scholarly journals Advances in Applying Computer-Aided Drug Design for Neurodegenerative Diseases

2021 ◽  
Vol 22 (9) ◽  
pp. 4688
Author(s):  
Mootaz M. Salman ◽  
Zaid Al-Obaidi ◽  
Philip Kitchen ◽  
Andrea Loreto ◽  
Roslyn M. Bill ◽  
...  
Keyword(s):  
Drug Design ◽  
Neurodegenerative Diseases ◽  
Docking Studies ◽  
New Drugs ◽  
Computer Aided Drug Design ◽  
Biological Assays ◽  
Advantages And Disadvantages ◽  
Computer Aided ◽  
Research Challenge ◽  
The Cost

Neurodegenerative diseases (NDs) including Alzheimer’s disease, Parkinson’s disease, amyotrophic lateral sclerosis, and Huntington’s disease are incurable and affect millions of people worldwide. The development of treatments for this unmet clinical need is a major global research challenge. Computer-aided drug design (CADD) methods minimize the huge number of ligands that could be screened in biological assays, reducing the cost, time, and effort required to develop new drugs. In this review, we provide an introduction to CADD and examine the progress in applying CADD and other molecular docking studies to NDs. We provide an updated overview of potential therapeutic targets for various NDs and discuss some of the advantages and disadvantages of these tools.

scholarly journals Computer-Aided Drug Design (CADD) to De-Orphanize Marine Molecules: Finding Potential Therapeutic Agents for Neurodegenerative and Cardiovascular Diseases

Marine Drugs ◽  
2022 ◽  
Vol 20 (1) ◽  
pp. 53
Author(s):  
Laura Llorach-Pares ◽  
Alfons Nonell-Canals ◽  
Conxita Avila ◽  
Melchor Sanchez-Martinez
Keyword(s):  
Natural Products ◽  
Drug Design ◽  
Therapeutic Potential ◽  
Marine Invertebrate ◽  
In Silico Analysis ◽  
New Drugs ◽  
Computer Aided Drug Design ◽  
Marine Habitats ◽  
Computer Aided ◽  
Promising Line

Computer-aided drug design (CADD) techniques allow the identification of compounds capable of modulating protein functions in pathogenesis-related pathways, which is a promising line on drug discovery. Marine natural products (MNPs) are considered a rich source of bioactive compounds, as the oceans are home to much of the planet’s biodiversity. Biodiversity is directly related to chemodiversity, which can inspire new drug discoveries. Therefore, natural products (NPs) in general, and MNPs in particular, have been used for decades as a source of inspiration for the design of new drugs. However, NPs present both opportunities and challenges. These difficulties can be technical, such as the need to dive or trawl to collect the organisms possessing the compounds, or biological, due to their particular marine habitats and the fact that they can be uncultivable in the laboratory. For all these difficulties, the contributions of CADD can play a very relevant role in simplifying their study, since, for example, no biological sample is needed to carry out an in-silico analysis. Therefore, the amount of natural product that needs to be used in the entire preclinical and clinical study is significantly reduced. Here, we exemplify how this combination between CADD and MNPs can help unlock their therapeutic potential. In this study, using a set of marine invertebrate molecules, we elucidate their possible molecular targets and associated therapeutic potential, establishing a pipeline that can be replicated in future studies.

scholarly journals Integration of Cassandra and Spark in Computer Aided Drug Design

2021 ◽  
pp. 68-73
Author(s):  
Nitha V R
Keyword(s):  
Big Data ◽  
Molecular Modeling ◽  
Drug Design ◽  
Programming Languages ◽  
New Drugs ◽  
Java Virtual Machine ◽  
Management Tool ◽  
Computer Aided Drug Design ◽  
Modeling Tool ◽  
Computer Aided

The primary purpose of this paper is to provide feasibility study of Cassandra and spark in Computer Aided Drug Design (CADD). The Apache Cassandra database is a big data management tool which can be used to store huge amount of data in different file formats. A huge database can be designed with details of all known molecules or compounds that are existing on earth. The information regarding the compounds such as selectivity, solubility, synthetic viability, affinity, adverse reactions, metabolism and environmental toxicity along with the 3 D structure of molecule can be stored in this big database. A data analytics tool “spark” can be efficiently used in mining and managing huge data stored in the database. Integrating big data in CADD helps in identifying the candidate drugs within minutes, not years. It may take eight to fifteen years to develop a new drug traditionally. Spark is written in Scala Programming Language which runs on Java Virtual Machine (JVM) and it supports Scala, Java and Python Programming languages .Cassandra can provide connectors to different programming languages, hence it’s very easy to integrate any other molecular modeling tool with Spark. A python based molecular modeling tool called Pymol can be easily implemented with Spark. CADD helps in identifying new drugs by computational means thus eliminating unnecessary cost incurred in chemical testing of drugs.

scholarly journals Chalcones as a basis for computer-aided drug design: innovative approaches to tackle malaria

2019 ◽  
Vol 11 (20) ◽  
pp. 2635-2646 ◽  
Author(s):  
Marilia NN Lima ◽  
Bruno J Neves ◽  
Gustavo C Cassiano ◽  
Marcelo N Gomes ◽  
Kaira CP Tomaz ◽  
...  
Keyword(s):  
Drug Design ◽  
Plasmodium Berghei ◽  
Experimental Validation ◽  
Docking Studies ◽  
Antiplasmodial Activity ◽  
Computer Aided Drug Design ◽  
Protein Targets ◽  
Computer Aided ◽  
Falciparum Protein

Aim: Computer-aided drug design approaches were applied to identify chalcones with antiplasmodial activity. Methodology: The virtual screening was performed as follows: structural standardization of in-house database of chalcones; identification of potential Plasmodium falciparum protein targets for the chalcones; homology modeling of the predicted P. falciparum targets; molecular docking studies; and in vitro experimental validation. Results: Using these models, we prioritized 16 chalcones with potential antiplasmodial activity, for further experimental evaluation. Among them, LabMol-86 and LabMol-87 showed potent in vitro antiplasmodial activity against P. falciparum, while LabMol-63 and LabMol-73 were potent inhibitors of Plasmodium berghei progression into mosquito stages. Conclusion: Our results encourage the exploration of chalcones in hit-to-lead optimization studies for tackling malaria.

scholarly journals In Silico Research of New Therapeutics Rotenoids Derivatives Against Leishmania Amazonensis Infection

2021 ◽  
Author(s):  
Adrián Vicente-Barrueco ◽  
Ángel Carlos Román ◽  
Trinidad Ruiz-Téllez ◽  
Francisco Centeno
Keyword(s):  
Drug Design ◽  
In Silico ◽  
Combinatorial Library ◽  
Leishmania Amazonensis ◽  
New Drugs ◽  
Ethnobotanical Knowledge ◽  
Computer Aided Drug Design ◽  
Computer Aided ◽  
Key Enzyme ◽  
The One

Yearly, 1,500,000 cases of leishmaniasis are diagnosed, causing thousands of deaths. To advance in its therapy, we present an interdisciplinary protocol that unifies ethnobotanical knowledge of natural compounds and the latest bioinformatics advances to respond to an orphan disease such as leishmaniasis and specifically the one caused by Leishmania amazonensis. The use of ethnobotanical information serves as a basis for the development of new drugs, a field in which computer-aided drug design (CADD) has been a revolution. Taking this information from Amazonian communities, located in the area with the highest prevalence of this disease, a protocol has been designed to verify new leads. Moreover, a method has been developed that allows the evaluation of lead molecules, and the improvement of their affinity and specificity against therapeutic targets. Through this approach, deguelin has been identified as a good lead to treat the infection due to its potential as an ornithine decarboxylase (ODC) inhibitor, a key enzyme in Leishmania development. Using an in silico-generated combinatorial library followed by docking approaches, we have found deguelin derivatives with better affinity and specificity against ODC than the original compound, suggesting that this approach could be adapted for developing new drugs against leishmaniasis.

scholarly journals Computer aided drug design using virtual screening and molecular energy calculation of a specific neurodegenerative diseases

2018 ◽  
Vol 7 (1.9) ◽  
pp. 141
Author(s):  
Bipin Nair B J ◽  
Akshay Rajendran
Keyword(s):  
Virtual Screening ◽  
Drug Design ◽  
Neurodegenerative Diseases ◽  
Neurodegenerative Disease ◽  
Data Bank ◽  
Binding Energies ◽  
Energy Calculation ◽  
Computer Aided Drug Design ◽  
Structure Of Molecules ◽  
Computer Aided

Computer-aided drug design (CADD) is designing a drug with the help of computational algorithms. Information technology advances to creates the structure of molecules, molecular modeling and calculate the binding energies of the drug to initiate a new medicine against neurodegenerative diseases. In our work, we implemented virtual screening of a drug-protein interaction is selected from drug data bank with potential drug bank inhibitory activity for a specific neurodegenerative disease. Here we analyze technical CADD studies of the neurodegenerative diseases. Finally selecting the best alkaloid for a specific neurodegenerative disease and predicting the efficiency using computation of alkaloid with molecular energy.

Computer-Aided Design of Coumarins for Neurodegenerative diseases: Trends of the Last Decade

2021 ◽  
Vol 21 ◽  
Author(s):  
Estela Guardado Yordi ◽  
Lourdes Santana ◽  
Eugenio Uriarte ◽  
Fernanda Borges ◽  
Maria J. Matos
Keyword(s):  
Neurodegenerative Diseases ◽  
Computer Aided Design ◽  
New Technologies ◽  
Chemical Properties ◽  
Docking Studies ◽  
New Drugs ◽  
Drug Candidates ◽  
New Drug ◽  
Computer Aided ◽  
Aided Design

: Computer-aided design of new drugs is an exponentially growing field, especially in the last decade. The support of theoretical tools may accelerate the drug discovery process, which is a long and very expensive journey. Tools as QSAR and docking calculations are on the top of the list for helping medicinal chemists to find more potent and selective molecules as potential leads for facing challenging diseases. Coumarins have been an important source of inspiration for the design of new drugs. Due to their chemical properties and their affinity to some targets, special attention has been paid to their role against neurodegenerative diseases. Therefore, the authors provide an overview of the scientific reports describing the research and development of new drug design tools supporting the discovery of coumarins as enzymatic inhibitors or receptor ligands involved in these diseases. This review emphasizes the rationale behind the design of new drug candidates, and particular attention is paid to the search for new leads over the last 10 years. QSAR and docking studies are discussed, as well as new technologies applied for the research in this field. The manuscripts discussed in this review have been collected from multiple electronic databases, including Pubmed, SciFinder, and Mendeley.

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