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Nascimento IJDS, de Aquino TM, da Silva-Júnior EF. The New Era of Drug Discovery: The Power of Computer-aided Drug
Design (CADD). LETT DRUG DES DISCOV 2022. [DOI: 10.2174/1570180819666220405225817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Abstract:
Drug design and discovery is a process that requires high financial costs and is timeconsuming.
For many years, this process focused on empirical pharmacology. However, over the years,
the target-based approach allowed a significant discovery in this field, initiating the rational design era. In
view, to decrease the time and financial cost, rational drug design is benefited by increasing computer
engineering and software development, and computer-aided drug design (CADD) emerges as a promising
alternative. Since the 1970s, this approach has been able to identify many important and revolutionary
compounds, like protease inhibitors, antibiotics, and others. Many anticancer compounds identified
through this approach have shown their importance, being CADD essential in any drug discovery campaign.
Thus, this perspective will present the prominent successful cases utilizing this approach and entering
into the next stage of drug design. We believe that drug discovery will follow the progress in bioinformatics,
using high-performance computing with molecular dynamics protocols faster and more effectively.
In addition, artificial intelligence and machine learning will be the next process in the rational design
of new drugs. Here, we hope that this paper generates new ideas and instigates research groups
worldwide to use these methods and stimulate progress in drug design.
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Affiliation(s)
| | | | - Edeildo Ferreira da Silva-Júnior
- Chemistry and Biotechnology Institute, Federal University of Alagoas, Maceió, Brazil
- Laboratory of Medicinal
Chemistry, Pharmaceutical Sciences Institute, Federal University of Alagoas, Maceió, Brazil
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An Improved Method for P2X7R Antagonist Screening. PLoS One 2015; 10:e0123089. [PMID: 25993132 PMCID: PMC4437783 DOI: 10.1371/journal.pone.0123089] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Accepted: 02/27/2015] [Indexed: 11/19/2022] Open
Abstract
ATP physiologically activates the P2X7 receptor (P2X7R), a member of the P2X ionotropic receptor family. When activated by high concentrations of ATP (i.e., at inflammation sites), this receptor is capable of forming a pore that allows molecules of up to 900 Da to pass through. This receptor is upregulated in several diseases, particularly leukemia, rheumatoid arthritis and Alzheimer's disease. A selective antagonist of this receptor could be useful in the treatment of P2X7R activation-related diseases. In the present study, we have evaluated several parameters using in vitro protocols to validate a high-throughput screening (HTS) method to identify P2X7R antagonists. We generated dose-response curves to determine the EC50 value of the known agonist ATP and the ICs50 values for the known antagonists Brilliant Blue G (BBG) and oxidized ATP (OATP). The values obtained were consistent with those found in the literature (0.7 ± 0.07 mM, 1.3-2.6 mM and 173-285 μM for ATP, BBG and OATP, respectively). The Z-factor, an important statistical tool that can be used to validate the robustness and suitability of an HTS assay, was 0.635 for PI uptake and 0.867 for LY uptake. No inter-operator variation was observed, and the results obtained using our improved method were reproducible. Our data indicate that our assay is suitable for the selective and reliable evaluation of P2X7 activity in multiwell plates using spectrophotometry-based methodology. This method might improve the high-throughput screening of conventional chemical or natural product libraries for possible candidate P2X7R antagonist or agonist
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Miura K, Satoh M, Kinouchi M, Yamamoto K, Hasegawa Y, Kakugawa Y, Kawai M, Uchimi K, Aizawa H, Ohnuma S, Kajiwara T, Sakurai H, Fujiya T. The use of natural products in colorectal cancer drug discovery. Expert Opin Drug Discov 2015; 10:411-26. [DOI: 10.1517/17460441.2015.1018174] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Koh Miura
- 1Miyagi Cancer Center, Department of Surgery, 47-1 Nodayama, Natori 981-1293, Japan ;
| | - Masayuki Satoh
- 2Miyagi Cancer Center, Department of Surgery, 47-1 Nodayama, Natori 981-1293, Japan
| | - Makoto Kinouchi
- 2Miyagi Cancer Center, Department of Surgery, 47-1 Nodayama, Natori 981-1293, Japan
| | - Kuniharu Yamamoto
- 2Miyagi Cancer Center, Department of Surgery, 47-1 Nodayama, Natori 981-1293, Japan
| | - Yasuhiro Hasegawa
- 2Miyagi Cancer Center, Department of Surgery, 47-1 Nodayama, Natori 981-1293, Japan
| | - Yoichiro Kakugawa
- 2Miyagi Cancer Center, Department of Surgery, 47-1 Nodayama, Natori 981-1293, Japan
| | - Masaaki Kawai
- 2Miyagi Cancer Center, Department of Surgery, 47-1 Nodayama, Natori 981-1293, Japan
| | - Kiyoshi Uchimi
- 3Miyagi Cancer Center, Department of Gastroenterology, 47-1 Nodayama, Natori 981-1293, Japan
| | - Hiroki Aizawa
- 3Miyagi Cancer Center, Department of Gastroenterology, 47-1 Nodayama, Natori 981-1293, Japan
| | - Shinobu Ohnuma
- 4Tohoku University Graduate School of Medicine, Department of Surgery, 1-1 Seiryo-machi, Sendai 980-8574, Japan
| | - Taiki Kajiwara
- 4Tohoku University Graduate School of Medicine, Department of Surgery, 1-1 Seiryo-machi, Sendai 980-8574, Japan
| | - Hiroto Sakurai
- 2Miyagi Cancer Center, Department of Surgery, 47-1 Nodayama, Natori 981-1293, Japan
| | - Tsuneaki Fujiya
- 2Miyagi Cancer Center, Department of Surgery, 47-1 Nodayama, Natori 981-1293, Japan
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Aminooxy analog of histamine is an efficient inhibitor of mammalian l-histidine decarboxylase: combined in silico and experimental evidence. Amino Acids 2013; 46:621-31. [DOI: 10.1007/s00726-013-1589-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Accepted: 08/27/2013] [Indexed: 12/20/2022]
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Okada O, Yamashita H, Takedomi K, Ono S, Sunada S, Kubodera H. Prediction of the binding affinity of compounds with diverse scaffolds by MP-CAFEE. Biophys Chem 2013; 180-181:119-26. [PMID: 23938954 DOI: 10.1016/j.bpc.2013.07.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Revised: 07/02/2013] [Accepted: 07/15/2013] [Indexed: 11/16/2022]
Abstract
Accurate methods to predict the binding affinities of compounds for target molecules are powerful tools in structure-based drug design (SBDD). A recently developed method called massively parallel computation of absolute binding free energy with a well-equilibrated system (MP-CAFEE) successfully predicted the binding affinities of compounds with relatively similar scaffolds. We investigate the applicability of MP-CAFEE for predicting the affinity of compounds having more diverse scaffolds for the target p38α, a mitogen-activated protein kinase. The calculated and experimental binding affinities correlate well, showing that MP-CAFEE can accurately rank the compounds with diverse scaffolds. We propose a method to determine the optimal number of sampling runs with respect to a predefined level of accuracy, which is established according to the stage in the SBDD process being considered. The optimal number of sampling runs for two key stages-lead identification and lead optimization-is estimated to be five and eight or more, respectively, in our model system using Cochrans sample size formula.
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Affiliation(s)
- Okimasa Okada
- Medicinal Chemistry Research Laboratories II, Mitsubishi Tanabe Pharma Corporation, Toda, Saitama 335-8505, Japan.
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Jacobson KA, Costanzi S. New insights for drug design from the X-ray crystallographic structures of G-protein-coupled receptors. Mol Pharmacol 2012; 82:361-71. [PMID: 22695719 DOI: 10.1124/mol.112.079335] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Methodological advances in X-ray crystallography have made possible the recent solution of X-ray structures of pharmaceutically important G protein-coupled receptors (GPCRs), including receptors for biogenic amines, peptides, a nucleoside, and a sphingolipid. These high-resolution structures have greatly increased our understanding of ligand recognition and receptor activation. Conformational changes associated with activation common to several receptors entail outward movements of the intracellular side of transmembrane helix 6 (TM6) and movements of TM5 toward TM6. Movements associated with specific agonists or receptors have also been described [e.g., extracellular loop (EL) 3 in the A(2A) adenosine receptor]. The binding sites of different receptors partly overlap but differ significantly in ligand orientation, depth, and breadth of contact areas in TM regions and the involvement of the ELs. A current challenge is how to use this structural information for the rational design of novel potent and selective ligands. For example, new chemotypes were discovered as antagonists of various GPCRs by subjecting chemical libraries to in silico docking in the X-ray structures. The vast majority of GPCR structures and their ligand complexes are still unsolved, and no structures are known outside of family A GPCRs. Molecular modeling, informed by supporting information from site-directed mutagenesis and structure-activity relationships, has been validated as a useful tool to extend structural insights to related GPCRs and to analyze docking of other ligands in already crystallized GPCRs.
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Affiliation(s)
- Kenneth A Jacobson
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0810, USA.
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Taboureau O, Baell JB, Fernández-Recio J, Villoutreix BO. Established and emerging trends in computational drug discovery in the structural genomics era. ACTA ACUST UNITED AC 2012; 19:29-41. [PMID: 22284352 DOI: 10.1016/j.chembiol.2011.12.007] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2011] [Revised: 12/05/2011] [Accepted: 12/08/2011] [Indexed: 12/01/2022]
Abstract
Bioinformatics and chemoinformatics approaches contribute to hit discovery, hit-to-lead optimization, safety profiling, and target identification and enhance our overall understanding of the health and disease states. A vast repertoire of computational methods has been reported and increasingly combined in order to address more and more challenging targets or complex molecular mechanisms in the context of large-scale integration of structure and bioactivity data produced by private and public drug research. This review explores some key computational methods directly linked to drug discovery and chemical biology with a special emphasis on compound collection preparation, virtual screening, protein docking, and systems pharmacology. A list of generally freely available software packages and online resources is provided, and examples of successful applications are briefly commented upon.
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Affiliation(s)
- Olivier Taboureau
- Center for Biological Sequences Analysis, Department of Systems Biology, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
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