scholarly journals Exploring protein hotspots by optimized fragment pharmacophores

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Dávid Bajusz ◽  
Warren S. Wade ◽  
Grzegorz Satała ◽  
Andrzej J. Bojarski ◽  
Janez Ilaš ◽  
...  
Keyword(s):  
Drug Target ◽  
Drug Targets ◽  
Chemical Space ◽  
General Concept ◽  
Small Fragment ◽  
Biochemical Screening ◽  
Main Protease ◽  
Design Protocol ◽  
Fragment Libraries ◽  
Early Drug

AbstractFragment-based drug design has introduced a bottom-up process for drug development, with improved sampling of chemical space and increased effectiveness in early drug discovery. Here, we combine the use of pharmacophores, the most general concept of representing drug-target interactions with the theory of protein hotspots, to develop a design protocol for fragment libraries. The SpotXplorer approach compiles small fragment libraries that maximize the coverage of experimentally confirmed binding pharmacophores at the most preferred hotspots. The efficiency of this approach is demonstrated with a pilot library of 96 fragment-sized compounds (SpotXplorer0) that is validated on popular target classes and emerging drug targets. Biochemical screening against a set of GPCRs and proteases retrieves compounds containing an average of 70% of known pharmacophores for these targets. More importantly, SpotXplorer0 screening identifies confirmed hits against recently established challenging targets such as the histone methyltransferase SETD2, the main protease (3CLPro) and the NSP3 macrodomain of SARS-CoV-2.

scholarly journals In Silico Screening of Some Antiviral Phytochemicals as Drug Leads Against Covid-19

2020 ◽  
Author(s):  
Monjur Ahmed Laskar ◽  
Moriom Begam ◽  
Manabendra Dutta Choudhury
Keyword(s):  
Drug Target ◽  
Drug Targets ◽  
Three Dimensional ◽  
Data Bank ◽  
Drug Candidate ◽  
Present Observation ◽  
Health It ◽  
Main Protease ◽  
And Control ◽  
Drug Leads

<p>Background: COVID-19 caused by SARS-CoV-2 in December 2019 has become a pandemic</p><p>hazard to the community health. It is a respiratory difficulty causing fever, dry cough, fatigue,</p><p>shortness of breath, muscle aches and some instances lead to pneumonia. Coronaviruses have</p><p>large viral RNA Genomes and are single-stranded positive-sense RNA viruses. The nsp10/nsp16</p><p>protein is an important target because it is essential for the virus to replicate, the papain-like</p><p>protease (Nsp3), the main protease (Nsp5), the primary RNA-dependent RNA polymerase</p><p>(Nsp12) are also attractive drug targets for this disease. The uses of phytochemicals as</p><p>therapeutic agents have been increasing in recent years. Some antiviral phytochemicals were</p><p>taken based on literature survey for this study.</p><p>Methods: ADME parameters and drug like nature of phytochemicals were screened using</p><p>SwissADME web tool. Three dimensional structures of targets are downloaded from Protein</p><p>Data Bank and docked with phytochemicals & control by using software FlexX.</p><p>Results: Morin shows significant results in ADME screening and Drug likeness prediction</p><p>studies, it shows stable bonding pattern with all four targets in compare to other phytochemicals</p><p>and control, shows least score in docking and forms maximum number of hydrogen bonds with</p><p>the active residues of the receptors.</p><p>Conclusion: Based on present observation of docking results, ADME parameters and drug like</p><p>nature, we suggest that morin may be a potent new drug candidate against Covid-19.</p><p>Keywords: COVID-19, coronavirus, drug target, phytochemicals, Drug likeness, ADME,</p><p>docking, morin</p>

scholarly journals In Silico Screening of Some Antiviral Phytochemicals as Drug Leads Against Covid-19

2020 ◽  
Author(s):  
Monjur Ahmed Laskar ◽  
Moriom Begam ◽  
Manabendra Dutta Choudhury
Keyword(s):  
Drug Target ◽  
Drug Targets ◽  
Three Dimensional ◽  
Data Bank ◽  
Drug Candidate ◽  
Present Observation ◽  
Health It ◽  
Main Protease ◽  
And Control ◽  
Drug Leads

<p>Background: COVID-19 caused by SARS-CoV-2 in December 2019 has become a pandemic</p><p>hazard to the community health. It is a respiratory difficulty causing fever, dry cough, fatigue,</p><p>shortness of breath, muscle aches and some instances lead to pneumonia. Coronaviruses have</p><p>large viral RNA Genomes and are single-stranded positive-sense RNA viruses. The nsp10/nsp16</p><p>protein is an important target because it is essential for the virus to replicate, the papain-like</p><p>protease (Nsp3), the main protease (Nsp5), the primary RNA-dependent RNA polymerase</p><p>(Nsp12) are also attractive drug targets for this disease. The uses of phytochemicals as</p><p>therapeutic agents have been increasing in recent years. Some antiviral phytochemicals were</p><p>taken based on literature survey for this study.</p><p>Methods: ADME parameters and drug like nature of phytochemicals were screened using</p><p>SwissADME web tool. Three dimensional structures of targets are downloaded from Protein</p><p>Data Bank and docked with phytochemicals & control by using software FlexX.</p><p>Results: Morin shows significant results in ADME screening and Drug likeness prediction</p><p>studies, it shows stable bonding pattern with all four targets in compare to other phytochemicals</p><p>and control, shows least score in docking and forms maximum number of hydrogen bonds with</p><p>the active residues of the receptors.</p><p>Conclusion: Based on present observation of docking results, ADME parameters and drug like</p><p>nature, we suggest that morin may be a potent new drug candidate against Covid-19.</p><p>Keywords: COVID-19, coronavirus, drug target, phytochemicals, Drug likeness, ADME,</p><p>docking, morin</p>

scholarly journals 4E Interacting Protein as a Potential Novel Drug Target for Nucleoside Analogues in Trypanosoma Brucei

2021 ◽  
Vol 9 (4) ◽  
pp. 826
Author(s):  
Dorien Mabille ◽  
Camila Cardoso Santos ◽  
Rik Hendrickx ◽  
Mathieu Claes ◽  
Peter Takac ◽  
...  
Keyword(s):  
Mode Of Action ◽  
Drug Target ◽  
Drug Targets ◽  
De Novo ◽  
Treatment Options ◽  
Adenosine Kinase ◽  
Nucleoside Analogues ◽  
Purine Salvage ◽  
Interacting Protein ◽  
Novel Drug

Human African trypanosomiasis is a neglected parasitic disease for which the current treatment options are quite limited. Trypanosomes are not able to synthesize purines de novo and thus solely depend on purine salvage from the host environment. This characteristic makes players of the purine salvage pathway putative drug targets. The activity of known nucleoside analogues such as tubercidin and cordycepin led to the development of a series of C7-substituted nucleoside analogues. Here, we use RNA interference (RNAi) libraries to gain insight into the mode-of-action of these novel nucleoside analogues. Whole-genome RNAi screening revealed the involvement of adenosine kinase and 4E interacting protein into the mode-of-action of certain antitrypanosomal nucleoside analogues. Using RNAi lines and gene-deficient parasites, 4E interacting protein was found to be essential for parasite growth and infectivity in the vertebrate host. The essential nature of this gene product and involvement in the activity of certain nucleoside analogues indicates that it represents a potential novel drug target.

Developing novel chemical entities for the treatment of lysosomal storage disorders: an academic perspective

2015 ◽  
Vol 309 (12) ◽  
pp. F996-F999 ◽  
Author(s):  
James A. Shayman
Keyword(s):  
Drug Targets ◽  
Lysosomal Storage ◽  
Federal Drug Administration ◽  
Drug Candidates ◽  
Gaucher Disease Type 1 ◽  
Biotechnology Companies ◽  
Approved Drugs ◽  
Novel Drug ◽  
Early Drug

Historically, most Federal Drug Administration-approved drugs were the result of “in-house” efforts within large pharmaceutical companies. Over the last two decades, this paradigm has steadily shifted as the drug industry turned to startups, small biotechnology companies, and academia for the identification of novel drug targets and early drug candidates. This strategic pivot has created new opportunities for groups less traditionally associated with the creation of novel therapeutics, including small academic laboratories, for engagement in the drug discovery process. A recent example of the successful development of a drug that had its origins in academia is eliglustat tartrate, an oral agent for Gaucher disease type 1.

scholarly journals Drug Target Prediction Based on the Herbs Components: The Study on the Multitargets Pharmacological Mechanism of Qishenkeli Acting on the Coronary Heart Disease

2012 ◽  
Vol 2012 ◽  
pp. 1-10 ◽  
Author(s):  
Yong Wang ◽  
Zhongyang Liu ◽  
Chun Li ◽  
Dong Li ◽  
Yulin Ouyang ◽  
...  
Keyword(s):  
Coronary Heart Disease ◽  
Heart Disease ◽  
Angiotensin Ii ◽  
Drug Target ◽  
Drug Targets ◽  
Target Prediction ◽  
Coronary Artery Ligation ◽  
Potential Drug ◽  
Drug Target Prediction ◽  
Potential Drug Targets

In this paper, we present a case study of Qishenkeli (QSKL) to research TCM’s underlying molecular mechanism, based on drug target prediction and analyses of TCM chemical components and following experimental validation. First, after determining the compositive compounds of QSKL, we use drugCIPHER-CS to predict their potential drug targets. These potential targets are significantly enriched with known cardiovascular disease-related drug targets. Then we find these potential drug targets are significantly enriched in the biological processes of neuroactive ligand-receptor interaction, aminoacyl-tRNA biosynthesis, calcium signaling pathway, glycine, serine and threonine metabolism, and renin-angiotensin system (RAAS), and so on. Then, animal model of coronary heart disease (CHD) induced by left anterior descending coronary artery ligation is applied to validate predicted pathway. RAAS pathway is selected as an example, and the results show that QSKL has effect on both rennin and angiotensin II receptor (AT1R), which eventually down regulates the angiotensin II (AngII). Bioinformatics combing with experiment verification can provide a credible and objective method to understand the complicated multitargets mechanism for Chinese herbal formula.

scholarly journals Translational and Clinical Pharmacology Considerations in Drug Repurposing for X-linked Adrenoleukodystrophy-A Rare Peroxisomal Disorder

2021 ◽  
Author(s):  
Julianne Tieu ◽  
Siddhee Sahasrabudhe ◽  
Paul Orchard ◽  
James Cloyd ◽  
Reena Kartha
Keyword(s):  
Drug Target ◽  
Drug Targets ◽  
Drug Repurposing ◽  
Pharmacokinetics And Pharmacodynamics ◽  
Drug Candidates ◽  
Target Patient Population ◽  
Site Of Action ◽  
Repurposed Drugs ◽  
Gait Disturbances ◽  
Spastic Quadriparesis

X-linked adrenoleukodystrophy (X-ALD) is an inherited, neurodegenerative rare disease that can result in devastating symptoms of blindness, gait disturbances, and spastic quadriparesis due to progressive demyelination. Typically, the disease progresses rapidly, causing death within the first decade of life. With limited treatments available, efforts to determine an effective therapy that can alter disease progression or mitigate symptoms have been undertaken for many years, particularly through drug repurposing. Repurposing has generally been guided through clinical experience and small trials. At this time, none of the drug candidates have been approved for use, which may be due, in part, to the lack of pharmacokinetic/pharmacodynamic (PK/PD) information on the repurposed medications in the target patient population. Greater consideration for the disease pathophysiology, drug pharmacology, and potential drug-target interactions, specifically at the site of action, would improve drug repurposing and facilitate development. Although there is a good understanding of X-ALD pathophysiology, the absence of information on drug targets, pharmacokinetics, and pharmacodynamics hinders the repurposing of drugs for this condition. Incorporating advanced translational and clinical pharmacological approaches in preclinical studies and early stages clinical trials will improve the success of repurposed drugs for X-ALD as well as other rare diseases.

scholarly journals Crystal structure of SARS-CoV-2 main protease in complex with a Chinese herb inhibitor shikonin

2020 ◽  
Author(s):  
Jian Li ◽  
Xuelan Zhou ◽  
Yan Zhang ◽  
Fanglin Zhong ◽  
Cheng Lin ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Conformational Changes ◽  
Drug Targets ◽  
Chinese Herb ◽  
Binding Modes ◽  
High Potency ◽  
Main Protease ◽  
Covalent Inhibitors ◽  
Catalytic Dyad ◽  
Important Drug

AbstractMain protease (Mpro, also known as 3CLpro) has a major role in the replication of coronavirus life cycle and is one of the most important drug targets for anticoronavirus agents. Here we report the crystal structure of main protease of SARS-CoV-2 bound to a previously identified Chinese herb inhibitor shikonin at 2.45 angstrom resolution. Although the structure revealed here shares similar overall structure with other published structures, there are several key differences which highlight potential features that could be exploited. The catalytic dyad His41-Cys145 undergoes dramatic conformational changes, and the structure reveals an unusual arrangement of oxyanion loop stabilized by the substrate. Binding to shikonin and binding of covalent inhibitors show different binding modes, suggesting a diversity in inhibitor binding. As we learn more about different binding modes and their structure-function relationships, it is probable that we can design more effective and specific drugs with high potency that can serve as effect SARS-CoV-2 anti-viral agents.

scholarly journals Drug Repurposing for Candidate SARS-CoV-2 Main Protease Inhibitors by a Novel in Silico Method

2020 ◽  
Author(s):  
Milan Sencanski ◽  
Vladimir Perovic ◽  
Snezana Pajovic ◽  
Miroslav Adzic ◽  
Slobodan Paessler ◽  
...  
Keyword(s):  
Protease Inhibitors ◽  
In Silico ◽  
Drug Target ◽  
Transmission Rate ◽  
Experimental Testing ◽  
Drug Repurposing ◽  
Global Public Health ◽  
Main Protease ◽  
Additional Approach ◽  
Drugbank Database

<p>The SARS-CoV-2 outbreak caused an unprecedented global public health threat, having a high transmission rate with currently no drugs or vaccines approved. An alternative powerful additional approach to counteract COVID-19 is <em>in silico</em> drug repurposing. The SARS-CoV-2 main protease is essential for viral replication and an attractive drug target. In this study, we used the virtual screening (VS) protocol with both long-range and short-range interactions to select candidate SARS-CoV-2 main protease inhibitors. First, the ISM applied for Small Molecules was used for searching the Drugbank database and further followed by molecular docking. After <em>in silico</em> screening of drug space, we identified 57 drugs as potential SARS-CoV-2 main protease inhibitors that we propose for further experimental testing.</p>

scholarly journals Compound2Drug – a Machine/deep Learning Tool for Predicting the Bioactivity of PubChem Compounds

2020 ◽  
Author(s):  
Ben Geoffrey A S ◽  
Pavan Preetham Valluri ◽  
Akhil Sanker ◽  
Rafal Madaj ◽  
Host Antony Davidd ◽  
...  
Keyword(s):  
Machine Learning ◽  
Deep Learning ◽  
Molecular Docking ◽  
Drug Target ◽  
Drug Targets ◽  
Learning Algorithms ◽  
Network Data ◽  
Ligand Interaction ◽  
Pubchem Compound ◽  
Protein Ligand Interaction

<p>Network data is composed of nodes and edges. Successful application of machine learning/deep learning algorithms on network data to make node classification and link prediction has been shown in the area of social networks through which highly customized suggestions are offered to social network users. Similarly one can attempt the use of machine learning/deep learning algorithms on biological network data to generate predictions of scientific usefulness. In the present work, compound-drug target interaction data set from bindingDB has been used to train machine learning/deep learning algorithms which are used to predict the drug targets for any PubChem compound queried by the user. The user is required to input the PubChem Compound ID (CID) of the compound the user wishes to gain information about its predicted biological activity and the tool outputs the RCSB PDB IDs of the predicted drug target. The tool also incorporates a feature to perform automated <i>In Silico</i> modelling for the compounds and the predicted drug targets to uncover their protein-ligand interaction profiles. The programs fetches the structures of the compound and the predicted drug targets, prepares them for molecular docking using standard AutoDock Scripts that are part of MGLtools and performs molecular docking, protein-ligand interaction profiling of the targets and the compound and stores the visualized results in the working folder of the user. The program is hosted, supported and maintained at the following GitHub repository </p> <p><a href="https://github.com/bengeof/Compound2Drug">https://github.com/bengeof/Compound2Drug</a></p>

scholarly journals An In-Silico Study on Selected Organosulfur Compounds as Potential Drugs for SARS-CoV-2 Infection via Binding Multiple Drug Targets

2020 ◽  
Author(s):  
Liya Thurakkal ◽  
Satyam Singh ◽  
Sushabhan Sadhukhan ◽  
Mintu Porel
Keyword(s):  
Drug Targets ◽  
Target Prediction ◽  
Multiple Drug ◽  
Organosulfur Compounds ◽  
Potential Candidate ◽  
Health Crisis ◽  
Drug Molecules ◽  
Main Protease

The emerging paradigm shift from ‘one molecule, one target, for one disease’ towards ‘multi-targeted small molecules’ has paved an ingenious pathway in drug discovery in recent years. This idea has been extracted for the investigation of competent drug molecules for the unprecedented COVID-19 pandemic which became the greatest global health crisis now. Perceiving the importance of organosulfur compounds against SARS-CoV-2 from the drugs under clinical trials, a class of organosulfur compounds effective against SARS-CoV were selected and studied the interaction with multiple proteins of the SARS-CoV-2. One compound displayed inhibition against five proteins (both structural and non-structural) of the virus namely, main protease, papain-like protease, spike protein, helicase and RNA dependent RNA polymerase. Consequently, this compound emanates as a potential candidate for treating the virulent disease. The pharmacokinetics, ADMET properties and target prediction studies carried out in this work further inflamed the versatility of the compound and urge to execute <i>in-vitro</i> and <i>in-vivo</i> analysis on SARS-CoV-2 in the future.<br>

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