In Silico Driven Prediction of MAPK14 Off-Targets Reveals Unrelated Proteins with High Accuracy

During the discovery and development of new drugs, candidates with undesired and potentially harmful side-effects can arise at all stages, which poses significant scientific and economic risks. Most of such phenotypic side-effects can be attributed to binding of the drug candidate to unintended proteins, so-called off-targets. The early identification of potential off-targets is therefore of utmost importance to mitigate any downstream risks. We showcase how the combination of knowledge-based in silico off-target screening and state-of-the-art biophysics can be applied to rapidly identify off-targets for a MAPK14 inhibitor. Out of 13 predicted off-targets, six proteins were confirmed to interact with the inhibitor in vitro, which translates to an exceptional hit rate of 46%. For two proteins, affinities in the lower micromolar range were obtained: The kinase IRE1 and the Hematopoietic Prostaglandin D Synthase, which is entirely unrelated to MAPK14 and is involved in different cell-regulatory processes. The whole off-target identification/validation pipeline can be completed as fast as within two months, excluding delivery times of proteins. These results emphasize how computational off-target screening in combination with MicroScale Thermophoresis can effectively reduce downstream development risks in a very competitive time frame and at low cost.

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In silico prospection of antineoplastic molecules from the Artemisia annua species

Revista Brasileira Militar de Ciências ◽

10.36414/rbmc.v7i19.105 ◽

2021 ◽

Vol 7 (19) ◽

Author(s):

Isabela Sacienti Lavezo ◽

Juracy Cirino de Souza Neto ◽

Túlio Nunes Pinto ◽

Leonardo Luiz Borges

Keyword(s):

In Silico ◽

Artemisia Annua ◽

Biological Effects ◽

Low Cost ◽

Target Prediction ◽

Molecular Target ◽

New Drugs ◽

Antineoplastic Activity

Lung cancer kills the most men and the second that kills the most women (behind only breast cancer). The in silico study makes it possible to search for new drugs at low cost, with a greater possibility of rapid manufacturing and a lower future cost for their manufacture. The objective of this study was to analyze an antineoplastic activity of the compounds of Artemisia annua to obtain an active substance that can reach the molecular target of the cancer cells. Compounds with antineoplastic effects were selected using Scielo, PubMed, and ScienceDirect platforms. Afterward, the first screening of compound compounds was performed with a high ability to predict biological and pharmacological activity through the PASS Prediction, Pubchem, and Swiss ADME platforms. After the current screening, we determined the toxicological and molecular target prediction by the Portox II and Swiss Target Prediction platforms. As a final part, molecular docking and redocking were performed for a compound using the PDB server and the GOLD Suite 5.7.0 program. For another, we completed the pharmacophoric mapping using the Binding DB and PharmaGist database. The compounds scopoletin and caffeic acid were the most promising structures in silico models capable of interacting with EGFR (epidermal growth factor) and MM-9 (metalloproteinase type 9), respectively. The results obtained that these structures are promising to be tested in in vitro and in vivo tests about the antineoplastic activity. In addition, in silico analyses help to understand the biological effects of A. annua extracts regarding antineoplastic evidence.

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Identification of Iminium Intermediates Generation in the Metabolism of Tepotinib Using LC-MS/MS: In Silico and Practical Approaches to Bioactivation Pathway Elucidation

Molecules ◽

10.3390/molecules25215004 ◽

2020 ◽

Vol 25 (21) ◽

pp. 5004 ◽

Cited By ~ 1

Author(s):

Ali S. Abdelhameed ◽

Mohamed W. Attwa ◽

Adnan A. Kadi

Keyword(s):

Side Effects ◽

Phase I ◽

In Silico ◽

Potassium Cyanide ◽

Reactive Intermediates ◽

Toxicity Assessment ◽

Human Liver Microsome ◽

New Drugs ◽

Piperidine Ring

Tepotinib (Tepmetko™, Merck) is a potent inhibitor of c-Met (mesenchymal−epithelial transition factor). In March 2020, tepotinib (TEP) was approved for use in Japan for the treatment of patients who suffered from non-small cell lung cancers (NSCLC) harboring an MET exon 14 skipping alteration and have progressed after platinum-based therapy. Practical and in silico experiments were used to screen for the metabolic profile and reactive intermediates of TEP. Knowing the bioactive center and structural alerts in the TEP structure helped in making targeted modifications to improve its safety. First, the prediction of metabolism vulnerable sites and reactivity metabolic pathways was performed using the StarDrop WhichP450™ module and the online Xenosite reactivity predictor tool, respectively. Subsequently, in silico data were used as a guide for the in vitro practical work. Second, in vitro phase I metabolites of TEP were generated from human liver microsome (HLM) incubations. Testing for the generation of unstable reactive intermediates was performed using potassium cyanide as a capturing agent forming stable cyano adduct that can be characterized and identified using liquid chromatography tandem mass spectrometry (LC-MS/MS). Third, in silico toxicity assessment of TEP metabolites was performed, and structural modification was proposed to decrease their side effects and to validate the proposed bioactivation pathway using the DEREK software. Four TEP phase I metabolites and four cyano adducts were characterized. The reactive intermediate generation mechanism of TEP may provide an explanation of its adverse reactions. The piperidine ring is considered a structural alert for toxicity as proposed by the DEREK software and a Xenosite reactivity model, which was confirmed by practical experiments. Steric hindrance or isosteric replacement at α-carbon of the piperidine ring stop the bioactivation sequence that was confirmed using the DEREK software. More drug discovery studies can be performed using this perception permitting the design of new drugs with an increased safety profile. To our knowledge, this is the first study for the identification of in vitro phase I metabolites and reactive intermediates in addition to toxicological properties of the metabolites for TEP that will be helpful for the evaluation of TEP side effects and drug–drug interactions in TEP-treated patients.

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Generation of High-Yield, Functional Oligodendrocytes from a c-myc Immortalized Neural Cell Line, Endowed with Staminal Properties

International Journal of Molecular Sciences ◽

10.3390/ijms22031124 ◽

2021 ◽

Vol 22 (3) ◽

pp. 1124

Author(s):

Mafalda Giovanna Reccia ◽

Floriana Volpicelli ◽

Eirkiur Benedikz ◽

Åsa Fex Svenningsen ◽

Luca Colucci-D’Amato

Keyword(s):

Cell Line ◽

Low Cost ◽

Neural Cell ◽

New Drugs ◽

High Yield ◽

Time Saving ◽

Interacting Protein ◽

Neuronal Marker ◽

Differentiation Status

Neural stem cells represent a powerful tool to study molecules involved in pathophysiology of Nervous System and to discover new drugs. Although they can be cultured and expanded in vitro as a primary culture, their use is hampered by their heterogeneity and by the cost and time needed for their preparation. Here we report that mes-c-myc A1 cells (A1), a neural cell line, is endowed with staminal properties. Undifferentiated/proliferating and differentiated/non-proliferating A1 cells are able to generate neurospheres (Ns) in which gene expression parallels the original differentiation status. In fact, Ns derived from undifferentiated A1 cells express higher levels of Nestin, Kruppel-like factor 4 (Klf4) and glial fibrillary protein (GFAP), markers of stemness, while those obtained from differentiated A1 cells show higher levels of the neuronal marker beta III tubulin. Interestingly, Ns differentiation, by Epidermal Growth Factors (EGF) and Fibroblast Growth Factor 2 (bFGF) withdrawal, generates oligodendrocytes at high-yield as shown by the expression of markers, Galactosylceramidase (Gal-C) Neuron-Glial antigen 2 (NG2), Receptor-Interacting Protein (RIP) and Myelin Basic Protein (MBP). Finally, upon co-culture, Ns-A1-derived oligodendrocytes cause a redistribution of contactin-associated protein (Caspr/paranodin) protein on neuronal cells, as primary oligodendrocytes cultures, suggesting that they are able to form compact myelin. Thus, Ns-A1-derived oligodendrocytes may represent a time-saving and low-cost tool to study the pathophysiology of oligodendrocytes and to test new drugs.

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A Study for the Access to a Semi-synthetic Regioisomer of Natural Fucosylated Chondroitin Sulfate with Fucosyl Branches on N-acetyl-Galactosamine Units

Marine Drugs ◽

10.3390/md17120655 ◽

2019 ◽

Vol 17 (12) ◽

pp. 655 ◽

Cited By ~ 1

Author(s):

Giulia Vessella ◽

Serena Traboni ◽

Anna V. A. Pirozzi ◽

Antonio Laezza ◽

Alfonso Iadonisi ◽

...

Keyword(s):

Chondroitin Sulfate ◽

Anticoagulant Activity ◽

The Body ◽

New Drugs ◽

Coagulation Cascade ◽

Drug Candidate ◽

Heterogeneous Structure ◽

Anticoagulant Drug ◽

Chemical Strategy

Fucosylated chondroitin sulfate (fCS) is a glycosaminoglycan found up to now exclusively in the body wall of sea cucumbers. It shows several interesting activities, with the anticoagulant and antithrombotic as the most attractive ones. Its different mechanism of action on the blood coagulation cascade with respect to heparin and the retention of its activity by oral administration make fCS a very promising anticoagulant drug candidate for heparin replacement. Nonetheless, its typically heterogeneous structure, the detection of some adverse effects and the preference for new drugs not sourced from animal tissues, explain how mandatory is to open an access to safer and less heterogeneous non-natural fCS species. Here we contribute to this aim by investigating a suitable chemical strategy to obtain a regioisomer of the natural fCS polysaccharide, with sulfated l-fucosyl branches placed at position O-6 of N-acetyl-d-galactosamine (GalNAc) units instead of O-3 of d-glucuronic acid (GlcA) ones, as in natural fCSs. This strategy is based on the structural modification of a microbial sourced chondroitin polysaccharide by regioselective insertion of fucosyl branches and sulfate groups on its polymeric structure. A preliminary in vitro evaluation of the anticoagulant activity of three of such semi-synthetic fCS analogues is also reported.

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[Ru(phen)2podppz]2+ significantly inhibits glioblastoma growth in vitro and vivo with fewer side-effects than cisplatin

Dalton Transactions ◽

10.1039/d0dt01877e ◽

2020 ◽

Vol 49 (26) ◽

pp. 8864-8871

Author(s):

Ruihao Li ◽

Yabin Ma ◽

Xiaochun Hu ◽

Wenjing Wu ◽

Xuewen Wu ◽

...

Keyword(s):

Side Effects ◽

Tumor Growth ◽

Drug Candidate ◽

Inhibit Tumor Growth ◽

New Drug

Ru1 could most effectively inhibit tumor growth and avoid any detectable side-effects compared with other ruthenium(ii) complexes and cisplatin, demonstrating its potential to be an exciting new drug candidate for glioblastoma treatment.

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FBDD: In-silico STRATEGY TO INHIBIT MPRO ACTIVITY USING DRUGS FROM PREVIOUS OUTBREAKS

Journal of Experimental Biology and Agricultural Sciences ◽

10.18006/2021.9(4).472.480 ◽

2021 ◽

Vol 9 (4) ◽

pp. 472-480

Author(s):

Gauravi N Trivedi ◽

◽

Janhavi T Karlekar ◽

Khushbu Dhimmar ◽

Hetal kumar Panchal ◽

...

Keyword(s):

Drug Development ◽

In Silico ◽

Drug Targets ◽

Transmission Rate ◽

Respiratory Illness ◽

Primary Treatment ◽

Rational Drug Design ◽

New Drugs ◽

Main Protease

Main protease (Mpro) and Spike (S) proteins are said potential drug targets of COVID-19. Pneumonia like respiratory illness caused by SARS-CoV-2 is spreading rapidly due to its replication and transmission rate. Protease is the protein that is involved in both replication and transcription. Since CoV-2 shares, genomic similarity with CoV and MERS-CoV, drugs from previous outbreaks are used as primary treatment of the disease. In-silico drug development strategies are said to be faster and effective than in-vitro with a lesser amount of risk factors. Fragment Based Drug Designing (FBDD), also known as rational drug design in which a potential target protein is selected and docked with a lead-like molecule that eventually leads to drug development. Nine (9) drugs that are currently being used to treat patients of coronavirus were selected in this study from the latest literature review and fragmented as per rules followed by crosslinking of drug fragments using editor tools. These native drugs and synthesized drugs were then docked against the main protease. Results of the study revealed that one of the crosslinked lead-like compounds showed a higher binding affinity (∆G) more than any of the native compounds. Further, the results of this study suggested that the combination of potential drugs can be an effective way to develop new drugs to treat a deadly disease.

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Efficacy of Spironolactone Treatment in Murine Models of Cutaneous and Visceral Leishmaniasis

Frontiers in Pharmacology ◽

10.3389/fphar.2021.636265 ◽

2021 ◽

Vol 12 ◽

Author(s):

Valter Viana Andrade-Neto ◽

Juliana da Silva Pacheco ◽

Job Domingos Inácio ◽

Elmo Eduardo Almeida-Amaral ◽

Eduardo Caio Torres-Santos ◽

...

Keyword(s):

Visceral Leishmaniasis ◽

Cutaneous Lesion ◽

Parasite Burden ◽

Parasite Load ◽

New Drugs ◽

Drug Candidate ◽

Success Rates ◽

Meglumine Antimoniate ◽

Future Possibility

Translational studies involving the reuse and association of drugs are approaches that can result in higher success rates in the discovery and development of drugs for serious public health problems, including leishmaniasis. If we consider the number of pathogenic species in relation to therapeutic options, this arsenal is still small, and each drug possesses a disadvantage in terms of toxicity, efficacy, price, or treatment regimen. In the search for new drugs, we performed a drug screening of L. amazonensis promastigotes and intracellular amastigotes of fifty available drugs belonging to several classes according to their pharmacophoric group. Spironolactone, a potassium-sparing diuretic, proved to be the most promising drug candidate. After demonstrating the in vitro antileishmanial activity, we evaluated the efficacy on a murine experimental model with L. amazonensis and L. infantum. The treatment controlled the cutaneous lesion and reduced the parasite burden of L. amazonensis significantly, as effectively as meglumine antimoniate. The treatment of experimental visceral leishmaniasis was effective in reducing the parasite load on the main affected organs (spleen and liver) via high doses of spironolactone. The association between spironolactone and meglumine antimoniate promoted better control of the parasite load in the spleen and liver compared to the group treated with meglumine antimoniate alone. These results reveal a possible benefit of the concomitant use of spironolactone and meglumine antimoniate that should be studied more in depth for the future possibility of repositioning for leishmaniasis co-therapy.

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A novel method of screening combinations of angiostatics identifies bevacizumab and temsirolimus as synergistic inhibitors of glioma-induced angiogenesis

PLoS ONE ◽

10.1371/journal.pone.0252233 ◽

2021 ◽

Vol 16 (6) ◽

pp. e0252233

Author(s):

Michael I. Dorrell ◽

Heidi R. Kast-Woelbern ◽

Ryan T. Botts ◽

Stephen A. Bravo ◽

Jacob R. Tremblay ◽

...

Keyword(s):

Side Effects ◽

Tumor Angiogenesis ◽

Clinical Success ◽

Low Cost ◽

Chorioallantoic Membrane ◽

Cellular Interactions ◽

Compensatory Mechanisms ◽

Chick Chorioallantoic Membrane

Tumor angiogenesis is critical for the growth and progression of cancer. As such, angiostasis is a treatment modality for cancer with potential utility for multiple types of cancer and fewer side effects. However, clinical success of angiostatic monotherapies has been moderate, at best, causing angiostatic treatments to lose their early luster. Previous studies demonstrated compensatory mechanisms that drive tumor vascularization despite the use of angiostatic monotherapies, as well as the potential for combination angiostatic therapies to overcome these compensatory mechanisms. We screened clinically approved angiostatics to identify specific combinations that confer potent inhibition of tumor-induced angiogenesis. We used a novel modification of the ex ovo chick chorioallantoic membrane (CAM) model that combined confocal and automated analyses to quantify tumor angiogenesis induced by glioblastoma tumor onplants. This model is advantageous due to its low cost and moderate throughput capabilities, while maintaining complex in vivo cellular interactions that are difficult to replicate in vitro. After screening multiple combinations, we determined that glioblastoma-induced angiogenesis was significantly reduced using a combination of bevacizumab (Avastin®) and temsirolimus (Torisel®) at doses below those where neither monotherapy demonstrated activity. These preliminary results were verified extensively, with this combination therapy effective even at concentrations further reduced 10-fold with a CI value of 2.42E-5, demonstrating high levels of synergy. Thus, combining bevacizumab and temsirolimus has great potential to increase the efficacy of angiostatic therapy and lower required dosing for improved clinical success and reduced side effects in glioblastoma patients.

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Genetically Encoded Sensor Cells for the Screening of Glucocorticoid Receptor (GR) Effectors in Herbal Extracts

Biosensors ◽

10.3390/bios11090341 ◽

2021 ◽

Vol 11 (9) ◽

pp. 341

Author(s):

Chungwon Kang ◽

Soyoun Kim ◽

Euiyeon Lee ◽

Jeahee Ryu ◽

Minhyeong Lee ◽

...

Keyword(s):

Drug Screening ◽

Low Cost ◽

Biologically Active ◽

Drug Candidate ◽

Fluorescence Signal ◽

Biologically Relevant ◽

Biological Targets ◽

Sensing Technology ◽

Medicinal Plant Extracts

Although in vitro sensors provide facile low-cost ways to screen for biologically active targets, their results may not accurately represent the molecular interactions in biological systems. Cell-based sensors have emerged as promising platforms to screen targets in biologically relevant environments. However, there are few examples where cell-based sensors have been practically applied for drug screening. Here, we used engineered cortisol-detecting sensor cells to screen for natural mimetics of cortisol. The sensor cells were designed to report the presence of a target through signal peptide activation and subsequent fluorescence signal translocation. The developed sensor cells were able to detect known biological targets from human-derived analytes as well as natural product extracts, such as deer antlers and ginseng. The multi-use capability and versatility to screen in different cellular environments were also demonstrated. The sensor cells were used to identify novel GR effectors from medicinal plant extracts. Our results suggest that decursin from dongquai had the GR effector function as a selective GR agonist (SEGRA), making it a potent drug candidate with anti-inflammatory activity. We demonstrated the superiority of cell-based sensing technology over in vitro screening, proving its potential for practical drug screening applications that leads to the function-based discovery of target molecules.

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In silico and antithrombotic studies of 1,3,4-oxadiazoles derived from benzimidazole

Bangladesh Journal of Pharmacology ◽

10.3329/bjp.v11i1.23981 ◽

2015 ◽

Vol 11 (1) ◽

pp. 67 ◽

Cited By ~ 2

Author(s):

B. Vishwanathan ◽

B. M. Gurupadayya ◽

K. Venkata Sairam

Keyword(s):

In Silico ◽

Factor Xa ◽

Docking Studies ◽

Negative Control ◽

Clot Lysis ◽

Drug Candidate ◽

Thrombolytic Activity ◽

Reference Drug ◽

Oxadiazole Derivatives

In the present study, a series of 1,3,4-oxadiazole derivatives (4a-4k) derived from benzimidazole were docked onto factor Xa (PDB: 1NFY) protein using SYBYLX 2.1. and also evaluated for in vitro clot lysis for thrombolytic activity. The synthesized molecules were also screened for in silico ADME studies. The molecular docking studies highlighted that the molecules showed high affinity towards 1NFY with higher docking score and the in silico ADME results were promising and indicated that the molecules holds great potential as a drug candidate. The thrombolytic evaluation was performed for decrease in solid clot weight by the clot lysis study at a concentration of 6.25, 12.5 and 25 µM strengths, respectively. The results of in vitro clot lysis for thrombolytic evaluation revealed that the tested compounds 4a-4k exhibited significant clot lysis with respect to negative control phosphate buffered saline and in comparison to the reference drug streptokinase (30,000 IU). Among all the tested compounds, compound 4j, 4d and 4g exhibited potent thrombolytic activity with EC50 value of 16.2, 18.1 and 23.7 µM, respectively. The thrombolytic efficacy investigation highlights that the synthesized compound 4j could be considered for further clinical studies to ascertain its possible hit as thrombolytic agents.

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