scholarly journals Ontological modeling and analysis of experimentally or clinically verified drugs against coronavirus infection

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Yingtong Liu ◽  
Junguk Hur ◽  
Wallace K. B. Chan ◽  
Zhigang Wang ◽  
Jiangan Xie ◽  
...  
Keyword(s):  
Drug Targets ◽  
Enrichment Analysis ◽  
Rational Drug Design ◽  
Knowledge Representation And Reasoning ◽  
Biological Processes ◽  
Protein Targets ◽  
Modeling And Analysis ◽  
Rational Drug

AbstractOur systematic literature collection and annotation identified 106 chemical drugs and 31 antibodies effective against the infection of at least one human coronavirus (including SARS-CoV, SAR-CoV-2, and MERS-CoV) in vitro or in vivo in an experimental or clinical setting. A total of 163 drug protein targets were identified, and 125 biological processes involving the drug targets were significantly enriched based on a Gene Ontology (GO) enrichment analysis. The Coronavirus Infectious Disease Ontology (CIDO) was used as an ontological platform to represent the anti-coronaviral drugs, chemical compounds, drug targets, biological processes, viruses, and the relations among these entities. In addition to new term generation, CIDO also adopted various terms from existing ontologies and developed new relations and axioms to semantically represent our annotated knowledge. The CIDO knowledgebase was systematically analyzed for scientific insights. To support rational drug design, a “Host-coronavirus interaction (HCI) checkpoint cocktail” strategy was proposed to interrupt the important checkpoints in the dynamic HCI network, and ontologies would greatly support the design process with interoperable knowledge representation and reasoning.

scholarly journals 1346. The Tetrazole VT-1598 Is Efficacious in a Murine Model of Invasive Aspergillosis with a PK/PD Expected of a Mold-Active CYP51 Inhibitor

2018 ◽  
Vol 5 (suppl_1) ◽  
pp. S411-S412
Author(s):  
Edward P Garvey ◽  
Andrew Sharp ◽  
Peter Warn ◽  
Christopher M Yates ◽  
Robert J Schotzinger
Keyword(s):  
Antifungal Activity ◽  
Invasive Aspergillosis ◽  
Murine Model ◽  
Pathogenic Fungi ◽  
Rational Drug Design ◽  
Fungal Burden ◽  
Delayed Treatment ◽  
Rational Drug

Abstract Background VT-1598 is a novel fungal CYP51 inhibitor with potent in vitro activity against yeast, mold, and endemic pathogenic fungi (Wiederhold, JAC, 2017). Its tetrazole-based rational drug design imparts much greater selectivity vs. human CYPs (Yates, BMCL, 2017), which could reduce human CYP-related side effects and DDIs. We report here VT-1598’s in vivo activity in an invasive aspergillosis (IA) model. Methods MIC was determined as outlined in CLSI M38-A2. Plasma PK was measured after 4 days of oral doses in neutropenic ICR mice without fungal inoculation. In vivo antifungal activity was determined in a tail-vein IA model in neutropenic mice inoculated with A. fumigatus (AF) ATCC 204305 (N = 10 per dose). Two separate studies were conducted, with oral VT-1598 treatment starting either 48 hours prior (prophylaxis) or 5 hours postinoculation (delayed), with 4 days of postinoculation dosing, and kidney fungal burden measured 1 day post last dose by both CFU and qPCR. Drug control was 10 mg/kg AmBisome i.v. Results The MIC for VT-1598 against AF 204305 was 0.25 μg/mL. The plasma PK of VT-1598 was linearly proportional between the 5 and 40 mg/kg once-daily doses, with AUCs of 155 and 1,033 μg h/mL for the two doses, respectively. VT-1598 was similarly effective in reducing fungal burden when given in delayed treatment compared with prophylaxis, and both studies demonstrated a full dose–response (i.e., no to full reduction of fungal burden). When comparing fungal burdens of each dose group to the fungal burden at the start of treatment, the dose of VT-1598 to achieve fungal stasis ranged from 20.5 to 25.9 mg/kg and to achieve a 1-log10 fungal kill ranged from 30.9 to 50.5 mg/kg. Using the previously measured mouse plasma binding (>99.9%), the free AUC /MIC values for stasis and 1-log10 kill ranged from 2.1–2.7 and 3.2–5.2, respectively. These values are within the range of 1–11 that have been reported for posaconazole and isavuconazole (Lepak, AAC, 2013). Conclusion VT-1598 had potent antifungal activity in a murine model of IA. The PK/PD relationship was the same as clinically used mold-active CYP51 agents, suggesting that it could have similar clinical efficacy. If correct, the tetrazole-based greater selectivity may significantly differentiate VT-1598 from current IA therapies. Disclosures E. P. Garvey, Viamet Pharmaceuticals, Inc.: Employee, Salary. A. Sharp, Evotec (UK) Ltd.: Employee, Salary. P. Warn, Evotec (UK) Ltd.: Employee, Salary. C. M. Yates, Viamet Pharmaceuticals, Inc.: Employee, Salary. R. J. Schotzinger, Viamet Pharmaceuticals, Inc.: Board Member and Employee, Salary.

Enzyme regulation by biological disulfides

1989 ◽  
Vol 9 (5) ◽  
pp. 593-604 ◽  
Author(s):  
Raul N. Ondarza
Keyword(s):  
Drug Design ◽  
Small Molecule ◽  
Regulatory Mechanism ◽  
Enzyme Regulation ◽  
Rational Drug Design ◽  
Host Cells ◽  
Disulfide Exchange ◽  
Rational Drug

More than a dozen enzymes have been found to be activated or inhibited in vitro by disulfide-exchange between the protein and small-molecule disulfides. Accordingly, thiol/disulfide ratio changes in vivo may be of great importance in the regulation of cellular metabolism. An awareness of this regulatory mechanism in both host cells and parasites, coupled with information on the presence or absence of key enzymes, may lead to rational drug design against certain diseases involving thiol intermediates, including trypanosomiasis.

From serendipity to rational drug design in brain disorders: in silico, in vitro, and in vivo approaches

2021 ◽  
Vol 60 ◽  
pp. 177-182
Author(s):  
Hyunjung Oh ◽  
Thomas D. Prevot ◽  
Dwight Newton ◽  
Etienne Sibille
Keyword(s):  
Drug Design ◽  
In Silico ◽  
Rational Drug Design ◽  
Brain Disorders ◽  
Rational Drug

scholarly journals Rational Drug Design of Targeted and Enzyme Cleavable Vitamin E Analogs as Neoadjuvant to Chemotherapy: In Vitro and In Vivo Evaluation on Reduction of Cardiotoxicity of Doxorubicin.

2021 ◽  
Author(s):  
Raghu S Pandurangi ◽  
Orsolya Cseh ◽  
Artee Luchman ◽  
siguang Xu ◽  
Cynthia Ma ◽  
...  
Keyword(s):  
Vitamin E ◽  
Drug Design ◽  
Cancer Cells ◽  
Water Solubility ◽  
Therapeutic Index ◽  
Rational Drug Design ◽  
In Vivo Evaluation ◽  
Rational Drug

Traditional drug design focus on specific target (s) expressed by cancer cells. However, cancer cells outsmart the interventions by activating survival pathways and/or downregulating cell death pathways. As the research in molecular biology of cancer grows exponentially, new methods of drug designs are needed to target multiple pathways/targets which are involved in survival of cancer cells. Vitamin E analogues including a-tocopheryl succinate (TOS) is a well-known anti-tumoregenic agent which is well studied both in vitro and in vivo tumor models. However, lack of targeting cancer cells and unexpected toxicity along with the poor water solubility of TOS compelled a rational drug design using both targeting and cleavable technologies incorporated in the new drug design. A plethora of Vitamin E derivatives (AMP-001, 002 and 003) were synthesized, characterized and studied for the improved efficacy and lowered toxicity in various cancer cells in vitro. Preliminary studies revealed AAAPT leading candidates reduced the invasive potential of brain tumor stem cells, synergized with different drugs and different treatments. AAAPT leading drug AMP-001 enhanced the therapeutic index of front-line drug Doxorubicin in triple negative breast cancer (TNBC) tumor rat model preserving the ventricular function when used as a neoadjuvant to Doxorubicin. These results may pave the way for reducing the cardiotoxicity of chemotherapy in clinical settings.

scholarly journals Bioinformatics Approaches to Natural Product Discovery

2021 ◽  
Vol 41 ◽  
pp. 02004
Author(s):  
Wisnu Ananta Kusuma
Keyword(s):  
Machine Learning ◽  
Natural Products ◽  
Enrichment Analysis ◽  
Network Pharmacology ◽  
Protein Targets ◽  
Link Type ◽  
Topological Features ◽  
Brown Adipose

Introduction: Bioinformatics is a multi-disciplinary field that usually uses approaches in Computer Science such as algorithms and machine learning to solve problems in the domains of Biology, Biochemistry, and other domains involving molecular biology data. This approach can also be used to screen natural products that have certain properties. Jamu or Indonesian herbal medicine works with the principle of multi-component multi-target. This principle focuses on the complex interactions of system components that describe how multi-components (compounds) can work together to affect multi-targets (protein targets). This mechanism is also popularly called Network Pharmacology. In this study, we introduce a workflow to screen herbal compounds based on Network Pharmacology and machine learning approach. Methods: The workflow starts by screening for proteins that have an important role in relation to a certain disease. The screening was conducted by applying clustering and utilizing network topological features which were represented as graphs [1]. Furthermore, we performed enrichment analysis by integrating the protein-protein interaction network with the Gene Ontology (GO) network covering biological processes, molecular functions, and cellular components into k-partite graph and analyzing them using soft clustering method [2]. From the results of this enrichment analysis, we determined which proteins are really relevant and have important role in a certain disease [3]. Next, from these screened proteins, we built a predictive models of compound-protein interactions from drug data collected from the DrugBank and SuperTarget databases and train the models using machine learning or deep learning methods [4]. This model was then used to predict Indonesian herbal compounds from the HerbalDB database (http://herbaldb.farmasi.ui.ac.id/v3/) and IJAH Analytics. Results: To demonstrate the effectiveness of the workflow, we applied it to analize some diseases, such as hyperinflamation in Covid-19 and obesity. We found several potential plants such as Andrographis paniculata (Sambiloto) to reduce the inflammatory effect on Covid-19 and Murraya paniculata (Kemuning) to activate Brown Adipose Tissue (BAT) which has the potential to treat obesity. Certainly all of this requires proof through in vitro, in vivo, and clinical trials. We have also implemented several processes in the workflow into the IJAH Analytics application. Some of the features of IJAH are finding herbal compounds or plant formulas based on specific disease or protein targets; and otherwise looking for the efficacy of several combinations of plants or herbal compounds. In addition, IJAH Analytics can also visualize pharmacological networks from plants-compound-protein-diseases. IJAH is available to the public at https://ijah.apps.cs.ipb.ac.id for free. Conclusion: This study shows the potential of using bioinformatics approaches based on network pharmacology and machine learning in discovering the potential of natural products from Indonesia’s biodiversity. In addition, IJAH Analytics, although still in the refinement stage, can be an alternative application that can support researchers to screen potential Indonesian natural products.

scholarly journals Weighted Gene Co-Expression Network Analysis Combined with Machine Learning Validation to Identify Key Modules and Hub Genes Associated with SARS-CoV-2 Infection

2021 ◽  
Vol 10 (16) ◽  
pp. 3567
Author(s):  
Hassan Karami ◽  
Afshin Derakhshani ◽  
Mohammad Ghasemigol ◽  
Mohammad Fereidouni ◽  
Ebrahim Miri-Moghaddam ◽  
...  
Keyword(s):  
Network Analysis ◽  
Signaling Pathway ◽  
Drug Targets ◽  
Experimental Studies ◽  
A549 Cells ◽  
Enrichment Analysis ◽  
Type I ◽  
Hub Genes

The coronavirus disease-2019 (COVID-19) pandemic has caused an enormous loss of lives. Various clinical trials of vaccines and drugs are being conducted worldwide; nevertheless, as of today, no effective drug exists for COVID-19. The identification of key genes and pathways in this disease may lead to finding potential drug targets and biomarkers. Here, we applied weighted gene co-expression network analysis and LIME as an explainable artificial intelligence algorithm to comprehensively characterize transcriptional changes in bronchial epithelium cells (primary human lung epithelium (NHBE) and transformed lung alveolar (A549) cells) during severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Our study detected a network that significantly correlated to the pathogenicity of COVID-19 infection based on identified hub genes in each cell line separately. The novel hub gene signature that was detected in our study, including PGLYRP4 and HEPHEL1, may shed light on the pathogenesis of COVID-19, holding promise for future prognostic and therapeutic approaches. The enrichment analysis of hub genes showed that the most relevant biological process and KEGG pathways were the type I interferon signaling pathway, IL-17 signaling pathway, cytokine-mediated signaling pathway, and defense response to virus categories, all of which play significant roles in restricting viral infection. Moreover, according to the drug–target network, we identified 17 novel FDA-approved candidate drugs, which could potentially be used to treat COVID-19 patients through the regulation of four hub genes of the co-expression network. In conclusion, the aforementioned hub genes might play potential roles in translational medicine and might become promising therapeutic targets. Further in vitro and in vivo experimental studies are needed to evaluate the role of these hub genes in COVID-19.

scholarly journals In Vitro and In Vivo Efficacies of the Linear and the Cyclic Version of an All-d-Enantiomeric Peptide Developed for the Treatment of Alzheimer’s Disease

2021 ◽  
Vol 22 (12) ◽  
pp. 6553
Author(s):  
Sarah Schemmert ◽  
Luana Cristina Camargo ◽  
Dominik Honold ◽  
Ian Gering ◽  
Janine Kutzsche ◽  
...  
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Amyloid Β ◽  
Pharmacokinetic Profile ◽  
Rational Drug Design ◽  
Multiple Sources ◽  
Aβ Oligomers ◽  
Rational Drug

Multiple sources of evidence suggest that soluble amyloid β (Aβ)-oligomers are responsible for the development and progression of Alzheimer’s disease (AD). In order to specifically eliminate these toxic Aβ-oligomers, our group has developed a variety of all-d-peptides over the past years. One of them, RD2, has been intensively studied and showed such convincing in vitro and in vivo properties that it is currently in clinical trials. In order to further optimize the compounds and to elucidate the characteristics of therapeutic d-peptides, several rational drug design approaches have been performed. Two of these d-peptides are the linear tandem (head-to-tail) d-peptide RD2D3 and its cyclized form cRD2D3. Tandemization and cyclization should result in an increased in vitro potency and increase pharmacokinetic properties, especially crossing the blood­–brain-barrier. In comparison, cRD2D3 showed a superior pharmacokinetic profile to RD2D3. This fact suggests that higher efficacy can be achieved in vivo at equally administered concentrations. To prove this hypothesis, we first established the in vitro profile of both d-peptides here. Subsequently, we performed an intraperitoneal treatment study. This study failed to provide evidence that cRD2D3 is superior to RD2D3 in vivo as in some tests cRD2D3 failed to show equal or higher efficacy.

Conjugates of Classical DNA/RNA Binder with Nucleobase: Chemical, Biochemical and Biomedical Applications

2019 ◽  
Vol 26 (30) ◽  
pp. 5609-5624
Author(s):  
Dijana Saftić ◽  
Željka Ban ◽  
Josipa Matić ◽  
Lidija-Marija Tumirv ◽  
Ivo Piantanida
Keyword(s):  
Molecular Weight ◽  
Small Molecules ◽  
Biomedical Applications ◽  
Protein Targets ◽  
New Class ◽  
Rna Targets ◽  
Covalently Linked ◽  
Structural Aspects

: Among the most intensively studied classes of small molecules (molecular weight < 650) in biomedical research are small molecules that non-covalently bind to DNA/RNA, and another intensively studied class is nucleobase derivatives. Both classes have been intensively elaborated in many books and reviews. However, conjugates consisting of DNA/RNA binder covalently linked to nucleobase are much less studied and have not been reviewed in the last two decades. Therefore, this review summarized reports on the design of classical DNA/RNA binder – nucleobase conjugates, as well as data about their interactions with various DNA or RNA targets, and even in some cases protein targets are involved. According to these data, the most important structural aspects of selective or even specific recognition between small molecule and target are proposed, and where possible related biochemical and biomedical aspects were discussed. The general conclusion is that this, rather new class of molecules showed an amazing set of recognition tools for numerous DNA or RNA targets in the last two decades, as well as few intriguing in vitro and in vivo selectivities. Several lead research lines show promising advancements toward either novel, highly selective markers or bioactive, potentially druggable molecules.

Current Status and Future Perspective for Research on Medicinal Plants with Anticancerous Activity and Minimum Cytotoxic Value

2019 ◽  
Vol 20 (12) ◽  
pp. 1227-1243
Author(s):  
Hina Qamar ◽  
Sumbul Rehman ◽  
D.K. Chauhan
Keyword(s):  
Side Effects ◽  
Medicinal Plants ◽  
Anticancer Agents ◽  
Drug Targets ◽  
Psidium Guajava ◽  
Current Status ◽  
Future Perspective ◽  
Wide Range

Cancer is the second leading cause of morbidity and mortality worldwide. Although chemotherapy and radiotherapy enhance the survival rate of cancerous patients but they have several acute toxic effects. Therefore, there is a need to search for new anticancer agents having better efficacy and lesser side effects. In this regard, herbal treatment is found to be a safe method for treating and preventing cancer. Here, an attempt has been made to screen some less explored medicinal plants like Ammania baccifera, Asclepias curassavica, Azadarichta indica, Butea monosperma, Croton tiglium, Hedera nepalensis, Jatropha curcas, Momordica charantia, Moringa oleifera, Psidium guajava, etc. having potent anticancer activity with minimum cytotoxic value (IC50 >3μM) and lesser or negligible toxicity. They are rich in active phytochemicals with a wide range of drug targets. In this study, these medicinal plants were evaluated for dose-dependent cytotoxicological studies via in vitro MTT assay and in vivo tumor models along with some more plants which are reported to have IC50 value in the range of 0.019-0.528 mg/ml. The findings indicate that these plants inhibit tumor growth by their antiproliferative, pro-apoptotic, anti-metastatic and anti-angiogenic molecular targets. They are widely used because of their easy availability, affordable price and having no or sometimes minimal side effects. This review provides a baseline for the discovery of anticancer drugs from medicinal plants having minimum cytotoxic value with minimal side effects and establishment of their analogues for the welfare of mankind.

Polyamines and Related Nitrogen Compounds in the Chemotherapy of Neglected Diseases Caused by Kinetoplastids

2018 ◽  
Vol 18 (5) ◽  
pp. 321-368 ◽  
Author(s):  
Juan A. Bisceglia ◽  
Maria C. Mollo ◽  
Nadia Gruber ◽  
Liliana R. Orelli
Keyword(s):  
Drug Targets ◽  
Redox Homeostasis ◽  
Cost Effective ◽  
Structural Features ◽  
Mammalian Host ◽  
Neglected Diseases ◽  
Nitrogen Compounds ◽  
Chemical Structures

Neglected diseases due to the parasitic protozoa Leishmania and Trypanosoma (kinetoplastids) affect millions of people worldwide, and the lack of suitable treatments has promoted an ongoing drug discovery effort to identify novel nontoxic and cost-effective chemotherapies. Polyamines are ubiquitous small organic molecules that play key roles in kinetoplastid parasites metabolism, redox homeostasis and in the normal progression of cell cycles, which differ from those found in the mammalian host. These features make polyamines attractive in terms of antiparasitic drug development. The present work provides a comprehensive insight on the use of polyamine derivatives and related nitrogen compounds in the chemotherapy of kinetoplastid diseases. The amount of literature on this subject is considerable, and a classification considering drug targets and chemical structures were made. Polyamines, aminoalcohols and basic heterocycles designed to target the relevant parasitic enzyme trypanothione reductase are discussed in the first section, followed by compounds directed to less common targets, like parasite SOD and the aminopurine P2 transporter. Finally, the third section comprises nitrogen compounds structurally derived from antimalaric agents. References on the chemical synthesis of the selected compounds are reported together with their in vivo and/or in vitro IC50 values, and structureactivity relationships within each group are analyzed. Some favourable structural features were identified from the SAR analyses comprising protonable sites, hydrophobic groups and optimum distances between them. The importance of certain pharmacophoric groups or amino acid residues in the bioactivity of polyamine derived compounds is also discussed.

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