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Yang L, Guo Q, Zhang L. AI-assisted chemistry research: a comprehensive analysis of evolutionary paths and hotspots through knowledge graphs. Chem Commun (Camb) 2024; 60:6977-6987. [PMID: 38910536 DOI: 10.1039/d4cc01892c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/25/2024]
Abstract
Artificial intelligence (AI) offers transformative potential for chemical research through its ability to optimize reactions and processes, enhance energy efficiency, and reduce waste. AI-assisted chemical research (AI + chem) has become a global hotspot. To better understand the current research status of "AI + chem", this study conducted a scientific bibliometric investigation using CiteSpace. The web of science core collection was utilized to retrieve original articles related to "AI + chem" published from 2000 to 2024. The obtained data allowed for the visualization of the knowledge background, current research status, and latest knowledge structure of "AI + chem". The "AI + chem" has entered a stage of explosive growth, and the number of papers will maintain long-term high-speed growth. This article systematically analyzes the latest progress in "AI + chem" and objectively predicts future trends, including molecular design, reaction prediction, materials design, drug design, and quantum chemistry. The outcomes of this study will provide readers with a comprehensive understanding of the overall landscape of "AI + chem".
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Affiliation(s)
- Lin Yang
- School of Intellectual Property, Dalian University of Technology, Dalian 116024, Liaoning, P. R. China
| | - Qingle Guo
- School of Intellectual Property, Dalian University of Technology, Dalian 116024, Liaoning, P. R. China
| | - Lijing Zhang
- School of Chemistry, Dalian University of Technology, Dalian 116024, Liaoning, P. R. China.
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2
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Kellogg GE, Cen Y, Dukat M, Ellis KC, Guo Y, Li J, May AE, Safo MK, Zhang S, Zhang Y, Desai UR. Merging cultures and disciplines to create a drug discovery ecosystem at Virginia commonwealth university: Medicinal chemistry, structural biology, molecular and behavioral pharmacology and computational chemistry. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2023; 28:255-269. [PMID: 36863508 PMCID: PMC10619687 DOI: 10.1016/j.slasd.2023.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 02/10/2023] [Accepted: 02/21/2023] [Indexed: 03/04/2023]
Abstract
The Department of Medicinal Chemistry, together with the Institute for Structural Biology, Drug Discovery and Development, at Virginia Commonwealth University (VCU) has evolved, organically with quite a bit of bootstrapping, into a unique drug discovery ecosystem in response to the environment and culture of the university and the wider research enterprise. Each faculty member that joined the department and/or institute added a layer of expertise, technology and most importantly, innovation, that fertilized numerous collaborations within the University and with outside partners. Despite moderate institutional support with respect to a typical drug discovery enterprise, the VCU drug discovery ecosystem has built and maintained an impressive array of facilities and instrumentation for drug synthesis, drug characterization, biomolecular structural analysis and biophysical analysis, and pharmacological studies. Altogether, this ecosystem has had major impacts on numerous therapeutic areas, such as neurology, psychiatry, drugs of abuse, cancer, sickle cell disease, coagulopathy, inflammation, aging disorders and others. Novel tools and strategies for drug discovery, design and development have been developed at VCU in the last five decades; e.g., fundamental rational structure-activity relationship (SAR)-based drug design, structure-based drug design, orthosteric and allosteric drug design, design of multi-functional agents towards polypharmacy outcomes, principles on designing glycosaminoglycans as drugs, and computational tools and algorithms for quantitative SAR (QSAR) and understanding the roles of water and the hydrophobic effect.
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Affiliation(s)
- Glen E Kellogg
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia, 23298-0540, USA.
| | - Yana Cen
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia, 23298-0540, USA
| | - Malgorzata Dukat
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia, 23298-0540, USA
| | - Keith C Ellis
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia, 23298-0540, USA
| | - Youzhong Guo
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia, 23298-0540, USA
| | - Jiong Li
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia, 23298-0540, USA
| | - Aaron E May
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia, 23298-0540, USA
| | - Martin K Safo
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia, 23298-0540, USA
| | - Shijun Zhang
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia, 23298-0540, USA
| | - Yan Zhang
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia, 23298-0540, USA
| | - Umesh R Desai
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia, 23298-0540, USA.
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3
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A Review on Artificial Intelligence Enabled Design, Synthesis, and Process Optimization of Chemical Products for Industry 4.0. Processes (Basel) 2023. [DOI: 10.3390/pr11020330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
With the development of Industry 4.0, artificial intelligence (AI) is gaining increasing attention for its performance in solving particularly complex problems in industrial chemistry and chemical engineering. Therefore, this review provides an overview of the application of AI techniques, in particular machine learning, in chemical design, synthesis, and process optimization over the past years. In this review, the focus is on the application of AI for structure-function relationship analysis, synthetic route planning, and automated synthesis. Finally, we discuss the challenges and future of AI in making chemical products.
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4
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Hawash M, Jaradat N, Abualhasan M, Qaoud MT, Joudeh Y, Jaber Z, Sawalmeh M, Zarour A, Mousa A, Arar M. Molecular docking studies and biological evaluation of isoxazole-carboxamide derivatives as COX inhibitors and antimicrobial agents. 3 Biotech 2022; 12:342. [PMID: 36345437 PMCID: PMC9636359 DOI: 10.1007/s13205-022-03408-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 10/23/2022] [Indexed: 11/06/2022] Open
Abstract
Non-steroidal anti-inflammatory drugs (NSAIDs) are considered one of the most commonly used medications globally. Seventeen isoxazole-containing compounds with various functional groups were evaluated in this work to identify which one was the most potent and which group was most selective toward COX-1 and COX-2 by using an in vitro COX inhibition assay kit. Their cytotoxicity was evaluated on the normal hepatic cell line (LX-2) utilizing the MTS assay. Moreover, these molecules' antibacterial and antifungal activities were evaluated using a microdilution assay against several bacterial and fungal species. In addition, molecular docking studies were conducted to identify the possible binding interactions between these compounds and their biological targets by using the X-ray crystal structure of the human COX enzyme and different proteins of bacterial and fungal strains. At the same time, the QiKProp module was used for ADME-T analysis. The results showed that all evaluated isoxazole derivatives showed moderate to potent activities against COX enzymes. The most potent compound against COX-1 and COX-2 enzymes was A13, with IC50 values of 64 and 13 nM, respectively, and a significant selectivity ratio of 4.63. It was clear that the 3,4-dimethoxy substitution on the first phenyl ring and the Cl atom on the other phenyl pushed the 5-methyl-isoxazole ring toward the secondary binding pocket and created the ideal binding interactions with the COX-2 enzyme in comparison with the other compounds. Compound A8 showed antibacterial and antifungal activities against Pseudomonas aeruginosa, Klebsiella pneumonia, and Candida albicans with MIC values of 2 mg/ml. In fact, this compound showed possible binding interactions with the elastase in P. aeruginosa and KPC-2 carbapenemase in K. pneumonia. Furthermore, for better understanding, molecular dynamics simulations were undertaken to study the change in dynamicity of the protein backbone and ligand after the ligand binds to the protein and to ensure the stability of ligand-protein complexes. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-022-03408-8.
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Affiliation(s)
- Mohammed Hawash
- Department of Pharmacy, Faculty of Medicine and Health Sciences, An-Najah National University, Nablus, Palestine
| | - Nidal Jaradat
- Department of Pharmacy, Faculty of Medicine and Health Sciences, An-Najah National University, Nablus, Palestine
| | - Murad Abualhasan
- Department of Pharmacy, Faculty of Medicine and Health Sciences, An-Najah National University, Nablus, Palestine
| | - Mohammed T. Qaoud
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Gazi University, 06330 Etiler, Ankara, Turkey
| | - Yara Joudeh
- Department of Pharmacy, Faculty of Medicine and Health Sciences, An-Najah National University, Nablus, Palestine
| | - Zeina Jaber
- Department of Pharmacy, Faculty of Medicine and Health Sciences, An-Najah National University, Nablus, Palestine
| | - Majd Sawalmeh
- Department of Pharmacy, Faculty of Medicine and Health Sciences, An-Najah National University, Nablus, Palestine
| | - Abdulraziq Zarour
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, An-Najah National University, 00970 Nablus, Palestine
| | - Ahmed Mousa
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, An-Najah National University, 00970 Nablus, Palestine
| | - Mohammed Arar
- Department of Pharmacy, Faculty of Medicine and Health Sciences, An-Najah National University, Nablus, Palestine
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5
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Woodward DJ, Bradley AR, van Hoorn WP. Coverage Score: A Model Agnostic Method to Efficiently Explore Chemical Space. J Chem Inf Model 2022; 62:4391-4402. [PMID: 35867814 DOI: 10.1021/acs.jcim.2c00258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Selecting the most appropriate compounds to synthesize and test is a vital aspect of drug discovery. Methods like clustering and diversity present weaknesses in selecting the optimal sets for information gain. Active learning techniques often rely on an initial model and computationally expensive semi-supervised batch selection. Herein, we describe a new subset-based selection method, Coverage Score, that combines Bayesian statistics and information entropy to balance representation and diversity to select a maximally informative subset. Coverage Score can be influenced by prior selections and desirable properties. In this paper, subsets selected through Coverage Score are compared against subsets selected through model-independent and model-dependent techniques for several datasets. In drug-like chemical space, Coverage Score consistently selects subsets that lead to more accurate predictions compared to other selection methods. Subsets selected through Coverage Score produced Random Forest models that have a root-mean-square-error up to 12.8% lower than subsets selected at random and can retain up to 99% of the structural dissimilarity of a diversity selection.
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Affiliation(s)
- Daniel J Woodward
- Exscientia plc, The Schrödinger Building, Oxford Science Park, Oxford OX4 4GE, U.K
| | - Anthony R Bradley
- Exscientia plc, The Schrödinger Building, Oxford Science Park, Oxford OX4 4GE, U.K
| | - Willem P van Hoorn
- Exscientia plc, The Schrödinger Building, Oxford Science Park, Oxford OX4 4GE, U.K
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Zięba A, Stępnicki P, Matosiuk D, Kaczor AA. What are the challenges with multi-targeted drug design for complex diseases? Expert Opin Drug Discov 2022; 17:673-683. [PMID: 35549603 DOI: 10.1080/17460441.2022.2072827] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
INTRODUCTION Current findings on multifactorial diseases with a complex pathomechanism confirm that multi-target drugs are more efficient ways in treating them as opposed to single-target drugs. However, to design multi-target ligands, a number of factors and challenges must be taken into account. AREAS COVERED In this perspective, we summarize the concept of application of multi-target drugs for the treatment of complex diseases such as neurodegenerative diseases, schizophrenia, diabetes, and cancer. We discuss the aspects of target selection for multifunctional ligands and the application of in silico methods in their design and optimization. Furthermore, we highlight other challenges such as balancing affinities to different targets and drug-likeness of obtained compounds. Finally, we present success stories in the design of multi-target ligands for the treatment of common complex diseases. EXPERT OPINION Despite numerous challenges resulting from the design of multi-target ligands, these efforts are worth making. Appropriate target selection, activity balancing, and ligand drug-likeness belong to key aspects in the design of ligands acting on multiple targets. It should be emphasized that in silico methods, in particular inverse docking, pharmacophore modeling, machine learning methods and approaches derived from network pharmacology are valuable tools for the design of multi-target drugs.
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Affiliation(s)
- Agata Zięba
- Department of Synthesis and Chemical Technology of Pharmaceutical Substances with Computer Modeling Laboratory, Faculty of Pharmacy, Medical University of Lublin, Lublin, Poland
| | - Piotr Stępnicki
- Department of Synthesis and Chemical Technology of Pharmaceutical Substances with Computer Modeling Laboratory, Faculty of Pharmacy, Medical University of Lublin, Lublin, Poland
| | - Dariusz Matosiuk
- Department of Synthesis and Chemical Technology of Pharmaceutical Substances with Computer Modeling Laboratory, Faculty of Pharmacy, Medical University of Lublin, Lublin, Poland
| | - Agnieszka A Kaczor
- Department of Synthesis and Chemical Technology of Pharmaceutical Substances with Computer Modeling Laboratory, Faculty of Pharmacy, Medical University of Lublin, Lublin, Poland.,School of Pharmacy, University of Eastern Finland, Kuopio, Finland
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7
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A Consensus Compound/Bioactivity Dataset for Data-Driven Drug Design and Chemogenomics. Molecules 2022; 27:molecules27082513. [PMID: 35458710 PMCID: PMC9028877 DOI: 10.3390/molecules27082513] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 03/31/2022] [Accepted: 04/10/2022] [Indexed: 02/01/2023] Open
Abstract
Publicly available compound and bioactivity databases provide an essential basis for data-driven applications in life-science research and drug design. By analyzing several bioactivity repositories, we discovered differences in compound and target coverage advocating the combined use of data from multiple sources. Using data from ChEMBL, PubChem, IUPHAR/BPS, BindingDB, and Probes & Drugs, we assembled a consensus dataset focusing on small molecules with bioactivity on human macromolecular targets. This allowed an improved coverage of compound space and targets, and an automated comparison and curation of structural and bioactivity data to reveal potentially erroneous entries and increase confidence. The consensus dataset comprised of more than 1.1 million compounds with over 10.9 million bioactivity data points with annotations on assay type and bioactivity confidence, providing a useful ensemble for computational applications in drug design and chemogenomics.
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8
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Thomas M, Boardman A, Garcia-Ortegon M, Yang H, de Graaf C, Bender A. Applications of Artificial Intelligence in Drug Design: Opportunities and Challenges. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2021; 2390:1-59. [PMID: 34731463 DOI: 10.1007/978-1-0716-1787-8_1] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Artificial intelligence (AI) has undergone rapid development in recent years and has been successfully applied to real-world problems such as drug design. In this chapter, we review recent applications of AI to problems in drug design including virtual screening, computer-aided synthesis planning, and de novo molecule generation, with a focus on the limitations of the application of AI therein and opportunities for improvement. Furthermore, we discuss the broader challenges imposed by AI in translating theoretical practice to real-world drug design; including quantifying prediction uncertainty and explaining model behavior.
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Affiliation(s)
- Morgan Thomas
- Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Andrew Boardman
- Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Miguel Garcia-Ortegon
- Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Cambridge, UK.,Department of Pure Mathematics and Mathematical Statistics, University of Cambridge, Cambridge, UK
| | - Hongbin Yang
- Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Cambridge, UK
| | | | - Andreas Bender
- Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Cambridge, UK.
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9
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Haywood AL, Redshaw J, Hanson-Heine MWD, Taylor A, Brown A, Mason AM, Gärtner T, Hirst JD. Kernel Methods for Predicting Yields of Chemical Reactions. J Chem Inf Model 2021; 62:2077-2092. [PMID: 34699222 DOI: 10.1021/acs.jcim.1c00699] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The use of machine learning methods for the prediction of reaction yield is an emerging area. We demonstrate the applicability of support vector regression (SVR) for predicting reaction yields, using combinatorial data. Molecular descriptors used in regression tasks related to chemical reactivity have often been based on time-consuming, computationally demanding quantum chemical calculations, usually density functional theory. Structure-based descriptors (molecular fingerprints and molecular graphs) are quicker and easier to calculate and are applicable to any molecule. In this study, SVR models built on structure-based descriptors were compared to models built on quantum chemical descriptors. The models were evaluated along the dimension of each reaction component in a set of Buchwald-Hartwig amination reactions. The structure-based SVR models outperformed the quantum chemical SVR models, along the dimension of each reaction component. The applicability of the models was assessed with respect to similarity to training. Prospective predictions of unseen Buchwald-Hartwig reactions are presented for synthetic assessment, to validate the generalizability of the models, with particular interest along the aryl halide dimension.
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Affiliation(s)
- Alexe L Haywood
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, U.K
| | - Joseph Redshaw
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, U.K
| | | | - Adam Taylor
- GlaxoSmithKline, Gunnels Wood Road, Stevenage SG1 2NY, U.K
| | - Alex Brown
- GlaxoSmithKline, Gunnels Wood Road, Stevenage SG1 2NY, U.K
| | - Andrew M Mason
- GlaxoSmithKline, Gunnels Wood Road, Stevenage SG1 2NY, U.K
| | - Thomas Gärtner
- Machine Learning Research Unit, TU Wien Informatics, Vienna 1040, Austria
| | - Jonathan D Hirst
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, U.K
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10
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Kim T, You BH, Han S, Shin HC, Chung KC, Park H. Quantum Artificial Neural Network Approach to Derive a Highly Predictive 3D-QSAR Model for Blood-Brain Barrier Passage. Int J Mol Sci 2021; 22:ijms222010995. [PMID: 34681653 PMCID: PMC8537149 DOI: 10.3390/ijms222010995] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 10/07/2021] [Accepted: 10/10/2021] [Indexed: 01/07/2023] Open
Abstract
A successful passage of the blood–brain barrier (BBB) is an essential prerequisite for the drug molecules designed to act on the central nervous system. The logarithm of blood–brain partitioning (LogBB) has served as an effective index of molecular BBB permeability. Using the three-dimensional (3D) distribution of the molecular electrostatic potential (ESP) as the numerical descriptor, a quantitative structure-activity relationship (QSAR) model termed AlphaQ was derived to predict the molecular LogBB values. To obtain the optimal atomic coordinates of the molecules under investigation, the pairwise 3D structural alignments were conducted in such a way to maximize the quantum mechanical cross correlation between the template and a target molecule. This alignment method has the advantage over the conventional atom-by-atom matching protocol in that the structurally diverse molecules can be analyzed as rigorously as the chemical derivatives with the same scaffold. The inaccuracy problem in the 3D structural alignment was alleviated in a large part by categorizing the molecules into the eight subsets according to the molecular weight. By applying the artificial neural network algorithm to associate the fully quantum mechanical ESP descriptors with the extensive experimental LogBB data, a highly predictive 3D-QSAR model was derived for each molecular subset with a squared correlation coefficient larger than 0.8. Due to the simplicity in model building and the high predictability, AlphaQ is anticipated to serve as an effective computational screening tool for molecular BBB permeability.
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Affiliation(s)
- Taeho Kim
- Department of Bioscience and Biotechnology, Sejong University, Kwangjin-gu, Seoul 05006, Korea;
| | - Byoung Hoon You
- Whan In Pharmaceutical Co., Ltd., 11, Songpa-gu, Seoul 05855, Korea; (B.H.Y.); (S.H.); (H.C.S.)
| | - Songhee Han
- Whan In Pharmaceutical Co., Ltd., 11, Songpa-gu, Seoul 05855, Korea; (B.H.Y.); (S.H.); (H.C.S.)
| | - Ho Chul Shin
- Whan In Pharmaceutical Co., Ltd., 11, Songpa-gu, Seoul 05855, Korea; (B.H.Y.); (S.H.); (H.C.S.)
| | - Kee-Choo Chung
- Department of Bioscience and Biotechnology, Sejong University, Kwangjin-gu, Seoul 05006, Korea;
- Correspondence: (K.-C.C.); (H.P.); Tel.: +82-2-2963-1635 (K.-C.C.); +82-2-3408-3766 (H.P.); Fax: +82-2-3408-4334 (K.-C.C. & H.P.)
| | - Hwangseo Park
- Department of Bioscience and Biotechnology, Sejong University, Kwangjin-gu, Seoul 05006, Korea;
- Correspondence: (K.-C.C.); (H.P.); Tel.: +82-2-2963-1635 (K.-C.C.); +82-2-3408-3766 (H.P.); Fax: +82-2-3408-4334 (K.-C.C. & H.P.)
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11
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Fu L, Yang ZY, Yang ZJ, Yin MZ, Lu AP, Chen X, Liu S, Hou TJ, Cao DS. QSAR-assisted-MMPA to expand chemical transformation space for lead optimization. Brief Bioinform 2021; 22:6071857. [PMID: 33418563 DOI: 10.1093/bib/bbaa374] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 10/25/2020] [Accepted: 11/25/2020] [Indexed: 11/13/2022] Open
Abstract
Matched molecular pairs analysis (MMPA) has become a powerful tool for automatically and systematically identifying medicinal chemistry transformations from compound/property datasets. However, accurate determination of matched molecular pair (MMP) transformations largely depend on the size and quality of existing experimental data. Lack of high-quality experimental data heavily hampers the extraction of more effective medicinal chemistry knowledge. Here, we developed a new strategy called quantitative structure-activity relationship (QSAR)-assisted-MMPA to expand the number of chemical transformations and took the logD7.4 property endpoint as an example to demonstrate the reliability of the new method. A reliable logD7.4 consensus prediction model was firstly established, and its applicability domain was strictly assessed. By applying the reliable logD7.4 prediction model to screen two chemical databases, we obtained more high-quality logD7.4 data by defining a strict applicability domain threshold. Then, MMPA was performed on the predicted data and experimental data to derive more chemical rules. To validate the reliability of the chemical rules, we compared the magnitude and directionality of the property changes of the predicted rules with those of the measured rules. Then, we compared the novel chemical rules generated by our proposed approach with the published chemical rules, and found that the magnitude and directionality of the property changes were consistent, indicating that the proposed QSAR-assisted-MMPA approach has the potential to enrich the collection of rule types or even identify completely novel rules. Finally, we found that the number of the MMP rules derived from the experimental data could be amplified by the predicted data, which is helpful for us to analyze the medicinal chemical rules in local chemical environment. In summary, the proposed QSAR-assisted-MMPA approach could be regarded as a very promising strategy to expand the chemical transformation space for lead optimization, especially when no enough experimental data can support MMPA.
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Affiliation(s)
- Li Fu
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha 410008, Hunan, P. R. China.,Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, Hunan, P. R. China
| | - Zi-Yi Yang
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, Hunan, P. R. China
| | - Zhi-Jiang Yang
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, Hunan, P. R. China
| | - Ming-Zhu Yin
- Department of Dermatology, Hunan Engineering Research Center of Skin Health and Disease, Hunan Key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital, Central South University, Changsha 410008, Hunan, P. R. China
| | - Ai-Ping Lu
- Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR 999077, P. R China
| | - Xiang Chen
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, P. R. China
| | - Shao Liu
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha 410008, Hunan, P. R. China
| | - Ting-Jun Hou
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, P. R. China
| | - Dong-Sheng Cao
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha 410008, Hunan, P. R. China.,Department of Dermatology, Hunan Engineering Research Center of Skin Health and Disease, Hunan Key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital, Central South University, Changsha 410008, Hunan, P. R. China.,Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR 999077, P. R China
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12
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Hatley RJD, Procopiou PA, McLachlan SP, Westendorf LE, Meanwell NA, Ewing WR, Macdonald SJF. Writing Your Next Medicinal Chemistry Article: Journal Bibliometrics and Guiding Principles for Industrial Authors. J Med Chem 2020; 63:14336-14356. [PMID: 33103431 DOI: 10.1021/acs.jmedchem.0c01159] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Writing scientific articles is immensely rewarding but challenging. This Perspective provides the medicinal chemist with background and advice on the art and process of writing manuscripts and complements the instructions to authors provided by journals. Included are many tips that we wish we had known when we first started writing. Bibliometric data from seven medicinal chemistry journals between 2000 and 2019 are collated including Bioorganic and Medicinal Chemistry Letters and the Journal of Medicinal Chemistry. Although the overall number of articles has doubled, the output from 23 large pharma companies in the past decade has dropped significantly. Commentary is given on the entire process of writing original scientific articles, opinion articles, and reviews. Examples from our own papers and experience are shared including what typically motivates the writer, challenges commonly encountered, and how we find time to write. Finally, the benefits derived from much wider publishing of industrial medicinal chemistry are described.
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Affiliation(s)
- Richard J D Hatley
- RGDscience Ltd, 2nd Floor, 2 Walsworth Road, Hitchin, Herts SG4 9SP, U.K
| | - Panayiotis A Procopiou
- School of Cancer and Pharmaceutical Science, Faculty of Life Sciences & Medicine, King's College London, 150 Stamford Street, London SE1 9NH, U.K
| | - Steven P McLachlan
- Data & Computational Science, GlaxoSmithKline Medicines Research Centre, Gunnels Wood Road, Stevenage SG1 2NY, U.K
| | - Laura E Westendorf
- Enterprise Information Management, Bristol Myers Squibb, 1 Squibb Drive, New Brunswick, New Jersey 08903, United States
| | - Nicholas A Meanwell
- Discovery Chemistry Platforms, Small Molecule Drug Discovery, Bristol Myers Squibb Research and Early Development, Princeton, New Jersey 08543-4000, United States
| | - William R Ewing
- Discovery Chemistry Platforms, Small Molecule Drug Discovery, Bristol Myers Squibb Research and Early Development, Princeton, New Jersey 08543-4000, United States
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13
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Zhao L, Ciallella HL, Aleksunes LM, Zhu H. Advancing computer-aided drug discovery (CADD) by big data and data-driven machine learning modeling. Drug Discov Today 2020; 25:1624-1638. [PMID: 32663517 PMCID: PMC7572559 DOI: 10.1016/j.drudis.2020.07.005] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 06/26/2020] [Accepted: 07/06/2020] [Indexed: 02/06/2023]
Abstract
Advancing a new drug to market requires substantial investments in time as well as financial resources. Crucial bioactivities for drug candidates, including their efficacy, pharmacokinetics (PK), and adverse effects, need to be investigated during drug development. With advancements in chemical synthesis and biological screening technologies over the past decade, a large amount of biological data points for millions of small molecules have been generated and are stored in various databases. These accumulated data, combined with new machine learning (ML) approaches, such as deep learning, have shown great potential to provide insights into relevant chemical structures to predict in vitro, in vivo, and clinical outcomes, thereby advancing drug discovery and development in the big data era.
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Affiliation(s)
- Linlin Zhao
- The Rutgers Center for Computational and Integrative Biology, Camden, NJ 08102, USA
| | - Heather L Ciallella
- The Rutgers Center for Computational and Integrative Biology, Camden, NJ 08102, USA
| | - Lauren M Aleksunes
- Department of Pharmacology and Toxicology, Ernest Mario School of Pharmacy, Rutgers University, Piscataway, NJ 08854, USA
| | - Hao Zhu
- The Rutgers Center for Computational and Integrative Biology, Camden, NJ 08102, USA; Department of Chemistry, Rutgers University, Camden, NJ 08102, USA.
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14
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Bordignon S, Cerreia Vioglio P, Amadio E, Rossi F, Priola E, Voinovich D, Gobetto R, Chierotti MR. Molecular Crystal Forms of Antitubercular Ethionamide with Dicarboxylic Acids: Solid-State Properties and a Combined Structural and Spectroscopic Study. Pharmaceutics 2020; 12:E818. [PMID: 32872201 PMCID: PMC7559828 DOI: 10.3390/pharmaceutics12090818] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 08/24/2020] [Accepted: 08/26/2020] [Indexed: 11/29/2022] Open
Abstract
We report on the preparation, characterization, and bioavailability properties of three new crystal forms of ethionamide, an antitubercular agent used in the treatment of drug-resistant tuberculosis. The new adducts were obtained by combining the active pharmaceutical ingredient with three dicarboxylic acids, namely glutaric, malonic and tartaric acid, in equimolar ratios. Crystal structures were obtained for all three adducts and were compared with two previously reported multicomponent systems of ethionamide with maleic and fumaric acid. The ethionamide-glutaric acid and the ethionamide-malonic acid adducts were thoroughly characterized by means of solid-state NMR (13C and 15N Cross-Polarization Magic Angle Spinning or CPMAS) to confirm the position of the carboxylic proton, and they were found to be a cocrystal and a salt, respectively; they were compared with two previously reported multicomponent systems of ethionamide with maleic and fumaric acid. Ethionamide-tartaric acid was found to be a rare example of kryptoracemic cocrystal. In vitro bioavailability enhancements up to a factor 3 compared to pure ethionamide were assessed for all obtained adducts.
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Affiliation(s)
- Simone Bordignon
- Department of Chemistry and NIS Centre, University of Torino, V. Giuria 7, 10125 Torino, Italy; (S.B.); (P.C.V.); (E.A.); (F.R.); (E.P.)
| | - Paolo Cerreia Vioglio
- Department of Chemistry and NIS Centre, University of Torino, V. Giuria 7, 10125 Torino, Italy; (S.B.); (P.C.V.); (E.A.); (F.R.); (E.P.)
| | - Elena Amadio
- Department of Chemistry and NIS Centre, University of Torino, V. Giuria 7, 10125 Torino, Italy; (S.B.); (P.C.V.); (E.A.); (F.R.); (E.P.)
| | - Federica Rossi
- Department of Chemistry and NIS Centre, University of Torino, V. Giuria 7, 10125 Torino, Italy; (S.B.); (P.C.V.); (E.A.); (F.R.); (E.P.)
| | - Emanuele Priola
- Department of Chemistry and NIS Centre, University of Torino, V. Giuria 7, 10125 Torino, Italy; (S.B.); (P.C.V.); (E.A.); (F.R.); (E.P.)
| | - Dario Voinovich
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, P.le Europa 1/via L. Giorgieri 1, 34127 Trieste, Italy;
| | - Roberto Gobetto
- Department of Chemistry and NIS Centre, University of Torino, V. Giuria 7, 10125 Torino, Italy; (S.B.); (P.C.V.); (E.A.); (F.R.); (E.P.)
| | - Michele R. Chierotti
- Department of Chemistry and NIS Centre, University of Torino, V. Giuria 7, 10125 Torino, Italy; (S.B.); (P.C.V.); (E.A.); (F.R.); (E.P.)
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15
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Mansbach RA, Leus IV, Mehla J, Lopez CA, Walker JK, Rybenkov VV, Hengartner NW, Zgurskaya HI, Gnanakaran S. Machine Learning Algorithm Identifies an Antibiotic Vocabulary for Permeating Gram-Negative Bacteria. J Chem Inf Model 2020; 60:2838-2847. [PMID: 32453589 DOI: 10.1021/acs.jcim.0c00352] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Drug discovery faces a crisis. The industry has used up the "obvious" space in which to find novel drugs for biomedical applications, and productivity is declining. One strategy to combat this is rational approaches to expand the search space without relying on chemical intuition, to avoid rediscovery of similar spaces. In this work, we present proof of concept of an approach to rationally identify a "chemical vocabulary" related to a specific drug activity of interest without employing known rules. We focus on the pressing concern of multidrug resistance in Pseudomonas aeruginosa by searching for submolecules that promote compound entry into this bacterium. By synergizing theory, computation, and experiment, we validate our approach, explain the molecular mechanism behind identified fragments promoting compound entry, and select candidate compounds from an external library that display good permeation ability.
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Affiliation(s)
- Rachael A Mansbach
- Department of Theoretical Biology and Biophysics, Los Alamos National Lab, MS-K710, P.O. Box 1663, Los Alamos, New Mexico 87545-0001, United States
| | - Inga V Leus
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, SLSRC, Rm 1000, Norman, Oklahoma 73019-5251, United States
| | - Jitender Mehla
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, SLSRC, Rm 1000, Norman, Oklahoma 73019-5251, United States
| | - Cesar A Lopez
- Department of Theoretical Biology and Biophysics, Los Alamos National Lab, MS-K710, P.O. Box 1663, Los Alamos, New Mexico 87545-0001, United States
| | - John K Walker
- Pharmacology and Physiological Science, School of Medicine, Saint Louis University, Schwitalla Hall, Room M362, St. Louis, Missouri 63104, United States
| | - Valentin V Rybenkov
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, SLSRC, Rm 1000, Norman, Oklahoma 73019-5251, United States
| | - Nicolas W Hengartner
- Department of Theoretical Biology and Biophysics, Los Alamos National Lab, MS-K710, P.O. Box 1663, Los Alamos, New Mexico 87545-0001, United States
| | - Helen I Zgurskaya
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, SLSRC, Rm 1000, Norman, Oklahoma 73019-5251, United States
| | - S Gnanakaran
- Department of Theoretical Biology and Biophysics, Los Alamos National Lab, MS-K710, P.O. Box 1663, Los Alamos, New Mexico 87545-0001, United States
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16
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Feijoo F, Palopoli M, Bernstein J, Siddiqui S, Albright TE. Key indicators of phase transition for clinical trials through machine learning. Drug Discov Today 2020; 25:414-421. [DOI: 10.1016/j.drudis.2019.12.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 12/22/2019] [Accepted: 12/30/2019] [Indexed: 02/08/2023]
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17
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Cova TFGG, Pais AACC. Deep Learning for Deep Chemistry: Optimizing the Prediction of Chemical Patterns. Front Chem 2019; 7:809. [PMID: 32039134 PMCID: PMC6988795 DOI: 10.3389/fchem.2019.00809] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 11/11/2019] [Indexed: 12/14/2022] Open
Abstract
Computational Chemistry is currently a synergistic assembly between ab initio calculations, simulation, machine learning (ML) and optimization strategies for describing, solving and predicting chemical data and related phenomena. These include accelerated literature searches, analysis and prediction of physical and quantum chemical properties, transition states, chemical structures, chemical reactions, and also new catalysts and drug candidates. The generalization of scalability to larger chemical problems, rather than specialization, is now the main principle for transforming chemical tasks in multiple fronts, for which systematic and cost-effective solutions have benefited from ML approaches, including those based on deep learning (e.g. quantum chemistry, molecular screening, synthetic route design, catalysis, drug discovery). The latter class of ML algorithms is capable of combining raw input into layers of intermediate features, enabling bench-to-bytes designs with the potential to transform several chemical domains. In this review, the most exciting developments concerning the use of ML in a range of different chemical scenarios are described. A range of different chemical problems and respective rationalization, that have hitherto been inaccessible due to the lack of suitable analysis tools, is thus detailed, evidencing the breadth of potential applications of these emerging multidimensional approaches. Focus is given to the models, algorithms and methods proposed to facilitate research on compound design and synthesis, materials design, prediction of binding, molecular activity, and soft matter behavior. The information produced by pairing Chemistry and ML, through data-driven analyses, neural network predictions and monitoring of chemical systems, allows (i) prompting the ability to understand the complexity of chemical data, (ii) streamlining and designing experiments, (ii) discovering new molecular targets and materials, and also (iv) planning or rethinking forthcoming chemical challenges. In fact, optimization engulfs all these tasks directly.
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Affiliation(s)
- Tânia F. G. G. Cova
- Coimbra Chemistry Centre, CQC, Department of Chemistry, Faculty of Sciences and Technology, University of Coimbra, Coimbra, Portugal
| | - Alberto A. C. C. Pais
- Coimbra Chemistry Centre, CQC, Department of Chemistry, Faculty of Sciences and Technology, University of Coimbra, Coimbra, Portugal
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18
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Davies IW. The digitization of organic synthesis. Nature 2019; 570:175-181. [DOI: 10.1038/s41586-019-1288-y] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 04/26/2019] [Indexed: 12/22/2022]
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Choi H, Kang H, Chung KC, Park H. Development and application of a comprehensive machine learning program for predicting molecular biochemical and pharmacological properties. Phys Chem Chem Phys 2019; 21:5189-5199. [PMID: 30775759 DOI: 10.1039/c8cp07002d] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
We establish a comprehensive quantitative structure-activity relationship (QSAR) model termed AlphaQ through the machine learning algorithm to associate the fully quantum mechanical molecular descriptors with various biochemical and pharmacological properties. Preliminarily, a novel method for molecular structural alignments was developed in such a way to maximize the quantum mechanical cross correlations among the molecules. Besides the improvement of structural alignments, three-dimensional (3D) distribution of the molecular electrostatic potential was introduced as the unique numerical descriptor for individual molecules. These dual modifications lead to a substantial accuracy enhancement in multifarious 3D-QSAR prediction models of AlphaQ. Most remarkably, AlphaQ has been proven to be applicable to structurally diverse molecules to the extent that it outperforms the conventional QSAR methods in estimating the inhibitory activity against thrombin, the water-cyclohexane distribution coefficient, the permeability across the membrane of the Caco-2 cell, and the metabolic stability in human liver microsomes. Due to the simplicity in model building and the high predictive capability for varying biochemical and pharmacological properties, AlphaQ is anticipated to serve as a valuable screening tool at both early and late stages of drug discovery.
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Affiliation(s)
- Hwanho Choi
- Department of Bioscience and Biotechnology, Sejong University, 209 Neungdong-ro, Kwangjin-gu, Seoul 05006, Korea.
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20
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Advances in Lead Generation. Bioorg Med Chem Lett 2019; 29:517-524. [DOI: 10.1016/j.bmcl.2018.12.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 11/28/2018] [Accepted: 12/01/2018] [Indexed: 11/21/2022]
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21
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Satpathy A, Datta P, Wu Y, Ayan B, Bayram E, Ozbolat IT. Developments with 3D bioprinting for novel drug discovery. Expert Opin Drug Discov 2018; 13:1115-1129. [PMID: 30384781 PMCID: PMC6494715 DOI: 10.1080/17460441.2018.1542427] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 10/26/2018] [Indexed: 02/06/2023]
Abstract
Introduction: Although there have been significant contributions from the pharmaceutical industry to clinical practice, several diseases remain unconquered, with the discovery of new drugs remaining a paramount objective. The actual process of drug discovery involves many steps including pre-clinical and clinical testing, which are highly time- and resource-consuming, driving researchers to improve the process efficiency. The shift of modelling technology from two-dimensions (2D) to three-dimensions (3D) is one of such advancements. 3D Models allow for close mimicry of cellular interactions and tissue microenvironments thereby improving the accuracy of results. The advent of bioprinting for fabrication of tissues has shown potential to improve 3D culture models. Areas covered: The present review provides a comprehensive update on a wide range of bioprinted tissue models and appraise them for their potential use in drug discovery research. Expert opinion: Efficiency, reproducibility, and standardization are some impediments of the bioprinted models. Vascularization of the constructs has to be addressed in the near future. While much progress has already been made with several seminal works, the next milestone will be the commercialization of these models after due regulatory approval.
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Affiliation(s)
- Aishwarya Satpathy
- a Centre for Healthcare Science and Technology , Indian Institute of Engineering Science and Technology Shibpur , Howrah , India
| | - Pallab Datta
- a Centre for Healthcare Science and Technology , Indian Institute of Engineering Science and Technology Shibpur , Howrah , India
| | - Yang Wu
- b Engineering Science and Mechanics Department , Penn State University , University Park , PA , USA
- c The Huck Institutes of the Life Sciences, Penn State University , USA
| | - Bugra Ayan
- b Engineering Science and Mechanics Department , Penn State University , University Park , PA , USA
- c The Huck Institutes of the Life Sciences, Penn State University , USA
| | - Ertugrul Bayram
- d Medical Oncology Department , Agri State Hospital , Agri , Turkey
| | - Ibrahim T Ozbolat
- b Engineering Science and Mechanics Department , Penn State University , University Park , PA , USA
- c The Huck Institutes of the Life Sciences, Penn State University , USA
- e Biomedical Engineering Department , Penn State University , University Park , PA , USA
- f Materials Research Institute, Penn State University , USA
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Spjuth O. Novel applications of Machine Learning in cheminformatics. J Cheminform 2018; 10:46. [PMID: 30191348 PMCID: PMC6127077 DOI: 10.1186/s13321-018-0301-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 08/30/2018] [Indexed: 12/26/2022] Open
Affiliation(s)
- Ola Spjuth
- Department of Pharmaceutical Biosciences, Uppsala University, Box 591, 751 24, Uppsala, Sweden.
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23
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Boström J, Brown DG, Young RJ, Keserü GM. Expanding the medicinal chemistry synthetic toolbox. Nat Rev Drug Discov 2018; 17:709-727. [DOI: 10.1038/nrd.2018.116] [Citation(s) in RCA: 267] [Impact Index Per Article: 44.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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24
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Foundations of data-driven medicinal chemistry. Future Sci OA 2018; 4:FSO320. [PMID: 30271612 PMCID: PMC6153455 DOI: 10.4155/fsoa-2018-0057] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 05/22/2018] [Indexed: 11/17/2022] Open
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