Computer-Based Approaches to Drug Design

1987 ◽  
pp. 73-96 ◽  
Author(s):  
Philip Loftus ◽  
Marvin Waldman ◽  
Robert F. Hout
Keyword(s):  
Drug Design ◽  
Computer Based

Experimental and Computational Approaches to Improve Binding Affinity in Chemical Biology and Drug Discovery

2020 ◽  
Vol 20 (19) ◽  
pp. 1651-1660
Author(s):  
Anuraj Nayarisseri
Keyword(s):  
Drug Discovery ◽  
Drug Design ◽  
Binding Affinity ◽  
Chemical Biology ◽  
De Novo ◽  
Structure Based Drug Design ◽  
Computational Approaches ◽  
Drug Designing ◽  
Traditional Drug ◽  
Computer Based

Drug discovery is one of the most complicated processes and establishment of a single drug may require multidisciplinary attempts to design efficient and commercially viable drugs. The main purpose of drug design is to identify a chemical compound or inhibitor that can bind to an active site of a specific cavity on a target protein. The traditional drug design methods involved various experimental based approaches including random screening of chemicals found in nature or can be synthesized directly in chemical laboratories. Except for the long cycle design and time, high cost is also the major issue of concern. Modernized computer-based algorithm including structure-based drug design has accelerated the drug design and discovery process adequately. Surprisingly from the past decade remarkable progress has been made concerned with all area of drug design and discovery. CADD (Computer Aided Drug Designing) based tools shorten the conventional cycle size and also generate chemically more stable and worthy compounds and hence reduce the drug discovery cost. This special edition of editorial comprises the combination of seven research and review articles set emphasis especially on the computational approaches along with the experimental approaches using a chemical synthesizing for the binding affinity in chemical biology and discovery as a salient used in de-novo drug designing. This set of articles exfoliates the role that systems biology and the evaluation of ligand affinity in drug design and discovery for the future.

Molecular Modeling Techniques Applied to the Design of Multitarget Drugs: Methods and Applications

2021 ◽  
Vol 21 ◽  
Author(s):  
Larissa Henriques Evangelista Castro ◽  
Carlos Mauricio R. Sant'Anna
Keyword(s):  
Drug Design ◽  
Similar Efficacy ◽  
Learning Approaches ◽  
Resistance Development ◽  
Multifactorial Diseases ◽  
Target Drug ◽  
Single Target ◽  
Modeling Techniques ◽  
Computer Based ◽  
New Challenges

: Multifactorial diseases, such as cancer and diabetes present a challenge for the traditional “one-target, one disease” paradigm due to their complex pathogenic mechanisms. Although a combination of drugs can be used, a multitarget drug may be a better choice face of its efficacy, lower adverse effects and lower chance of resistance development. The computer-based design of these multitarget drugs can explore the same techniques used for single-target drug design, but the difficulties associated to the obtention of drugs that are capable of modulating two or more targets with similar efficacy impose new challenges, whose solutions involve the adaptation of known techniques and also to the development of new ones, including machine-learning approaches. In this review, some SBDD and LBDD techniques for the multitarget drug design are discussed, together with some cases where the application of such techniques led to effective multitarget ligands.

scholarly journals Computer-Based Drug Design of Positive Modulators of Store-Operated Calcium Channels to Prevent Synaptic Dysfunction in Alzheimer’s Disease

2021 ◽  
Vol 22 (24) ◽  
pp. 13618
Author(s):  
Lernik Hunanyan ◽  
Viktor Ghamaryan ◽  
Ani Makichyan ◽  
Elena Popugaeva
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Drug Design ◽  
Dendritic Spines ◽  
Structural Features ◽  
Fine Tuning ◽  
3D Structures ◽  
Drug Candidates ◽  
Store Operated Calcium Entry ◽  
Computer Based

Store-operated calcium entry (SOCE) constitutes a fine-tuning mechanism responsible for the replenishment of intracellular stores. Hippocampal SOCE is regulated by store-operated channels (SOC) organized in tripartite complex TRPC6/ORAI2/STIM2. It is suggested that in neurons, SOCE maintains intracellular homeostatic Ca2+ concentration at resting conditions and is needed to support the structure of dendritic spines. Recent evidence suggests that positive modulators of SOC are prospective drug candidates to treat Alzheimer’s disease (AD) at early stages. Although STIM2 and ORAI2 are definitely involved in the regulation of nSOC amplitude and a play major role in AD pathogenesis, growing evidence suggest that it is not easy to target these proteins pharmacologically. Existing positive modulators of TRPC6 are unsuitable for drug development due to either bad pharmacokinetics or side effects. Thus, we concentrate the review on perspectives to develop specific nSOC modulators based on available 3D structures of TRPC6, ORAI2, and STIM2. We shortly describe the structural features of existing models and the methods used to prepare them. We provide commonly used steps applied for drug design based on 3D structures of target proteins that might be used to develop novel AD preventing therapy.

The Importance of Anthraquinone and Its Analogues and Molecular Docking Calculation

2019 ◽  
pp. 177-205 ◽  
Author(s):  
Sefa Celik ◽  
Funda Ozkok ◽  
Sevim Akyuz ◽  
Aysen E. Ozel
Keyword(s):  
Molecular Docking ◽  
Drug Design ◽  
Molecular Conformation ◽  
Biological Activities ◽  
Cell Interaction ◽  
Structure Based Drug Design ◽  
Wide Range ◽  
Tumor Killing ◽  
Computer Based ◽  
Dna Strand

In drug-delivery systems containing nano-drug structures, targeting the tumorous tissue by anthraquinone molecules with high biological activity, and reaching and destroying tumors by their tumor-killing effect reveals remarkable results for the treatment of tumors. The various biological activities of anthraquinones and their derivatives depend on molecular conformation; hence, their intra-cell interaction mechanisms including deoxyribonucleic acid (DNA), ribonucleic acid (RNA), enzymes, and hormones. Computer-based drug design plays an important role in the design of drugs and the determination of goals for them. Molecular docking has been widely used in structure-based drug design. The effects of anthraquinone analogues in tumor cells as a result of their interaction with DNA strand has increased the number of studies done on them, and they have been shown to have a wide range of applications in chemistry, medicine, pharmacy, materials, and especially in the field of biomolecules.

Integrated Teaching of Structure-Based Drug Design and Biopharmaceutics: A Computer-Based Approach

2011 ◽  
Vol 89 (1) ◽  
pp. 45-51 ◽  
Author(s):  
Brian T. Sutch ◽  
Rebecca M. Romero ◽  
Nouri Neamati ◽  
Ian S. Haworth
Keyword(s):  
Drug Design ◽  
Structure Based Drug Design ◽  
Computer Based

Integrating computer-based de novo drug design and multidimensional filtering for desirable drugs

TARGETS ◽  
2002 ◽  
Vol 1 (6) ◽  
pp. 196-205 ◽  
Author(s):  
Jun Shimada ◽  
Sean Ekins ◽  
Carl Elkin ◽  
Eugene I. Shakhnovich ◽  
Jean-Pierre Wery
Keyword(s):  
Drug Design ◽  
De Novo ◽  
De Novo Drug Design ◽  
Multidimensional Filtering ◽  
Computer Based

Cell morphology, volume, and surface area determinations from multilevel contouring within HVEM micrographs of serial sections and whole-cell mounts

1987 ◽  
Vol 45 ◽  
pp. 588-589
Author(s):  
M. Marko ◽  
A. Leith ◽  
D. Parsons
Keyword(s):  
Surface Area ◽  
Electron Micrographs ◽  
Cell Morphology ◽  
Individual Variation ◽  
Serial Section ◽  
Stereo Pair ◽  
Complex Structures ◽  
Serial Sections ◽  
Surface Areas ◽  
Computer Based

The use of serial sections and computer-based 3-D reconstruction techniques affords an opportunity not only to visualize the shape and distribution of the structures being studied, but also to determine their volumes and surface areas. Up until now, this has been done using serial ultrathin sections.The serial-section approach differs from the stereo logical methods of Weibel in that it is based on the Information from a set of single, complete cells (or organelles) rather than on a random 2-dimensional sampling of a population of cells. Because of this, it can more easily provide absolute values of volume and surface area, especially for highly-complex structures. It also allows study of individual variation among the cells, and study of structures which occur only infrequently.We have developed a system for 3-D reconstruction of objects from stereo-pair electron micrographs of thick specimens.

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