police Forces, Tianjin, People’s Republic of China
| | - Hanzhong Wang
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, People’s Republic of China
| | - Zhenhua Zheng
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, People’s Republic of China, Zhenhua Zheng CAS Key Laboratory of Special Pathogens and Biosafety, Center for Emerging Infectious Diseases, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan430071, People’s Republic of China
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139
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Tiwari PC, Pal R, Chaudhary MJ, Nath R. Artificial intelligence revolutionizing drug development: Exploring opportunities and challenges. Drug Dev Res 2023; 84:1652-1663. [PMID: 37712494 DOI: 10.1002/ddr.22115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 08/14/2023] [Accepted: 09/04/2023] [Indexed: 09/16/2023]
Abstract
By harnessing artificial intelligence (AI) algorithms and machine learning techniques, the entire drug discovery process stands to undergo a profound transformation, offering a myriad of advantages. Foremost among these is the ability of AI to conduct swift and efficient screenings of expansive compound libraries, significantly augmenting the identification of potential drug candidates. Moreover, AI algorithms can prove instrumental in predicting the efficacy and safety profiles of candidate compounds, thus endowing invaluable insights and reducing reliance on extensive preclinical and clinical testing. This predictive capacity of AI has the potential to streamline the drug development pipeline and enhance the success rate of clinical trials, ultimately resulting in the emergence of more efficacious and safer therapeutic agents. However, the deployment of AI in drug discovery introduces certain challenges that warrant attention. A primary hurdle entails the imperative acquisition of high-quality and diverse data. Furthermore, ensuring the interpretability of AI models assumes critical importance in securing regulatory endorsement and cultivating trust within scientific and medical communities. Addressing ethical considerations, including data privacy and mitigating bias, represents an additional momentous challenge, requiring assiduous navigation. In this review, we provide an intricate and comprehensive overview of the multifaceted challenges intrinsic to conventional drug development paradigms, while simultaneously interrogating the efficacy of AI in effectively surmounting these formidable obstacles.
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Affiliation(s)
- Prafulla C Tiwari
- Department of Pharmacology and Therapeutics, King George's Medical University, Lucknow, Uttar Pradesh, India
| | - Rishi Pal
- Department of Pharmacology and Therapeutics, King George's Medical University, Lucknow, Uttar Pradesh, India
| | - Manju J Chaudhary
- Department of Physiology, Government Medical College, Kannauj, Uttar Pradesh, India
| | - Rajendra Nath
- Department of Pharmacology and Therapeutics, King George's Medical University, Lucknow, Uttar Pradesh, India
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Bortolasci CC, Kidnapillai S, Spolding B, Truong TTT, Connor T, Swinton C, Panizzutti B, Liu ZSJ, Sanigorski A, Dean OM, Crowley T, Richardson M, Bozaoglu K, Vlahos K, Cowdery S, Watmuff B, Steyn SF, Wolmarans DW, Engelbrecht BJ, Perry C, Drummond K, Pang T, Jamain S, Gray L, McGee SL, Harvey BH, Kim JH, Leboyer M, Berk M, Walder K. Use of a gene expression signature to identify trimetazidine for repurposing to treat bipolar depression. Bipolar Disord 2023; 25:661-670. [PMID: 36890661 PMCID: PMC10946906 DOI: 10.1111/bdi.13319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/10/2023]
Abstract
OBJECTIVES The aim of this study was to repurpose a drug for the treatment of bipolar depression. METHODS A gene expression signature representing the overall transcriptomic effects of a cocktail of drugs widely prescribed to treat bipolar disorder was generated using human neuronal-like (NT2-N) cells. A compound library of 960 approved, off-patent drugs were then screened to identify those drugs that affect transcription most similar to the effects of the bipolar depression drug cocktail. For mechanistic studies, peripheral blood mononuclear cells were obtained from a healthy subject and reprogrammed into induced pluripotent stem cells, which were then differentiated into co-cultured neurons and astrocytes. Efficacy studies were conducted in two animal models of depressive-like behaviours (Flinders Sensitive Line rats and social isolation with chronic restraint stress rats). RESULTS The screen identified trimetazidine as a potential drug for repurposing. Trimetazidine alters metabolic processes to increase ATP production, which is thought to be deficient in bipolar depression. We showed that trimetazidine increased mitochondrial respiration in cultured human neuronal-like cells. Transcriptomic analysis in induced pluripotent stem cell-derived neuron/astrocyte co-cultures suggested additional mechanisms of action via the focal adhesion and MAPK signalling pathways. In two different rodent models of depressive-like behaviours, trimetazidine exhibited antidepressant-like activity with reduced anhedonia and reduced immobility in the forced swim test. CONCLUSION Collectively our data support the repurposing of trimetazidine for the treatment of bipolar depression.
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Affiliation(s)
- Chiara C. Bortolasci
- IMPACTThe Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Deakin UniversityGeelongAustralia
| | - Srisaiyini Kidnapillai
- IMPACTThe Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Deakin UniversityGeelongAustralia
| | - Briana Spolding
- IMPACTThe Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Deakin UniversityGeelongAustralia
| | - Trang T. T. Truong
- IMPACTThe Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Deakin UniversityGeelongAustralia
| | - Timothy Connor
- IMPACTThe Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Deakin UniversityGeelongAustralia
| | - Courtney Swinton
- IMPACTThe Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Deakin UniversityGeelongAustralia
| | - Bruna Panizzutti
- IMPACTThe Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Deakin UniversityGeelongAustralia
| | - Zoe S. J. Liu
- IMPACTThe Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Deakin UniversityGeelongAustralia
| | - Andrew Sanigorski
- IMPACTThe Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Deakin UniversityGeelongAustralia
| | - Olivia M. Dean
- IMPACTThe Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Deakin UniversityGeelongAustralia
- The Florey Institute of Neuroscience and Mental HealthParkvilleAustralia
| | - Tamsyn Crowley
- IMPACTThe Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Deakin UniversityGeelongAustralia
- Bioinformatics Core Research Facility (BCRF)Deakin UniversityGeelongAustralia
| | - Mark Richardson
- Bioinformatics Core Research Facility (BCRF)Deakin UniversityGeelongAustralia
| | - Kiymet Bozaoglu
- Murdoch Children's Research InstituteParkvilleVictoriaAustralia
- Department of PaediatricsUniversity of MelbourneParkvilleVictoriaAustralia
| | - Katerina Vlahos
- Murdoch Children's Research InstituteParkvilleVictoriaAustralia
| | - Stephanie Cowdery
- IMPACTThe Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Deakin UniversityGeelongAustralia
| | - Brad Watmuff
- IMPACTThe Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Deakin UniversityGeelongAustralia
| | - Stephan F. Steyn
- Centre of Excellence for Pharmaceutical Sciences, Faculty of Health SciencesNorth‐West UniversityPotchefstroomSouth Africa
| | - De Wet Wolmarans
- Centre of Excellence for Pharmaceutical Sciences, Faculty of Health SciencesNorth‐West UniversityPotchefstroomSouth Africa
| | - Barend J. Engelbrecht
- Centre of Excellence for Pharmaceutical Sciences, Faculty of Health SciencesNorth‐West UniversityPotchefstroomSouth Africa
| | - Christina Perry
- The Florey Institute of Neuroscience and Mental HealthParkvilleAustralia
| | - Katherine Drummond
- The Florey Institute of Neuroscience and Mental HealthParkvilleAustralia
| | - Terence Pang
- The Florey Institute of Neuroscience and Mental HealthParkvilleAustralia
| | - Stéphane Jamain
- Univ Paris Est Créteil, INSERM, IMRB, Translational Neuropsychiatry, AP‐HP, DMU IMPACT, FHU ADAPTFondation FondaMentalCréteilFrance
| | - Laura Gray
- IMPACTThe Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Deakin UniversityGeelongAustralia
- The Florey Institute of Neuroscience and Mental HealthParkvilleAustralia
| | - Sean L. McGee
- IMPACTThe Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Deakin UniversityGeelongAustralia
| | - Brian H. Harvey
- Centre of Excellence for Pharmaceutical Sciences, Faculty of Health SciencesNorth‐West UniversityPotchefstroomSouth Africa
- SAMRC Unit on Risk and Resilience in Mental Disorders, Department of Psychiatry and Mental Health and Neuroscience InstituteUniversity of Cape TownCape TownSouth Africa
| | - Jee Hyun Kim
- IMPACTThe Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Deakin UniversityGeelongAustralia
- The Florey Institute of Neuroscience and Mental HealthParkvilleAustralia
| | - Marion Leboyer
- Univ Paris Est Créteil, INSERM, IMRB, Translational Neuropsychiatry, AP‐HP, DMU IMPACT, FHU ADAPTFondation FondaMentalCréteilFrance
| | - Michael Berk
- IMPACTThe Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Deakin UniversityGeelongAustralia
- The Florey Institute of Neuroscience and Mental HealthParkvilleAustralia
- Orygen, The National Centre of Excellence in Youth Mental HealthParkvilleAustralia
| | - Ken Walder
- IMPACTThe Institute for Mental and Physical Health and Clinical Translation, School of Medicine, Deakin UniversityGeelongAustralia
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Zheng B, Su B, Ahmadi-Abhari S, Kapogiannis D, Tzoulaki I, Riboli E, Middleton L. Dementia risk in patients with type 2 diabetes: Comparing metformin with no pharmacological treatment. Alzheimers Dement 2023; 19:5681-5689. [PMID: 37395154 DOI: 10.1002/alz.13349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 04/26/2023] [Accepted: 05/19/2023] [Indexed: 07/04/2023]
Abstract
INTRODUCTION Metformin has been suggested as a therapeutic agent for dementia, but the relevant evidence has been partial and inconsistent. METHODS We established a national cohort of 210,237 type 2 diabetes patients in the UK Clinical Practice Research Datalink. Risks of incident dementia were compared between metformin initiators and those who were not prescribed any anti-diabetes medication during follow-up. RESULTS Compared with metformin initiators (n = 114,628), patients who received no anti-diabetes medication (n = 95,609) had lower HbA1c and better cardiovascular health at baseline. Both Cox regression and propensity score weighting analysis showed metformin initiators had lower risk of dementia compared to those non-users (adjusted hazard ratio = 0.88 [95% confidence interval: 0.84-0.92] and 0.90 [0.84-0.96]). Patients on long-term metformin treatment had an even lower risk of dementia. DISCUSSION Metformin may act beyond its glycemic effect and reduce dementia risk to an even lower level than that of patients with milder diabetes and better health profiles. HIGHLIGHTS Metformin initiators had a significantly lower risk of dementia compared with patients not receiving anti-diabetes medication. Compared with metformin initiators, diabetes patients not receiving pharmacological treatment had better glycemic profiles at baseline and during follow-up. Patients on long-term metformin treatment had an even lower risk of subsequent dementia incidence. Metformin may act beyond its effect on hyperglycemia and has the potential of being repurposed for dementia prevention.
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Affiliation(s)
- Bang Zheng
- Ageing Epidemiology Research Unit, School of Public Health, Imperial College London, London, UK
- Department of Non-communicable Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK
| | - Bowen Su
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
| | - Sara Ahmadi-Abhari
- Ageing Epidemiology Research Unit, School of Public Health, Imperial College London, London, UK
| | - Dimitrios Kapogiannis
- Laboratory of Clinical Investigation, Intramural Research Program, National Institute on Aging, Baltimore, USA
| | - Ioanna Tzoulaki
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
| | - Elio Riboli
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
- Public Health Directorate, Imperial College NHS Healthcare Trust, London, UK
| | - Lefkos Middleton
- Ageing Epidemiology Research Unit, School of Public Health, Imperial College London, London, UK
- Public Health Directorate, Imperial College NHS Healthcare Trust, London, UK
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Schumacher J, Nienhaus A, Heber S, Matylitsky J, Chaves-Olarte E, Rodríguez C, Barth H, Papatheodorou P. Exploring the inhibitory potential of the antiarrhythmic drug amiodarone against Clostridioides difficile toxins TcdA and TcdB. Gut Microbes 2023; 15:2256695. [PMID: 37749884 PMCID: PMC10524773 DOI: 10.1080/19490976.2023.2256695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 09/05/2023] [Indexed: 09/27/2023] Open
Abstract
The intestinal pathogen Clostridioides difficile is the leading cause of antibiotic-associated diarrhea and pseudomembranous colitis in humans. The symptoms of C. difficile-associated diseases (CDADs) are directly associated with the pathogen's toxins TcdA and TcdB, which enter host cells and inactivate Rho and/or Ras GTPases by glucosylation. Membrane cholesterol is crucial during the intoxication process of TcdA and TcdB, and likely involved during pore formation of both toxins in endosomal membranes, a key step after cellular uptake for the translocation of the glucosyltransferase domain of both toxins from endosomes into the host cell cytosol. The licensed drug amiodarone, a multichannel blocker commonly used in the treatment of cardiac dysrhythmias, is also capable of inhibiting endosomal acidification and, as shown recently, cholesterol biosynthesis. Thus, we were keen to investigate in vitro with cultured cells and human intestinal organoids, whether amiodarone preincubation protects from TcdA and/or TcdB intoxication. Amiodarone conferred protection against both toxins independently and in combination as well as against toxin variants from the clinically relevant, epidemic C. difficile strain NAP1/027. Further mechanistic studies suggested that amiodarone's mode-of-inhibition involves also interference with the translocation pore of both toxins. Our study opens the possibility of repurposing the licensed drug amiodarone as a novel pan-variant antitoxin therapeutic in the context of CDADs.
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Affiliation(s)
- Judith Schumacher
- Institute of Experimental and Clinical Pharmacology, Toxicology and Pharmacology of Natural Products, Ulm University Medical Center, Ulm, Germany
| | - Astrid Nienhaus
- Institute of Experimental and Clinical Pharmacology, Toxicology and Pharmacology of Natural Products, Ulm University Medical Center, Ulm, Germany
| | - Sebastian Heber
- Institute of Experimental and Clinical Pharmacology, Toxicology and Pharmacology of Natural Products, Ulm University Medical Center, Ulm, Germany
| | - Jauheni Matylitsky
- Institute of Experimental and Clinical Pharmacology, Toxicology and Pharmacology of Natural Products, Ulm University Medical Center, Ulm, Germany
| | - Esteban Chaves-Olarte
- Centro de Investigación en Enfermedades Tropicales and Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
| | - César Rodríguez
- Centro de Investigación en Enfermedades Tropicales and Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
| | - Holger Barth
- Institute of Experimental and Clinical Pharmacology, Toxicology and Pharmacology of Natural Products, Ulm University Medical Center, Ulm, Germany
| | - Panagiotis Papatheodorou
- Institute of Experimental and Clinical Pharmacology, Toxicology and Pharmacology of Natural Products, Ulm University Medical Center, Ulm, Germany
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Daisy Precilla S, Kuduvalli SS, Biswas I, Bhavani K, Pillai AB, Thomas JM, Anitha TS. Repurposing synthetic and natural derivatives induces apoptosis in an orthotopic glioma-induced xenograft model by modulating WNT/β-catenin signaling. Fundam Clin Pharmacol 2023; 37:1179-1197. [PMID: 37458120 DOI: 10.1111/fcp.12932] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 05/09/2023] [Accepted: 06/09/2023] [Indexed: 07/18/2023]
Abstract
BACKGROUND Glioblastomas arise from multistep tumorigenesis of the glial cells. Despite the current state-of-art treatment, tumor recurrence is inevitable. Among the innovations blooming up against glioblastoma, drug repurposing could provide profound premises for treatment enhancement. While considering this strategy, the efficacy of the repurposed drugs as monotherapies were not up to par; hence, the focus has now shifted to investigate the multidrug combinations. AIM To investigate the efficacy of a quadruple-combinatorial treatment comprising temozolomide along with chloroquine, naringenin, and phloroglucinol in an orthotopic glioma-induced xenograft model. METHODS Antiproliferative effect of the drugs was assessed by immunostaining. The expression profiles of WNT/β-catenin and apoptotic markers were evaluated by qRT-PCR, immunoblotting, and ELISA. Patterns of mitochondrial depolarization was determined by flow cytometry. TUNEL assay was performed to affirm apoptosis induction. In vivo drug detection study was carried out by ESI-Q-TOF MS analysis. RESULTS The quadruple-drug treatment had significantly hampered glioma proliferation and had induced apoptosis by modulating the WNT/β-catenin signaling. Interestingly, the induction of apoptosis was associated with mitochondrial depolarization. The quadruple-drug cocktail had breached the blood-brain barrier and was detected in the brain tissue and plasma samples. CONCLUSION The quadruple-drug combination served as a promising adjuvant therapy to combat glioblastoma lethality in vivo and can be probed for translation from bench to bedside.
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Affiliation(s)
- Senthilathiban Daisy Precilla
- Mahatma Gandhi Medical Advanced Research Institute (MGMARI), Sri Balaji Vidyapeeth (Deemed to-be University), Puducherry, 607 403, India
| | - Shreyas S Kuduvalli
- Mahatma Gandhi Medical Advanced Research Institute (MGMARI), Sri Balaji Vidyapeeth (Deemed to-be University), Puducherry, 607 403, India
| | - Indrani Biswas
- Mahatma Gandhi Medical Advanced Research Institute (MGMARI), Sri Balaji Vidyapeeth (Deemed to-be University), Puducherry, 607 403, India
| | - Krishnamurthy Bhavani
- Department of Pathology, Mahatma Gandhi Medical College and Research Institute (MGMCRI), Sri Balaji Vidyapeeth (Deemed to-be University), Puducherry, 607 403, India
| | - Agieshkumar Balakrishna Pillai
- Mahatma Gandhi Medical Advanced Research Institute (MGMARI), Sri Balaji Vidyapeeth (Deemed to-be University), Puducherry, 607 403, India
| | - Jisha Mary Thomas
- Catalysis and Energy Laboratory, Department of Chemistry, Pondicherry University, Puducherry, 605 014, India
| | - Thirugnanasambandhar Sivasubramanian Anitha
- Mahatma Gandhi Medical Advanced Research Institute (MGMARI), Sri Balaji Vidyapeeth (Deemed to-be University), Puducherry, 607 403, India
- Department of Biochemistry and Molecular Biology, Pondicherry University, Puducherry, 605 014, India
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André N, Bailey S, Peyrl A. Successfully targeting the cancer system with metronomics for medulloblastoma. Trends Cancer 2023; 9:989-991. [PMID: 37940401 DOI: 10.1016/j.trecan.2023.10.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 10/17/2023] [Accepted: 10/20/2023] [Indexed: 11/10/2023]
Abstract
The prognosis of the patients with medulloblastoma who relapse after initial treatment including radiotherapy remains dismal. A recent study by Peyrl et al. in JAMA Oncology suggests that the metronomic multidrug combination used in the medulloblastoma European multitarget metronomic antiangiogenic trial (MEMMAT) given at relapse can improve long-term survival.
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Affiliation(s)
- Nicolas André
- Department of Pediatric Oncology, Timone Hospital, Assistance Publique Hôpitaux de Marseille (AP-HM), Marseille, France; Reverse Molecular Pharmacology in Pediatric Oncology, Centre de Recherche en Cancérologie de Marseille (CRCM), Aix-Marseille Université, Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Marseille, France; Metronomics Global Health Initiative, Marseille, France.
| | - Simon Bailey
- Great North Children's Hospital, Queen Victoria Road, Newcastle upon Tyne NE1 4LP, UK; Wolfson Childhood Cancer Research Centre, Newcastle University Centre for Cancer, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Andreas Peyrl
- Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Waehringer Guertel 18-20, 1090 Vienna, Austria; Comprehensive Center for Pediatrics, Medical University of Vienna, 1090 Vienna, Austria
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Pedini G, Chen CL, Achsel T, Bagni C. Cancer drug repurposing in autism spectrum disorder. Trends Pharmacol Sci 2023; 44:963-977. [PMID: 37940430 DOI: 10.1016/j.tips.2023.09.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 09/20/2023] [Accepted: 09/20/2023] [Indexed: 11/10/2023]
Abstract
Autism spectrum disorder (ASD) is a complex neurodevelopmental condition with uncertain origins. Understanding of the mechanisms underlying ASD remains limited, and treatments are lacking. Genetic diversity complicates drug development. Given the complexity and severity of ASD symptoms and the rising number of diagnoses, exploring novel therapeutic strategies is essential. Here, we focus on shared molecular pathways between ASD and cancer and highlight recent progress on the repurposing of cancer drugs for ASD treatment, such as mTOR inhibitors, histone deacetylase inhibitors, and anti-inflammatory agents. We discuss how to improve trial design considering drug dose and patient age. Lastly, the discussion explores the critical aspects of side effects, commercial factors, and the efficiency of drug-screening pipelines; all of which are essential considerations in the pursuit of repurposing cancer drugs for addressing core features of ASD.
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Affiliation(s)
- Giorgia Pedini
- University of Rome Tor Vergata, Department of Biomedicine and Prevention, Via Montpellier 1, 00133, Rome, Italy
| | - Chin-Lin Chen
- University of Lausanne, Department of Fundamental Neurosciences, Rue du Bugnon 9, 1005, Lausanne, Switzerland
| | - Tilmann Achsel
- University of Lausanne, Department of Fundamental Neurosciences, Rue du Bugnon 9, 1005, Lausanne, Switzerland
| | - Claudia Bagni
- University of Rome Tor Vergata, Department of Biomedicine and Prevention, Via Montpellier 1, 00133, Rome, Italy; University of Lausanne, Department of Fundamental Neurosciences, Rue du Bugnon 9, 1005, Lausanne, Switzerland.
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Keller SA, Chen Z, Gaponova A, Korzinkin M, Berquez M, Luciani A. Drug discovery and therapeutic perspectives for proximal tubulopathies. Kidney Int 2023; 104:1103-1112. [PMID: 37783447 DOI: 10.1016/j.kint.2023.08.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Revised: 07/11/2023] [Accepted: 08/03/2023] [Indexed: 10/04/2023]
Abstract
The efficient reabsorption of essential nutrients by epithelial cells in the proximal tubule of the kidney is crucial for maintaining homeostasis. This process relies heavily on a complex ecosystem of vesicular trafficking pathways. At the center of this network, the lysosome plays a pivotal role in processing incoming molecules, sensing nutrient availability, sorting receptors and transporters, and balancing differentiation and proliferation in the tubular epithelial cells. Disruptions in these fundamental processes can lead to proximal tubulopathy-a condition characterized by the dysfunction of the tubular cells followed by the presence of low-molecular-weight proteins and solutes in urine. If left untreated, proximal tubulopathy can progress to chronic kidney disease and severe complications. Functional studies of rare inherited disorders affecting the proximal tubule have gleaned actionable insights into fundamental mechanisms of homeostasis while revealing drug targets for therapeutic discovery and development. In this mini review, we explore hereditary proximal tubulopathies as a paradigm of kidney homeostasis disorders, discussing the factors contributing to tubular dysfunction. In addition, we shed light on the current landscape of drug discovery approaches used to identify actionable targets and summarize the preclinical pipeline of potential therapeutic agents. These efforts may ultimately lead to new treatment avenues for proximal tubulopathies, which are currently inadequately tackled by existing therapies. Through this article, our hope is to promote academia-industry partnerships and advocate for research consortia that can accelerate the effective translation of knowledge advances into innovative therapies addressing the huge unmet needs of individuals with these debilitating diseases.
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Affiliation(s)
- Svenja A Keller
- Mechanisms of Inherited Kidney Disorders Group, Institute of Physiology, University of Zurich, Zurich, Switzerland
| | - Zhiyong Chen
- Mechanisms of Inherited Kidney Disorders Group, Institute of Physiology, University of Zurich, Zurich, Switzerland
| | - Anna Gaponova
- Insilico Medicine, Hong Kong Science and Technology Park, Hong Kong, China
| | - Mikhail Korzinkin
- Insilico Medicine, Hong Kong Science and Technology Park, Hong Kong, China
| | - Marine Berquez
- Mechanisms of Inherited Kidney Disorders Group, Institute of Physiology, University of Zurich, Zurich, Switzerland
| | - Alessandro Luciani
- Mechanisms of Inherited Kidney Disorders Group, Institute of Physiology, University of Zurich, Zurich, Switzerland.
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Caputo WL, de Souza MC, Basso CR, Pedrosa VDA, Seiva FRF. Comprehensive Profiling and Therapeutic Insights into Differentially Expressed Genes in Hepatocellular Carcinoma. Cancers (Basel) 2023; 15:5653. [PMID: 38067357 PMCID: PMC10705715 DOI: 10.3390/cancers15235653] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 11/02/2023] [Accepted: 11/04/2023] [Indexed: 02/16/2024] Open
Abstract
Background: Drug repurposing is a strategy that complements the conventional approach of developing new drugs. Hepatocellular carcinoma (HCC) is a highly prevalent type of liver cancer, necessitating an in-depth understanding of the underlying molecular alterations for improved treatment. Methods: We searched for a vast array of microarray experiments in addition to RNA-seq data. Through rigorous filtering processes, we have identified highly representative differentially expressed genes (DEGs) between tumor and non-tumor liver tissues and identified a distinct class of possible new candidate drugs. Results: Functional enrichment analysis revealed distinct biological processes associated with metal ions, including zinc, cadmium, and copper, potentially implicating chronic metal ion exposure in tumorigenesis. Conversely, up-regulated genes are associated with mitotic events and kinase activities, aligning with the relevance of kinases in HCC. To unravel the regulatory networks governing these DEGs, we employed topological analysis methods, identifying 25 hub genes and their regulatory transcription factors. In the pursuit of potential therapeutic options, we explored drug repurposing strategies based on computational approaches, analyzing their potential to reverse the expression patterns of key genes, including AURKA, CCNB1, CDK1, RRM2, and TOP2A. Potential therapeutic chemicals are alvocidib, AT-7519, kenpaullone, PHA-793887, JNJ-7706621, danusertibe, doxorubicin and analogues, mitoxantrone, podofilox, teniposide, and amonafide. Conclusion: This multi-omic study offers a comprehensive view of DEGs in HCC, shedding light on potential therapeutic targets and drug repurposing opportunities.
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Affiliation(s)
- Wesley Ladeira Caputo
- Post Graduation Program in Experimental Pathology, State University of Londrina (UEL), Londrina 86057-970, PR, Brazil; (W.L.C.); (M.C.d.S.)
| | - Milena Cremer de Souza
- Post Graduation Program in Experimental Pathology, State University of Londrina (UEL), Londrina 86057-970, PR, Brazil; (W.L.C.); (M.C.d.S.)
| | - Caroline Rodrigues Basso
- Department of Chemical and Biological Sciences, Institute of Bioscience, São Paulo State University (UNESP), Botucatu 18610-034, SP, Brazil; (C.R.B.); (V.d.A.P.)
| | - Valber de Albuquerque Pedrosa
- Department of Chemical and Biological Sciences, Institute of Bioscience, São Paulo State University (UNESP), Botucatu 18610-034, SP, Brazil; (C.R.B.); (V.d.A.P.)
| | - Fábio Rodrigues Ferreira Seiva
- Post Graduation Program in Experimental Pathology, State University of Londrina (UEL), Londrina 86057-970, PR, Brazil; (W.L.C.); (M.C.d.S.)
- Department of Chemical and Biological Sciences, Institute of Bioscience, São Paulo State University (UNESP), Botucatu 18610-034, SP, Brazil; (C.R.B.); (V.d.A.P.)
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Alotaibi HF, Alotaibi H, Darwish KM, Khafagy ES, Abu Lila AS, Ali MAM, Hegazy WAH, Alshawwa SZ. The Anti-Virulence Activities of the Antihypertensive Drug Propranolol in Light of Its Anti-Quorum Sensing Effects against Pseudomonas aeruginosa and Serratia marcescens. Biomedicines 2023; 11:3161. [PMID: 38137382 PMCID: PMC10741015 DOI: 10.3390/biomedicines11123161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 11/17/2023] [Accepted: 11/24/2023] [Indexed: 12/24/2023] Open
Abstract
The development of bacterial resistance is an increasing global concern that requires discovering new antibacterial agents and strategies. Bacterial quorum sensing (QS) systems play important roles in controlling bacterial virulence, and their targeting could lead to diminishing bacterial pathogenesis. In this context, targeting QS systems without significant influence on bacterial growth is assumed as a promising strategy to overcome resistance development. This study aimed at evaluating the anti-QS and anti-virulence activities of the β-adrenoreceptor antagonist propranolol at sub-minimal inhibitory concentrations (sub-MIC) against two Gram-negative bacterial models Pseudomonas aeruginosa and Serratia marcescens. The effect of propranolol on the expression of QS-encoding genes was evaluated. Additionally, the affinity of propranolol to QS receptors was virtually attested. The influence of propranolol at sub-MIC on biofilm formation, motility, and production of virulent factors was conducted. The outcomes of the propranolol combination with different antibiotics were assessed. Finally, the in vivo protection assay in mice was performed to assess propranolol's effect on lessening the bacterial pathogenesis. The current findings emphasized the significant ability of propranolol at sub-MIC to reduce the formation of biofilms, motility, and production of virulence factors. In addition, propranolol at sub-MIC decreased the capacity of tested bacteria to induce pathogenesis in mice. Furthermore, propranolol significantly downregulated the QS-encoding genes and showed significant affinity to QS receptors. Finally, propranolol at sub-MIC synergistically decreased the MICs of different antibiotics against tested bacteria. In conclusion, propranolol might serve as a plausible adjuvant therapy with antibiotics for the treatment of serious bacterial infections after further pharmacological and pharmaceutical studies.
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Affiliation(s)
- Hadil Faris Alotaibi
- Department of Pharmaceutical Sciences, College of Pharmacy, Princess Nourah bint Abdulrahman University, Riyadh 11671, Saudi Arabia
| | - Haifa Alotaibi
- Department of Family Medicine, Prince Sultan Military Medical City, Riyadh 12624, Saudi Arabia
| | - Khaled M. Darwish
- Department of Medicinal Chemistry, Faculty of Pharmacy, Suez Canal University, Ismailia 41522, Egypt
| | - El-Sayed Khafagy
- Department of Pharmaceutics, College of Pharmacy, Prince Sattam bin Abdulaziz University, Al-kharj 11942, Saudi Arabia
- Department of Pharmaceutics and Industrial Pharmacy, Faculty of Pharmacy, Suez Canal University, Ismailia 41522, Egypt
| | - Amr S. Abu Lila
- Department of Pharmaceutics, College of Pharmacy, University of Hail, Hail 81442, Saudi Arabia
- Molecular Diagnostics and Personalized Therapeutics Unit, University of Hail, Hail 81442, Saudi Arabia
- Department of Pharmaceutics and Industrial Pharmacy, Faculty of Pharmacy, Zagazig University, Zagazig 44519, Egypt
| | - Mohamed A. M. Ali
- Department of Biology, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh 11623, Saudi Arabia
- Department of Biochemistry, Faculty of Science, Ain Shams University, Abbassia, Cairo 11566, Egypt
| | - Wael A. H. Hegazy
- Department of Microbiology and Immunology, Faculty of Pharmacy, Zagazig University, Zagazig 44519, Egypt
- Pharmacy Program, Department of Pharmaceutical Sciences, Oman College of Health Sciences, Muscat 113, Oman
| | - Samar Zuhair Alshawwa
- Department of Pharmaceutical Sciences, College of Pharmacy, Princess Nourah bint Abdulrahman University, Riyadh 11671, Saudi Arabia
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149
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Makeeva VS, Dyrkheeva NS, Lavrik OI, Zakian SM, Malakhova AA. Mutant-Huntingtin Molecular Pathways Elucidate New Targets for Drug Repurposing. Int J Mol Sci 2023; 24:16798. [PMID: 38069121 PMCID: PMC10706709 DOI: 10.3390/ijms242316798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 11/18/2023] [Accepted: 11/24/2023] [Indexed: 12/18/2023] Open
Abstract
The spectrum of neurodegenerative diseases known today is quite extensive. The complexities of their research and treatment lie not only in their diversity. Even many years of struggle and narrowly focused research on common pathologies such as Alzheimer's, Parkinson's, and other brain diseases have not brought cures for these illnesses. What can be said about orphan diseases? In particular, Huntington's disease (HD), despite affecting a smaller part of the human population, still attracts many researchers. This disorder is known to result from a mutation in the HTT gene, but having this information still does not simplify the task of drug development and studying the mechanisms of disease progression. Nonetheless, the data accumulated over the years and their analysis provide a good basis for further research. Here, we review studies devoted to understanding the mechanisms of HD. We analyze genes and molecular pathways involved in HD pathogenesis to describe the action of repurposed drugs and try to find new therapeutic targets.
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Affiliation(s)
- Vladlena S. Makeeva
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 10 Akad. Lavrentiev Ave., 630090 Novosibirsk, Russia; (V.S.M.); (S.M.Z.); (A.A.M.)
| | - Nadezhda S. Dyrkheeva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 8 Akad. Lavrentiev Ave., 630090 Novosibirsk, Russia;
| | - Olga I. Lavrik
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 8 Akad. Lavrentiev Ave., 630090 Novosibirsk, Russia;
| | - Suren M. Zakian
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 10 Akad. Lavrentiev Ave., 630090 Novosibirsk, Russia; (V.S.M.); (S.M.Z.); (A.A.M.)
| | - Anastasia A. Malakhova
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 10 Akad. Lavrentiev Ave., 630090 Novosibirsk, Russia; (V.S.M.); (S.M.Z.); (A.A.M.)
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150
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Alyami MH, Musallam AA, Ibrahim TM, Mahdy MA, Elnahas HM, Aldeeb RA. The Exploitation of pH-Responsive Eudragit-Coated Mesoporous Silica Nanostructures in the Repurposing of Terbinafine Hydrochloride for Targeted Colon Cancer Inhibition: Design Optimization, In Vitro Characterization, and Cytotoxicity Assessment. Pharmaceutics 2023; 15:2677. [PMID: 38140018 PMCID: PMC10747614 DOI: 10.3390/pharmaceutics15122677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 11/13/2023] [Accepted: 11/23/2023] [Indexed: 12/24/2023] Open
Abstract
Targeted drug delivery is achieving great success in cancer therapy due to its potential to deliver drugs directly to the action site. Terbinafine hydrochloride (TER) is a broad-spectrum anti-fungal drug that has been found to have some potential anti-tumor effects in the treatment of colon cancer. We aimed here to design and develop pH-sensitive Eudragit (Eud)-coated mesoporous silica nanostructures (MSNs) to control drug release in response to changes in pH. The diffusion-supported loading (DiSupLo) technique was applied for loading TER into the MSNs. The formulation was optimized by a D-optimal design, which permits the concurrent assessment of the influence of drug/MSN%, coat concentration, and MSN type on the drug entrapment efficiency (EE) and its release performance. The optimal formula displayed a high EE of 96.49%, minimizing the release in pH 1.2 to 16.15% and maximizing the release in pH 7.4 to 78.09%. The cytotoxicity of the optimal formula on the colon cancer cells HT-29 was higher than it was with TER alone by 2.8-fold. Apoptosis in cancer cells exposed to the optimum formula was boosted as compared to what it was with the plain TER by 1.2-fold and it was more efficient in arresting cells during the G0/G1 and S stages of the cell cycle. Accordingly, the repurposing of TER utilizing Eud/MSNs is a promising technique for targeted colon cancer therapy.
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Affiliation(s)
- Mohammad H. Alyami
- Department of Pharmaceutics, College of Pharmacy, Najran University, Najran 66462, Saudi Arabia
| | - Abeer A. Musallam
- Department of Pharmaceutics, College of Pharmaceutical Sciences and Drug Manufacturing, Misr University for Science and Technology, 6th of October City 12582, Egypt
| | - Tarek M. Ibrahim
- Department of Pharmaceutics, Faculty of Pharmacy, Zagazig University, Zagazig 44519, Egypt
| | - Mahmoud A. Mahdy
- Department of Pharmaceutics, Faculty of Pharmacy, Zagazig University, Zagazig 44519, Egypt
| | - Hanan M. Elnahas
- Department of Pharmaceutics, Faculty of Pharmacy, Zagazig University, Zagazig 44519, Egypt
| | - Reem A. Aldeeb
- Department of Pharmaceutics, College of Pharmaceutical Sciences and Drug Manufacturing, Misr University for Science and Technology, 6th of October City 12582, Egypt
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