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Llorach-Pares L, Nonell-Canals A, Avila C, Sanchez-Martinez M. Computer-Aided Drug Design (CADD) to De-Orphanize Marine Molecules: Finding Potential Therapeutic Agents for Neurodegenerative and Cardiovascular Diseases. Mar Drugs 2022; 20:53. [PMID: 35049908 PMCID: PMC8781171 DOI: 10.3390/md20010053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 12/24/2021] [Accepted: 12/27/2021] [Indexed: 11/30/2022] Open
Abstract
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.
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Affiliation(s)
- Laura Llorach-Pares
- Mind the Byte S.L., 08028 Barcelona, Catalonia, Spain; (L.L.-P.); (A.N.-C.)
- Department of Evolutionary Biology, Ecology and Environmental Sciences, Faculty of Biology and Biodiversity Research Institute (IRBio), University of Barcelona, 08028 Barcelona, Catalonia, Spain;
| | | | - Conxita Avila
- Department of Evolutionary Biology, Ecology and Environmental Sciences, Faculty of Biology and Biodiversity Research Institute (IRBio), University of Barcelona, 08028 Barcelona, Catalonia, Spain;
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102
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Present and future challenges in therapeutic designing using computational approaches. COMPUTATIONAL APPROACHES FOR NOVEL THERAPEUTIC AND DIAGNOSTIC DESIGNING TO MITIGATE SARS-COV-2 INFECTION 2022. [PMCID: PMC9300749 DOI: 10.1016/b978-0-323-91172-6.00020-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Currently, various computational methods are being used for the purpose of therapeutic design. The advent of the Coronavirus disease-2019 (COVID-19) pandemic has created a lot of problems due to which the development of effective treatment options is urgently needed. Computational intelligence is used in the control, prevention, prediction, diagnosis, and treatment of the disease. Several important drug targets have been identified in severe acute respiratory syndrome-Coronavirus-2 using in silico methods. Computer-aided drug design includes a variety of theoretical and computational approaches that are part of modern drug discovery. Advances in machine learning methods and their applications speed up the drug discovery process. Exploration of nucleic acid-based therapeutics is playing an important role in healthcare also. But a lot of challenges have also been seen that complicate the therapeutic design. Therefore, investigation of challenges associated with therapeutic design is important, and the present chapter is aimed to cover various therapeutic design approaches and challenges associated with them. Moreover, the role of computational strategies in the exploration of potential therapeutics against COVID-19 has been investigated.
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103
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Applications of machine learning in computer-aided drug discovery. QRB DISCOVERY 2022. [PMID: 37529294 PMCID: PMC10392679 DOI: 10.1017/qrd.2022.12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Abstract
Machine learning (ML) has revolutionised the field of structure-based drug design (SBDD) in recent years. During the training stage, ML techniques typically analyse large amounts of experimentally determined data to create predictive models in order to inform the drug discovery process. Deep learning (DL) is a subfield of ML, that relies on multiple layers of a neural network to extract significantly more complex patterns from experimental data, and has recently become a popular choice in SBDD. This review provides a thorough summary of the recent DL trends in SBDD with a particular focus on de novo drug design, binding site prediction, and binding affinity prediction of small molecules.
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104
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Ai R, Jin X, Tang B, Yang G, Niu Z, Fang EF. Aging and Alzheimer’s Disease. Artif Intell Med 2022. [DOI: 10.1007/978-3-030-64573-1_74] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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105
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Forrest RM, Greer AL. Machine-learning improves understanding of glass formation in metallic systems. DIGITAL DISCOVERY 2022; 1:476-489. [PMID: 36091413 PMCID: PMC9358760 DOI: 10.1039/d2dd00026a] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 06/13/2022] [Indexed: 11/19/2022]
Abstract
Glass-forming ability (GFA) in metallic systems remains a little-understood property. Experimental work on bulk metallic glasses (BMGs) is guided by many empirical criteria, which are often of limited predictive value. This work uses machine-learning both to produce predictive models for the GFA of alloy compositions, and to reveal insights useful for furthering theoretical understanding of GFA. Our machine-learning models apply a novel neural-network architecture to predict simultaneously the liquidus temperature, glass-transition temperature, crystallization-onset temperature, maximum glassy casting diameter, and probability of glass formation, for any given alloy. Feature permutation is used to identify the features of importance in the black-box neural network, recovering Inoue's empirical rules, and highlighting the effect of discontinuous Wigner–Seitz boundary electron-densities on atomic radii. With certain combinations of elements, atomic radii of different species contract and expand to balance electron-density discontinuities such that the overall difference in atomic radii increases, improving GFA. We calculate adjusted radii via the Thomas–Fermi model and use this insight to propose promising novel glass-forming alloy systems. We train a neural-network model for glass formation in metallic systems, and probe its inner workings to extract theoretical insights.![]()
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Affiliation(s)
- Robert M. Forrest
- Department of Materials Science and Metallurgy, University of Cambridge, UK
| | - A. Lindsay Greer
- Department of Materials Science and Metallurgy, University of Cambridge, UK
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106
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Verma S, Pathak RK. Discovery and optimization of lead molecules in drug designing. Bioinformatics 2022. [DOI: 10.1016/b978-0-323-89775-4.00004-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
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107
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Ajjarapu SM, Tiwari A, Ramteke PW, Singh DB, Kumar S. Ligand-based drug designing. Bioinformatics 2022. [DOI: 10.1016/b978-0-323-89775-4.00018-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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108
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Abstract
The appearance on the free market of synthetic cannabinoids raised the researchers’ interest in establishing their molecular similarity by QSAR analysis. A rigorous criterion for classifying drugs is their chemical structure. Therefore, this article presents the structural similarity of two groups of drugs: benzoylindoles and phenylacetylindoles. Statistical analysis and clustering of the molecules are performed based on their numerical characteristics extracted using Cheminformatics methods. Their similarities/dissimilarities are emphasized using the dendrograms and heat map. The highest discrepancies are found in the phenylacetylindoles group.
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109
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Overcoming Depression with 5-HT2A Receptor Ligands. Int J Mol Sci 2021; 23:ijms23010010. [PMID: 35008436 PMCID: PMC8744644 DOI: 10.3390/ijms23010010] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 12/17/2021] [Accepted: 12/18/2021] [Indexed: 01/25/2023] Open
Abstract
Depression is a multifactorial disorder that affects millions of people worldwide, and none of the currently available therapeutics can completely cure it. Thus, there is a need for developing novel, potent, and safer agents. Recent medicinal chemistry findings on the structure and function of the serotonin 2A (5-HT2A) receptor facilitated design and discovery of novel compounds with antidepressant action. Eligible papers highlighting the importance of 5-HT2A receptors in the pathomechanism of the disorder were identified in the content-screening performed on the popular databases (PubMed, Google Scholar). Articles were critically assessed based on their titles and abstracts. The most accurate papers were chosen to be read and presented in the manuscript. The review summarizes current knowledge on the applicability of 5-HT2A receptor signaling modulators in the treatment of depression. It provides an insight into the structural and physiological features of this receptor. Moreover, it presents an overview of recently conducted virtual screening campaigns aiming to identify novel, potent 5-HT2A receptor ligands and additional data on currently synthesized ligands acting through this protein.
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110
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Leveraging nonstructural data to predict structures and affinities of protein-ligand complexes. Proc Natl Acad Sci U S A 2021; 118:2112621118. [PMID: 34921117 PMCID: PMC8713799 DOI: 10.1073/pnas.2112621118] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/15/2021] [Indexed: 01/02/2023] Open
Abstract
Structure-based drug design depends on the ability to predict both the three-dimensional structures of candidate molecules bound to their targets and the associated binding affinities. We demonstrate that one can substantially improve the accuracy of these predictions using easily obtained data about completely different molecules that bind to the same target without requiring any target-bound structures of these molecules. The approach we developed to integrate physical and data-driven modeling may find a variety of applications in the rapidly growing field of artificial intelligence for drug discovery. Over the past five decades, tremendous effort has been devoted to computational methods for predicting properties of ligands—i.e., molecules that bind macromolecular targets. Such methods, which are critical to rational drug design, fall into two categories: physics-based methods, which directly model ligand interactions with the target given the target’s three-dimensional (3D) structure, and ligand-based methods, which predict ligand properties given experimental measurements for similar ligands. Here, we present a rigorous statistical framework to combine these two sources of information. We develop a method to predict a ligand’s pose—the 3D structure of the ligand bound to its target—that leverages a widely available source of information: a list of other ligands that are known to bind the same target but for which no 3D structure is available. This combination of physics-based and ligand-based modeling improves pose prediction accuracy across all major families of drug targets. Using the same framework, we develop a method for virtual screening of drug candidates, which outperforms standard physics-based and ligand-based virtual screening methods. Our results suggest broad opportunities to improve prediction of various ligand properties by combining diverse sources of information through customized machine-learning approaches.
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111
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Tetteh J, Bai S, Kubelka J, Piri M. Surfactant-induced wettability reversal on oil-wet calcite surfaces: Experimentation and molecular dynamics simulations with scaled-charges. J Colloid Interface Sci 2021; 609:890-900. [PMID: 34848057 DOI: 10.1016/j.jcis.2021.11.080] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 11/03/2021] [Accepted: 11/15/2021] [Indexed: 01/29/2023]
Abstract
HYPOTHESIS Surfactant flooding is the leading approach for reversing the wettability of oil-wet carbonate reservoirs, which is critical for the recovery of the remaining oil. Combination of molecular dynamics (MD) simulations with experiments on simplified model systems can uncover the molecular mechanisms of wettability reversal and identify key molecular properties for systematic design of new, effective chemical formulations for the enhanced oil recovery. EXPERIMENTS/SIMULATIONS Wettability reversal by a series of surfactant solutions was studied experimentally using contact angle measurements on aged calcite chips, and a novel MD simulation methodology with scaled-charges that provides superior description of the ionic interactions in aqueous solutions. FINDINGS The MD simulation results were in excellent agreement with the experiments. Cationic surfactants were the most effective in reversing the calcite wettability, resulting in complete detachment of the oil from the surface. Some nonionic surfactants also altered the wettability, but to a lesser degree, while the amphoteric and anionic surfactants had no effect. From the tested cationic surfactants, the double-tailed one was the least effective, but the experiments were inconclusive due to its poor solubility. Contributions of specific interactions to the wettability reversal process and implications for the design and optimization of surfactants for the enhanced oil recovery are discussed.
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Affiliation(s)
- Julius Tetteh
- Center of Innovation for Flow Through Porous Media, Department of Petroleum Engineering, University of Wyoming, Laramie, WY 82071, United States
| | - Shixun Bai
- Center of Innovation for Flow Through Porous Media, Department of Petroleum Engineering, University of Wyoming, Laramie, WY 82071, United States
| | - Jan Kubelka
- Center of Innovation for Flow Through Porous Media, Department of Petroleum Engineering, University of Wyoming, Laramie, WY 82071, United States.
| | - Mohammad Piri
- Center of Innovation for Flow Through Porous Media, Department of Petroleum Engineering, University of Wyoming, Laramie, WY 82071, United States
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112
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In vitro cytotoxicity assay, mushroom tyrosinase inhibitory activity and release analysis of kojic monooleate nanodelivery system and in silico molecular docking study against 2Y9X target enzyme. J Drug Deliv Sci Technol 2021. [DOI: 10.1016/j.jddst.2021.102764] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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113
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Dembitsky VM. In Silico Prediction of Steroids and Triterpenoids as Potential Regulators of Lipid Metabolism. Mar Drugs 2021; 19:650. [PMID: 34822521 PMCID: PMC8618826 DOI: 10.3390/md19110650] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 11/12/2021] [Accepted: 11/19/2021] [Indexed: 12/12/2022] Open
Abstract
This review focuses on a rare group of steroids and triterpenoids that share common properties as regulators of lipid metabolism. This group of compounds is divided by the type of chemical structure, and they represent: aromatic steroids, steroid phosphate esters, highly oxygenated steroids such as steroid endoperoxides and hydroperoxides, α,β-epoxy steroids, and secosteroids. In addition, subgroups of carbon-bridged steroids, neo steroids, miscellaneous steroids, as well as synthetic steroids containing heteroatoms S (epithio steroids), Se (selena steroids), Te (tellura steroids), and At (astatosteroids) were presented. Natural steroids and triterpenoids have been found and identified from various sources such as marine sponges, soft corals, starfish, and other marine invertebrates. In addition, this group of rare lipids is found in fungi, fungal endophytes, and plants. The pharmacological profile of the presented steroids and triterpenoids was determined using the well-known computer program PASS, which is currently available online for all interested scientists and pharmacologists and is currently used by research teams from more than 130 countries of the world. Our attention has been focused on the biological activities of steroids and triterpenoids associated with the regulation of cholesterol metabolism and related processes such as anti-hyperlipoproteinemic activity, as well as the treatment of atherosclerosis, lipoprotein disorders, or inhibitors of cholesterol synthesis. In addition, individual steroids and triterpenoids were identified that demonstrated rare or unique biological activities such as treating neurodegenerative diseases, Alzheimer's, and Parkinson's diseases with a high degree of certainty over 95 percent. For individual steroids or triterpenoids or a group of compounds, 3D drawings of their predicted biological activities are presented.
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Affiliation(s)
- Valery M Dembitsky
- Centre for Applied Research, Innovation and Entrepreneurship, Lethbridge College, 3000 College Drive South, Lethbridge, AB T1K 1L6, Canada
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114
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Sarma H, Upadhyaya M, Gogoi B, Phukan M, Kashyap P, Das B, Devi R, Sharma HK. Cardiovascular Drugs: an Insight of In Silico Drug Design Tools. J Pharm Innov 2021. [DOI: 10.1007/s12247-021-09587-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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115
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Joshi RP, Kumar N. Artificial Intelligence for Autonomous Molecular Design: A Perspective. Molecules 2021; 26:6761. [PMID: 34833853 PMCID: PMC8619999 DOI: 10.3390/molecules26226761] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 10/23/2021] [Accepted: 10/29/2021] [Indexed: 11/23/2022] Open
Abstract
Domain-aware artificial intelligence has been increasingly adopted in recent years to expedite molecular design in various applications, including drug design and discovery. Recent advances in areas such as physics-informed machine learning and reasoning, software engineering, high-end hardware development, and computing infrastructures are providing opportunities to build scalable and explainable AI molecular discovery systems. This could improve a design hypothesis through feedback analysis, data integration that can provide a basis for the introduction of end-to-end automation for compound discovery and optimization, and enable more intelligent searches of chemical space. Several state-of-the-art ML architectures are predominantly and independently used for predicting the properties of small molecules, their high throughput synthesis, and screening, iteratively identifying and optimizing lead therapeutic candidates. However, such deep learning and ML approaches also raise considerable conceptual, technical, scalability, and end-to-end error quantification challenges, as well as skepticism about the current AI hype to build automated tools. To this end, synergistically and intelligently using these individual components along with robust quantum physics-based molecular representation and data generation tools in a closed-loop holds enormous promise for accelerated therapeutic design to critically analyze the opportunities and challenges for their more widespread application. This article aims to identify the most recent technology and breakthrough achieved by each of the components and discusses how such autonomous AI and ML workflows can be integrated to radically accelerate the protein target or disease model-based probe design that can be iteratively validated experimentally. Taken together, this could significantly reduce the timeline for end-to-end therapeutic discovery and optimization upon the arrival of any novel zoonotic transmission event. Our article serves as a guide for medicinal, computational chemistry and biology, analytical chemistry, and the ML community to practice autonomous molecular design in precision medicine and drug discovery.
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Affiliation(s)
| | - Neeraj Kumar
- Computational Biology Group, Biological Science Division, Pacific Northwest National Laboratory, 902 Battelle Blvd, Richland, WA 99352, USA;
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116
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Tayara H, Abdelbaky I, To Chong K. Recent omics-based computational methods for COVID-19 drug discovery and repurposing. Brief Bioinform 2021; 22:6355836. [PMID: 34423353 DOI: 10.1093/bib/bbab339] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 07/09/2021] [Indexed: 12/22/2022] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is the main reason for the increasing number of deaths worldwide. Although strict quarantine measures were followed in many countries, the disease situation is still intractable. Thus, it is needed to utilize all possible means to confront this pandemic. Therefore, researchers are in a race against the time to produce potential treatments to cure or reduce the increasing infections of COVID-19. Computational methods are widely proving rapid successes in biological related problems, including diagnosis and treatment of diseases. Many efforts in recent months utilized Artificial Intelligence (AI) techniques in the context of fighting the spread of COVID-19. Providing periodic reviews and discussions of recent efforts saves the time of researchers and helps to link their endeavors for a faster and efficient confrontation of the pandemic. In this review, we discuss the recent promising studies that used Omics-based data and utilized AI algorithms and other computational tools to achieve this goal. We review the established datasets and the developed methods that were basically directed to new or repurposed drugs, vaccinations and diagnosis. The tools and methods varied depending on the level of details in the available information such as structures, sequences or metabolic data.
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Affiliation(s)
- Hilal Tayara
- School of international Engineering and Science, Jeonbuk National University, Jeonju 54896, Republic of Korea
| | - Ibrahim Abdelbaky
- Artificial Intelligence Department, Faculty of Computers and Artificial Intelligence, Benha University, Banha 13518, Egypt
| | - Kil To Chong
- Department of Electronics and Information Engineering, Jeonbuk National University, Jeonju, Jeollabukdo 54896, Republic of Korea.,Advances Electronics and Information Research Center, Jeonbuk National University, Jeonju 54896, Republic of Korea
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117
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Abstract
Knowledge of protein structure is crucial to our understanding of biological function and is routinely used in drug discovery. High-resolution techniques to determine the three-dimensional atomic coordinates of proteins are available. However, such methods are frequently limited by experimental challenges such as sample quantity, target size, and efficiency. Structural mass spectrometry (MS) is a technique in which structural features of proteins are elucidated quickly and relatively easily. Computational techniques that convert sparse MS data into protein models that demonstrate agreement with the data are needed. This review features cutting-edge computational methods that predict protein structure from MS data such as chemical cross-linking, hydrogen-deuterium exchange, hydroxyl radical protein footprinting, limited proteolysis, ion mobility, and surface-induced dissociation. Additionally, we address future directions for protein structure prediction with sparse MS data. Expected final online publication date for the Annual Review of Physical Chemistry, Volume 73 is April 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Sarah E Biehn
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, Ohio 43210, USA;
| | - Steffen Lindert
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, Ohio 43210, USA;
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118
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Wei YP, Yao LY, Wu YY, Liu X, Peng LH, Tian YL, Ding JH, Li KH, He QG. Critical Review of Synthesis, Toxicology and Detection of Acyclovir. Molecules 2021; 26:molecules26216566. [PMID: 34770975 PMCID: PMC8587948 DOI: 10.3390/molecules26216566] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 10/25/2021] [Accepted: 10/27/2021] [Indexed: 02/02/2023] Open
Abstract
Acyclovir (ACV) is an effective and selective antiviral drug, and the study of its toxicology and the use of appropriate detection techniques to control its toxicity at safe levels are extremely important for medicine efforts and human health. This review discusses the mechanism driving ACV’s ability to inhibit viral coding, starting from its development and pharmacology. A comprehensive summary of the existing preparation methods and synthetic materials, such as 5-aminoimidazole-4-carboxamide, guanine and its derivatives, and other purine derivatives, is presented to elucidate the preparation of ACV in detail. In addition, it presents valuable analytical procedures for the toxicological studies of ACV, which are essential for human use and dosing. Analytical methods, including spectrophotometry, high performance liquid chromatography (HPLC), liquid chromatography/tandem mass spectrometry (LC-MS/MS), electrochemical sensors, molecularly imprinted polymers (MIPs), and flow injection–chemiluminescence (FI-CL) are also highlighted. A brief description of the characteristics of each of these methods is also presented. Finally, insight is provided for the development of ACV to drive further innovation of ACV in pharmaceutical applications. This review provides a comprehensive summary of the past life and future challenges of ACV.
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Affiliation(s)
- Yan-Ping Wei
- School of Life Science and Chemistry, Hunan University of Technology, Zhuzhou 412007, China; (Y.-P.W.); (Y.-Y.W.); (L.-H.P.); (Y.-L.T.)
- Zhuzhou People’s Hospital, Zhuzhou 412001, China; (X.L.); (J.-H.D.)
- Hunan Qianjin Xiangjiang Pharmaceutical Joint Stock Co., Ltd., Zhuzhou 412001, China;
| | - Liang-Yuan Yao
- Hunan Qianjin Xiangjiang Pharmaceutical Joint Stock Co., Ltd., Zhuzhou 412001, China;
| | - Yi-Yong Wu
- School of Life Science and Chemistry, Hunan University of Technology, Zhuzhou 412007, China; (Y.-P.W.); (Y.-Y.W.); (L.-H.P.); (Y.-L.T.)
| | - Xia Liu
- Zhuzhou People’s Hospital, Zhuzhou 412001, China; (X.L.); (J.-H.D.)
| | - Li-Hong Peng
- School of Life Science and Chemistry, Hunan University of Technology, Zhuzhou 412007, China; (Y.-P.W.); (Y.-Y.W.); (L.-H.P.); (Y.-L.T.)
| | - Ya-Ling Tian
- School of Life Science and Chemistry, Hunan University of Technology, Zhuzhou 412007, China; (Y.-P.W.); (Y.-Y.W.); (L.-H.P.); (Y.-L.T.)
| | - Jian-Hua Ding
- Zhuzhou People’s Hospital, Zhuzhou 412001, China; (X.L.); (J.-H.D.)
| | - Kang-Hua Li
- Zhuzhou People’s Hospital, Zhuzhou 412001, China; (X.L.); (J.-H.D.)
- Correspondence: (K.-H.L.); (Q.-G.H.); Tel./Fax: +86-731-2218-3426 (Q.-G.H.)
| | - Quan-Guo He
- School of Life Science and Chemistry, Hunan University of Technology, Zhuzhou 412007, China; (Y.-P.W.); (Y.-Y.W.); (L.-H.P.); (Y.-L.T.)
- Zhuzhou People’s Hospital, Zhuzhou 412001, China; (X.L.); (J.-H.D.)
- Hunan Qianjin Xiangjiang Pharmaceutical Joint Stock Co., Ltd., Zhuzhou 412001, China;
- Correspondence: (K.-H.L.); (Q.-G.H.); Tel./Fax: +86-731-2218-3426 (Q.-G.H.)
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119
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da Silva TH, Hachigian TZ, Lee J, King MD. Using computers to ESKAPE the antibiotic resistance crisis. Drug Discov Today 2021; 27:456-470. [PMID: 34688913 DOI: 10.1016/j.drudis.2021.10.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Revised: 08/01/2021] [Accepted: 10/15/2021] [Indexed: 12/16/2022]
Abstract
Since the discovery of penicillin, the development and use of antibiotics have promoted safe and effective control of bacterial infections. However, the number of antibiotic-resistance cases has been ever increasing over time. Thus, the drug discovery process demands fast, efficient and cost-effective alternative approaches for developing lead candidates with outstanding performance. Computational approaches are appealing techniques to develop lead candidates in an in silico fashion. In this review, we provide an overview of the implementation of current in silico state-of-the-art techniques, including machine learning (ML) and deep learning (DL), in drug discovery. We also discuss the development of quantum computing and its potential benefits for antibiotics research and current bottlenecks that limit computational drug discovery advancement.
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Affiliation(s)
- Thiago H da Silva
- Micron School of Materials Science and Engineering, Boise State University, Boise, ID 83725, USA
| | - Timothy Z Hachigian
- Micron School of Materials Science and Engineering, Boise State University, Boise, ID 83725, USA
| | - Jeunghoon Lee
- Micron School of Materials Science and Engineering, Boise State University, Boise, ID 83725, USA; Department of Chemistry and Biochemistry, Boise State University, Boise, ID 83725, USA
| | - Matthew D King
- Micron School of Materials Science and Engineering, Boise State University, Boise, ID 83725, USA; Department of Chemistry and Biochemistry, Boise State University, Boise, ID 83725, USA.
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Rizzuti B, Lan W, Santofimia-Castaño P, Zhou Z, Velázquez-Campoy A, Abián O, Peng L, Neira JL, Xia Y, Iovanna JL. Design of Inhibitors of the Intrinsically Disordered Protein NUPR1: Balance between Drug Affinity and Target Function. Biomolecules 2021; 11:biom11101453. [PMID: 34680086 PMCID: PMC8533202 DOI: 10.3390/biom11101453] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 09/16/2021] [Accepted: 09/28/2021] [Indexed: 12/22/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) are emerging as attractive drug targets by virtue of their physiological ubiquity and their prevalence in various diseases, including cancer. NUPR1 is an IDP that localizes throughout the whole cell, and is involved in the development and progression of several tumors. We have previously repurposed trifluoperazine (TFP) as a drug targeting NUPR1 and, by using a ligand-based approach, designed the drug ZZW-115 starting from the TFP scaffold. Such derivative compound hinders the development of pancreatic ductal adenocarcinoma (PDAC) in mice, by hampering nuclear translocation of NUPR1. Aiming to further improve the activity of ZZW-115, here we have used an indirect drug design approach to modify its chemical features, by changing the substituent attached to the piperazine ring. As a result, we have synthesized a series of compounds based on the same chemical scaffold. Isothermal titration calorimetry (ITC) showed that, with the exception of the compound preserving the same chemical moiety at the end of the alkyl chain as ZZW-115, an increase of the length by a single methylene group (i.e., ethyl to propyl) significantly decreased the affinity towards NUPR1 measured in vitro, whereas maintaining the same length of the alkyl chain and adding heterocycles favored the binding affinity. However, small improvements of the compound affinity towards NUPR1, as measured by ITC, did not result in a corresponding improvement in their inhibitory properties and in cellulo functions, as proved by measuring three different biological effects: hindrance of the nuclear translocation of the protein, sensitization of cells against DNA damage mediated by NUPR1, and prevention of cancer cell growth. Our findings suggest that a delicate compromise between favoring ligand affinity and controlling protein function may be required to successfully design drugs against NUPR1, and likely other IDPs.
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Affiliation(s)
- Bruno Rizzuti
- CNR-NANOTEC, SS Rende (CS), Department of Physics, University of Calabria, Via P. Bucci, Cubo 31 C, 87036 Rende, Cosenza, Italy;
- Instituto de Biocomputación y Física de Sistemas Complejos, Joint Units IQFR-CSIC-BIFI, and GBsC-CSIC-BIFI, Universidad de Zaragoza, 50018 Zaragoza, Spain; (A.V.-C.); (O.A.); (J.L.N.)
| | - Wenjun Lan
- Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Institut Paoli-Calmettes, Aix-Marseille Université, 13288 Marseille, France; (W.L.); (P.S.-C.)
- Aix-Marseille Université, CNRS, Centre Interdisciplinaire de Nanoscience de Marseille, UMR 7325, «Equipe Labellisée Ligue Contre le Cancer», 13288 Marseille, France;
| | - Patricia Santofimia-Castaño
- Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Institut Paoli-Calmettes, Aix-Marseille Université, 13288 Marseille, France; (W.L.); (P.S.-C.)
| | - Zhengwei Zhou
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China;
| | - Adrián Velázquez-Campoy
- Instituto de Biocomputación y Física de Sistemas Complejos, Joint Units IQFR-CSIC-BIFI, and GBsC-CSIC-BIFI, Universidad de Zaragoza, 50018 Zaragoza, Spain; (A.V.-C.); (O.A.); (J.L.N.)
- Aragon Institute for Health Research (IIS Aragon), 50009 Zaragoza, Spain
- Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), 28029 Barcelona, Spain
- Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, 50009 Zaragoza, Spain
- Fundacion ARAID, Government of Aragon, 50018 Zaragoza, Spain
| | - Olga Abián
- Instituto de Biocomputación y Física de Sistemas Complejos, Joint Units IQFR-CSIC-BIFI, and GBsC-CSIC-BIFI, Universidad de Zaragoza, 50018 Zaragoza, Spain; (A.V.-C.); (O.A.); (J.L.N.)
- Aragon Institute for Health Research (IIS Aragon), 50009 Zaragoza, Spain
- Instituto Aragonés de Ciencias de la Salud (IACS), 50009 Zaragoza, Spain
| | - Ling Peng
- Aix-Marseille Université, CNRS, Centre Interdisciplinaire de Nanoscience de Marseille, UMR 7325, «Equipe Labellisée Ligue Contre le Cancer», 13288 Marseille, France;
| | - José L. Neira
- Instituto de Biocomputación y Física de Sistemas Complejos, Joint Units IQFR-CSIC-BIFI, and GBsC-CSIC-BIFI, Universidad de Zaragoza, 50018 Zaragoza, Spain; (A.V.-C.); (O.A.); (J.L.N.)
- IDIBE, Universidad Miguel Hernández, 03202 Elche, Alicante, Spain
| | - Yi Xia
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China;
- Correspondence: (Y.X.); (J.L.I.)
| | - Juan L. Iovanna
- Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Institut Paoli-Calmettes, Aix-Marseille Université, 13288 Marseille, France; (W.L.); (P.S.-C.)
- Correspondence: (Y.X.); (J.L.I.)
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Dawn Woodfield J, Bhardwaj A, Bergman C, Wuest F. Synthesis, Binding Affinity Analysis, and 18 F Radiosynthesis of Small-Molecular-Weight HIF-1α-Binding Compounds. ChemMedChem 2021; 17:e202100544. [PMID: 34595843 DOI: 10.1002/cmdc.202100544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 09/25/2021] [Indexed: 11/07/2022]
Abstract
Eleven small-molecular-weight compounds and three cyclic peptides were synthesized and evaluated for binding to hypoxia-inducible factor-1α (HIF-1α). Microscale thermophoresis analysis identified peptide [19 F]SFB-link-c-(Ppg)LLFVY 3 and small-molecule inhibitor 5 as potent HIF-1α binding compounds with KD values of 0.46±0.2 μM and 7.8±3.4 μM, respectively. Both compounds represent novel HIF-1α-targeting compounds that are predicted to interact with the PAS-B region of HIF-1α, as confirmed with molecular docking studies. Lead structures 3 and 5 were further radiolabelled with fluorine-18 for positron emission tomography (PET) imaging agents targeting HIF-1α in vivo.
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Affiliation(s)
- Jenilee Dawn Woodfield
- Department of Oncology, Cross Cancer Institute, University of Alberta, T6G 1Z2, Edmonton, AB, Canada
| | - Atul Bhardwaj
- Department of Oncology, Cross Cancer Institute, University of Alberta, T6G 1Z2, Edmonton, AB, Canada
| | - Cody Bergman
- Department of Oncology, Cross Cancer Institute, University of Alberta, T6G 1Z2, Edmonton, AB, Canada
| | - Frank Wuest
- Department of Oncology, Cross Cancer Institute, University of Alberta, T6G 1Z2, Edmonton, AB, Canada.,Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, T6G 2E1, Edmonton, AB, Canada.,Department of Chemistry, University of Alberta, 11227 Saskatchewan Drive, T6G 2G2, Edmonton, AB, Canada
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Pharmacophore-Based Virtual Screening, Quantum Mechanics Calculations, and Molecular Dynamics Simulation Approaches Identified Potential Natural Antiviral Drug Candidates against MERS-CoV S1-NTD. Molecules 2021; 26:molecules26164961. [PMID: 34443556 PMCID: PMC8401589 DOI: 10.3390/molecules26164961] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 05/06/2021] [Accepted: 05/07/2021] [Indexed: 11/16/2022] Open
Abstract
Middle East respiratory syndrome coronavirus (MERS-CoV) is a highly infectious zoonotic virus first reported into the human population in September 2012 on the Arabian Peninsula. The virus causes severe and often lethal respiratory illness in humans with an unusually high fatality rate. The N-terminal domain (NTD) of receptor-binding S1 subunit of coronavirus spike (S) proteins can recognize a variety of host protein and mediates entry into human host cells. Blocking the entry by targeting the S1-NTD of the virus can facilitate the development of effective antiviral drug candidates against the pathogen. Therefore, the study has been designed to identify effective antiviral drug candidates against the MERS-CoV by targeting S1-NTD. Initially, a structure-based pharmacophore model (SBPM) to the active site (AS) cavity of the S1-NTD has been generated, followed by pharmacophore-based virtual screening of 11,295 natural compounds. Hits generated through the pharmacophore-based virtual screening have re-ranked by molecular docking and further evaluated through the ADMET properties. The compounds with the best ADME and toxicity properties have been retrieved, and a quantum mechanical (QM) based density-functional theory (DFT) has been performed to optimize the geometry of the selected compounds. Three optimized natural compounds, namely Taiwanhomoflavone B (Amb23604132), 2,3-Dihydrohinokiflavone (Amb23604659), and Sophoricoside (Amb1153724), have exhibited substantial docking energy >-9.00 kcal/mol, where analysis of frontier molecular orbital (FMO) theory found the low chemical reactivity correspondence to the bioactivity of the compounds. Molecular dynamics (MD) simulation confirmed the stability of the selected natural compound to the binding site of the protein. Additionally, molecular mechanics generalized born surface area (MM/GBSA) predicted the good value of binding free energies (ΔG bind) of the compounds to the desired protein. Convincingly, all the results support the potentiality of the selected compounds as natural antiviral candidates against the MERS-CoV S1-NTD.
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Hariono M, Wijaya DBE, Chandra T, Frederick N, Putri AB, Herawati E, Warastika LA, Permatasari M, Putri ADA, Ardyantoro S. A Decade of Indonesian Atmosphere in Computer-Aided Drug Design. J Chem Inf Model 2021; 62:5276-5288. [DOI: 10.1021/acs.jcim.1c00607] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Maywan Hariono
- Drug Discovery Student Club, Faculty of Pharmacy, Sanata Dharma University, Campus III, Paingan, Maguwoharjo, Depok, Sleman 55282, Yogyakarta, Indonesia
| | - Dominikus B. E. Wijaya
- Drug Discovery Student Club, Faculty of Pharmacy, Sanata Dharma University, Campus III, Paingan, Maguwoharjo, Depok, Sleman 55282, Yogyakarta, Indonesia
| | - Teddy Chandra
- Drug Discovery Student Club, Faculty of Pharmacy, Sanata Dharma University, Campus III, Paingan, Maguwoharjo, Depok, Sleman 55282, Yogyakarta, Indonesia
| | - Nico Frederick
- Drug Discovery Student Club, Faculty of Pharmacy, Sanata Dharma University, Campus III, Paingan, Maguwoharjo, Depok, Sleman 55282, Yogyakarta, Indonesia
| | - Agnes B. Putri
- Drug Discovery Student Club, Faculty of Pharmacy, Sanata Dharma University, Campus III, Paingan, Maguwoharjo, Depok, Sleman 55282, Yogyakarta, Indonesia
| | - Erlia Herawati
- Drug Discovery Student Club, Faculty of Pharmacy, Sanata Dharma University, Campus III, Paingan, Maguwoharjo, Depok, Sleman 55282, Yogyakarta, Indonesia
| | - Luthfi A. Warastika
- Drug Discovery Student Club, Faculty of Pharmacy, Sanata Dharma University, Campus III, Paingan, Maguwoharjo, Depok, Sleman 55282, Yogyakarta, Indonesia
| | - Merry Permatasari
- Drug Discovery Student Club, Faculty of Pharmacy, Sanata Dharma University, Campus III, Paingan, Maguwoharjo, Depok, Sleman 55282, Yogyakarta, Indonesia
| | - Agata D. A. Putri
- Drug Discovery Student Club, Faculty of Pharmacy, Sanata Dharma University, Campus III, Paingan, Maguwoharjo, Depok, Sleman 55282, Yogyakarta, Indonesia
| | - Satrio Ardyantoro
- Drug Discovery Student Club, Faculty of Pharmacy, Sanata Dharma University, Campus III, Paingan, Maguwoharjo, Depok, Sleman 55282, Yogyakarta, Indonesia
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124
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Liu Y, Liu H, Liu C. Nanosize Hydroxyapatite Significantly Repairs the Bone Damage Caused by Several Genes. INT J PHARMACOL 2021. [DOI: 10.3923/ijp.2021.621.633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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125
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Abstract
This review provides the feasible literature on drug discovery through ML tools and techniques that are enforced in every phase of drug development to accelerate the research process and deduce the risk and expenditure in clinical trials. Machine learning techniques improve the decision-making in pharmaceutical data across various applications like QSAR analysis, hit discoveries, de novo drug architectures to retrieve accurate outcomes. Target validation, prognostic biomarkers, digital pathology are considered under problem statements in this review. ML challenges must be applicable for the main cause of inadequacy in interpretability outcomes that may restrict the applications in drug discovery. In clinical trials, absolute and methodological data must be generated to tackle many puzzles in validating ML techniques, improving decision-making, promoting awareness in ML approaches, and deducing risk failures in drug discovery.
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Affiliation(s)
- Suresh Dara
- Department of Computer Science and Engineering, B V Raju Institute of Technology, Narsapur, Medak, 502313 Telangana India
| | - Swetha Dhamercherla
- Department of Computer Science and Engineering, B V Raju Institute of Technology, Narsapur, Medak, 502313 Telangana India
| | - Surender Singh Jadav
- Centre for Molecular Cancer Research (CMCR) and Vishnu Institute of Pharmaceutical Education and Research (VIPER), Narsapur, Medak, 502313 Telangana India
| | - CH Madhu Babu
- Department of Computer Science and Engineering, B V Raju Institute of Technology, Narsapur, Medak, 502313 Telangana India
| | - Mohamed Jawed Ahsan
- Department of Pharmaceutical Chemistry, Maharishi Arvind College of Pharmacy, Jaipur, 302023 Rajasthan India
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126
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Lan L, Sun Y, Jin X, Xie L, Liu L, Cheng L. A Light‐Controllable Chemical Modulation of m
6
A RNA Methylation. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202103854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Ling Lan
- Beijing National Laboratory for Molecular Sciences (BNLMS) CAS Key Laboratory of Molecular Recognition and Function CAS Research/Education Center for Excellence in Molecular Sciences Institute of Chemistry Chinese Academy of Sciences Beijing 100190 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Ying‐Jie Sun
- Beijing National Laboratory for Molecular Sciences (BNLMS) CAS Key Laboratory of Molecular Recognition and Function CAS Research/Education Center for Excellence in Molecular Sciences Institute of Chemistry Chinese Academy of Sciences Beijing 100190 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Xiao‐Yang Jin
- Beijing National Laboratory for Molecular Sciences (BNLMS) CAS Key Laboratory of Molecular Recognition and Function CAS Research/Education Center for Excellence in Molecular Sciences Institute of Chemistry Chinese Academy of Sciences Beijing 100190 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Li‐Jun Xie
- Beijing National Laboratory for Molecular Sciences (BNLMS) CAS Key Laboratory of Molecular Recognition and Function CAS Research/Education Center for Excellence in Molecular Sciences Institute of Chemistry Chinese Academy of Sciences Beijing 100190 China
| | - Li Liu
- Beijing National Laboratory for Molecular Sciences (BNLMS) CAS Key Laboratory of Molecular Recognition and Function CAS Research/Education Center for Excellence in Molecular Sciences Institute of Chemistry Chinese Academy of Sciences Beijing 100190 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Liang Cheng
- Beijing National Laboratory for Molecular Sciences (BNLMS) CAS Key Laboratory of Molecular Recognition and Function CAS Research/Education Center for Excellence in Molecular Sciences Institute of Chemistry Chinese Academy of Sciences Beijing 100190 China
- Hangzhou Institute for Advanced Study University of Chinese Academy of Sciences Hangzhou 310024 China
- University of Chinese Academy of Sciences Beijing 100049 China
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127
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Liu Y, Cong L, Han C, Li B, Dai R. Recent Progress in the Drug Development for the Treatment of Alzheimer's Disease Especially on Inhibition of Amyloid-peptide Aggregation. Mini Rev Med Chem 2021; 21:969-990. [PMID: 33245270 DOI: 10.2174/1389557520666201127104539] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 08/25/2020] [Accepted: 09/14/2020] [Indexed: 11/22/2022]
Abstract
As the world 's population is aging, Alzheimer's disease (AD) has become a big concern since AD has started affecting younger people and the population of AD patients is increasing worldwide. It has been revealed that the neuropathological hallmarks of AD are typically characterized by the presence of neurotoxic extracellular amyloid plaques in the brain, which are surrounded by tangles of neuronal fibers. However, the causes of AD have not been completely understood yet. Currently, there is no drug to effectively prevent AD or to completely reserve the symptoms in the patients. This article reviews the pathological features associated with AD, the recent progress in research on the drug development to treat AD, especially on the discovery of natural product derivatives to inhibit Aβ peptide aggregation as well as the design and synthesis of Aβ peptide aggregation inhibitors to treat AD.
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Affiliation(s)
- Yuanyuan Liu
- Advanced Research Institute of Multidisciplinary Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Lin Cong
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, School of Life Science, Beijing Institute of Technology, Beijing, 10081, China
| | - Chu Han
- Advanced Research Institute of Multidisciplinary Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Bo Li
- Advanced Research Institute of Multidisciplinary Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Rongji Dai
- Beijing Key Laboratory for Separation and Analysis in Biomedicine and Pharmaceuticals, School of Life Science, Beijing Institute of Technology, Beijing, 10081, China
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128
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Bisht N, Sah AN, Bisht S, Joshi H. Emerging Need of Today: Significant Utilization of Various Databases and Softwares in Drug Design and Development. Mini Rev Med Chem 2021; 21:1025-1032. [PMID: 33319657 DOI: 10.2174/1389557520666201214101329] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 10/05/2020] [Accepted: 10/09/2020] [Indexed: 11/22/2022]
Abstract
In drug discovery, in silico methods have become a very important part of the process. These approaches impact the entire development process by discovering and identifying new target proteins as well as designing potential ligands with a significant reduction of time and cost. Furthermore, in silico approaches are also preferred because of reduction in the experimental use of animals as; in vivo testing for safer drug design and repositioning of known drugs. Novel software-based discovery and development such as direct/indirect drug design, molecular modelling, docking, screening, drug-receptor interaction, and molecular simulation studies are very important tools for the predictions of ligand-target interaction pattern, pharmacodynamics as well as pharmacokinetic properties of ligands. On the other part, the computational approaches can be numerous, requiring interdisciplinary studies and the application of advanced computer technology to design effective and commercially feasible drugs. This review mainly focuses on the various databases and software used in drug design and development to speed up the process.
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Affiliation(s)
- Neema Bisht
- Assistant Professor, College of Pharmacy, Graphic Era Hill University, Bhimtal Campus, Sattal Road, Bhimtal, Uttarakhand 263136, India
| | - Archana N Sah
- Head and Dean, Department of Pharmaceutical Sciences, Faculty of Technology, Sir J.C. Bose Technical Campus, Bhimtal, Kumaun University Nainital, Uttarakhand 263136, India
| | - Sandeep Bisht
- Assistant Professor, School of Management, Graphic Era Hill University, Bhimtal Campus, Sattal Road, Bhimtal, Uttarakhand 263136, India
| | - Himanshu Joshi
- Professor, College of Pharmacy, Graphic Era Hill University, Bhimtal Campus, Sattal Road, Bhimtal, Uttarakhand 263136, India
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129
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The Psychonauts' Benzodiazepines; Quantitative Structure-Activity Relationship (QSAR) Analysis and Docking Prediction of Their Biological Activity. Pharmaceuticals (Basel) 2021; 14:ph14080720. [PMID: 34451817 PMCID: PMC8398354 DOI: 10.3390/ph14080720] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 07/19/2021] [Accepted: 07/20/2021] [Indexed: 12/28/2022] Open
Abstract
Designer benzodiazepines (DBZDs) represent a serious health concern and are increasingly reported in polydrug consumption-related fatalities. When new DBZDs are identified, very limited information is available on their pharmacodynamics. Here, computational models (i.e., quantitative structure-activity relationship/QSAR and Molecular Docking) were used to analyse DBZDs identified online by an automated web crawler (NPSfinder®) and to predict their possible activity/affinity on the gamma-aminobutyric acid A receptors (GABA-ARs). The computational software MOE was used to calculate 2D QSAR models, perform docking studies on crystallised GABA-A receptors (6HUO, 6HUP) and generate pharmacophore queries from the docking conformational results. 101 DBZDs were identified online by NPSfinder®. The validated QSAR model predicted high biological activity values for 41% of these DBDZs. These predictions were supported by the docking studies (good binding affinity) and the pharmacophore modelling confirmed the importance of the presence and location of hydrophobic and polar functions identified by QSAR. This study confirms once again the importance of web-based analysis in the assessment of drug scenarios (DBZDs), and how computational models could be used to acquire fast and reliable information on biological activity for index novel DBZDs, as preliminary data for further investigations.
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130
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Jalalvand A, Khatouni SB, Najafi ZB, Fatahinia F, Ismailzadeh N, Farahmand B. Computational drug repurposing study of antiviral drugs against main protease, RNA polymerase, and spike proteins of SARS-CoV-2 using molecular docking method. J Basic Clin Physiol Pharmacol 2021; 33:85-95. [PMID: 34265888 DOI: 10.1515/jbcpp-2020-0369] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 05/16/2021] [Indexed: 12/23/2022]
Abstract
OBJECTIVES The new Coronavirus (SARS-CoV-2) created a pandemic in the world in late 2019 and early 2020. Unfortunately, despite the increasing prevalence of the disease, there is no effective drug for the treatment. A computational drug repurposing study would be an appropriate and rapid way to provide an effective drug in the treatment of the coronavirus disease of 2019 (COVID-19) pandemic. In this study, the inhibitory potential of more than 50 antiviral drugs on three important proteins of SARS-CoV-2, was investigated using the molecular docking method. METHODS By literature review, three important proteins, including main protease, RNA-dependent RNA polymerase (RdRp), and spike, were selected as the drug targets. The three-dimensional (3D) structure of protease, spike, and RdRp proteins was obtained from the Protein Data Bank. Proteins were energy minimized. More than 50 antiviral drugs were considered as candidates for protein inhibition, and their 3D structure was obtained from Drug Bank. Molecular docking settings were defined using Autodock 4.2 software and the algorithm was executed. RESULTS Based on the estimated binding energy of docking and hydrogen bond analysis and the position of drug binding, five drugs including, indinavir, lopinavir, saquinavir, nelfinavir, and remdesivir, had the highest inhibitory potential for all three proteins. CONCLUSIONS According to the results, among the mentioned drugs, saquinavir and lopinavir showed the highest inhibitory potential for all three proteins compared to the other drugs. This study suggests that saquinavir and lopinavir could be included in the laboratory phase studies as a two-drug treatment for SARS-CoV-2 inhibition.
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Affiliation(s)
- Alireza Jalalvand
- Department of Influenza and Other Respiratory Viruses, Pasteur Institute of Iran, Tehran, Iran
| | - Somayeh Behjat Khatouni
- Department of Influenza and Other Respiratory Viruses, Pasteur Institute of Iran, Tehran, Iran.,Department of Plant Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Zahra Bahri Najafi
- Department of Influenza and Other Respiratory Viruses, Pasteur Institute of Iran, Tehran, Iran.,Division of Genetics, Department of Cell and Molecular Biology, Faculty of Science and Technology, University of Isfahan, Isfahan, Iran
| | - Foroozan Fatahinia
- Department of Influenza and Other Respiratory Viruses, Pasteur Institute of Iran, Tehran, Iran.,Department of Biology, Faculty of Science, University of Mohaghegh Ardabili, Ardabil, Iran
| | - Narges Ismailzadeh
- Department of Influenza and Other Respiratory Viruses, Pasteur Institute of Iran, Tehran, Iran.,Department of Chemistry, Faculty of Science, University of Tarbiat Modarres, Tehran, Iran
| | - Behrokh Farahmand
- Department of Influenza and Other Respiratory Viruses, Pasteur Institute of Iran, Tehran, Iran
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131
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Sabe VT, Ntombela T, Jhamba LA, Maguire GEM, Govender T, Naicker T, Kruger HG. Current trends in computer aided drug design and a highlight of drugs discovered via computational techniques: A review. Eur J Med Chem 2021; 224:113705. [PMID: 34303871 DOI: 10.1016/j.ejmech.2021.113705] [Citation(s) in RCA: 165] [Impact Index Per Article: 55.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 07/12/2021] [Accepted: 07/12/2021] [Indexed: 12/30/2022]
Abstract
Computer-aided drug design (CADD) is one of the pivotal approaches to contemporary pre-clinical drug discovery, and various computational techniques and software programs are typically used in combination, in a bid to achieve the desired outcome. Several approved drugs have been developed with the aid of CADD. On SciFinder®, we evaluated more than 600 publications through systematic searching and refining, using the terms, virtual screening; software methods; computational studies and publication year, in order to obtain data concerning particular aspects of CADD. The primary focus of this review was on the databases screened, virtual screening and/or molecular docking software program used. Furthermore, we evaluated the studies that subsequently performed molecular dynamics (MD) simulations and we reviewed the software programs applied, the application of density functional theory (DFT) calculations and experimental assays. To represent the latest trends, the most recent data obtained was between 2015 and 2020, consequently the most frequently employed techniques and software programs were recorded. Among these, the ZINC database was the most widely preferred with an average use of 31.2%. Structure-based virtual screening (SBVS) was the most prominently used type of virtual screening and it accounted for an average of 57.6%, with AutoDock being the preferred virtual screening/molecular docking program with 41.8% usage. Following the screening process, 38.5% of the studies performed MD simulations to complement the virtual screening and GROMACS with 39.3% usage, was the popular MD software program. Among the computational techniques, DFT was the least applied whereby it only accounts for 0.02% average use. An average of 36.5% of the studies included reports on experimental evaluations following virtual screening. Ultimately, since the inception and application of CADD in pre-clinical drug discovery, more than 70 approved drugs have been discovered, and this number is steadily increasing over time.
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Affiliation(s)
- Victor T Sabe
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, 4001, South Africa.
| | - Thandokuhle Ntombela
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, 4001, South Africa.
| | - Lindiwe A Jhamba
- HIV Pathogenesis Program, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, 4001, South Africa
| | - Glenn E M Maguire
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, 4001, South Africa; School of Chemistry and Physics, University of KwaZulu-Natal, Durban, 4001, South Africa
| | - Thavendran Govender
- Faculty of Science and Agriculture, Department of Chemistry, University of Zululand, KwaDlangezwa, 3886, South Africa
| | - Tricia Naicker
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, 4001, South Africa
| | - Hendrik G Kruger
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, 4001, South Africa.
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Lan L, Sun YJ, Jin XY, Xie LJ, Liu L, Cheng L. A Light-Controllable Chemical Modulation of m 6 A RNA Methylation. Angew Chem Int Ed Engl 2021; 60:18116-18121. [PMID: 34107156 DOI: 10.1002/anie.202103854] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 05/27/2021] [Indexed: 12/21/2022]
Abstract
Bioactive small molecules with photo-removable protecting groups have provided spatial and temporal control of corresponding biological effects. We present the design, synthesis, computational and experimental evaluation of the first photo-activatable small-molecule methyltransferase agonist. By blocking the functional N-H group on MPCH with a photo-removable ortho-nitrobenzyl moiety, we have developed a promising photo-caged compound that had completely concealed its biological activity. Short UV light exposure of cells treated with that caged molecule in a few minutes resulted in a considerable hypermethylation of m6 A modification in transcriptome RNAs, implicating a rapid release of the parent active compound. This study validates for the first time the photo-activatable small organic molecular concept in the field of RNA epigenetic research, which represents a novel tool in spatiotemporal and cellular modulation approaches.
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Affiliation(s)
- Ling Lan
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Molecular Recognition and Function, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ying-Jie Sun
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Molecular Recognition and Function, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiao-Yang Jin
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Molecular Recognition and Function, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Li-Jun Xie
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Molecular Recognition and Function, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
| | - Li Liu
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Molecular Recognition and Function, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Liang Cheng
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Molecular Recognition and Function, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China.,Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
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133
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Norouzi-Barough L, Bayat A. Validation strategies for identifying drug targets in dermal fibrotic disorders. Drug Discov Today 2021; 26:2474-2485. [PMID: 34229083 DOI: 10.1016/j.drudis.2021.06.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 05/19/2021] [Accepted: 06/29/2021] [Indexed: 11/16/2022]
Abstract
Fibrotic skin disorders, such as keloid disease (KD), are common clinically challenging disorders with unknown etiopathogenesis and ill-defined treatment strategies that affect millions of people worldwide. Thus, there is an urgent need to discover novel therapeutics. The validation of potential drug targets is an obligatory step in discovering and developing new therapeutic agents for the successful treatment of dermal fibrotic conditions, such as KD. The integration of multi-omics data with traditional and modern technological approaches, such as RNA interference (RNAi) and genome-editing tools, would provide unique opportunities to identify and validate novel targets in KD during early drug development. Thus, in this review, we summarize the current and emerging drug discovery process with a focus on validation strategies of potential drug targets identified in dermal fibrosis.
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Affiliation(s)
- Leyla Norouzi-Barough
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Ardeshir Bayat
- Centre for Dermatology Research, NIHR Manchester Biomedical Research Centre, Stopford Building, University of Manchester, Oxford Road, Manchester M13 9PT, UK; Medical Research Council-Wound Healing Unit, Division of Dermatology, University of Cape Town, Cape Town, South Africa.
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134
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Sharma S, Bhatia V. Nanoscale Drug Delivery Systems for Glaucoma: Experimental and In Silico Advances. Curr Top Med Chem 2021; 21:115-125. [PMID: 32962618 DOI: 10.2174/1568026620666200922114210] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 07/21/2020] [Accepted: 07/23/2020] [Indexed: 12/25/2022]
Abstract
In this review, nanoscale-based drug delivery systems, particularly in relevance to the antiglaucoma drugs, have been discussed. In addition to that, the latest computational/in silico advances in this field are examined in brief. Using nanoscale materials for drug delivery is an ideal option to target tumours, and the drug can be released in areas of the body where traditional drugs may fail to act. Nanoparticles, polymeric nanomaterials, single-wall carbon nanotubes (SWCNTs), quantum dots (QDs), liposomes and graphene are the most important nanomaterials used for drug delivery. Ocular drug delivery is one of the most common and difficult tasks faced by pharmaceutical scientists because of many challenges like circumventing the blood-retinal barrier, corneal epithelium and the blood-aqueous barrier. Authors found compelling empirical evidence of scientists relying on in-silico approaches to develop novel drugs and drug delivery systems for treating glaucoma. This review in nanoscale drug delivery systems will help us understand the existing queries and evidence gaps and will pave the way for the effective design of novel ocular drug delivery systems.
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Affiliation(s)
- Smriti Sharma
- Department of Chemistry, Miranda House, University of Delhi, Delhi, India
| | - Vinayak Bhatia
- ICARE Eye Hospital and Postgraduate Institute, Noida, UP, India
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135
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Roy H, Nayak BS, Nandi S. In Silico Factorial Screening and Optimization of Chitosan Based Gel for Urapidil Loaded Microparticle using Reduced Factorial Design. Comb Chem High Throughput Screen 2021; 23:1049-1063. [PMID: 32598248 DOI: 10.2174/1386207323666200628110552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Revised: 03/02/2020] [Accepted: 04/21/2020] [Indexed: 11/22/2022]
Abstract
OBJECTIVE Literature study revealed the poor mechanical strength of chitosan-based microparticles. Our research aimed at developing sufficient strength of microparticle with a suitable concentration of chitosan and non-ionic surfactants such as poloxamer-188 (pluronic). It also aimed to develop and study the effect of variables for prepared microparticles utilizing insilico screening methodology, such as reduced factorial design, followed by optimization. METHODS Preliminary trial batches were prepared with variable concentration of chitosan and poloxamer-188 utilizing cross-linked ion-gelation technique. A 20% w/v sodium citrate solution was used as a cross-linking solution. The resolution-IV of 24-1 reduced factorial design was selected to screen the possible and significant independent variables or factors in the dosage form design. A total number of eight runs were suggested by statistical software and responses were recorded. The responses such as spreadability, pH, viscosity and percentage of drug released at 12 h were considered in the screening study. Based on the result, selected factors were included in the optimization technique, including graphical and numerical methods. RESULTS The signified factors based on reduced two-level factorial screening design with randomized subtype, were identified by Half-normal and Pareto chart. Mathematical fitting and analysis were performed by the factorial equation during the optimization process. The validation and fitting of models were suggested and evaluated by p-value, adjusted R2, and predicted R2 values. The significant and non-significant terms were evaluated, followed by finding the optimal concentration and region with yellow color highlighted in an overlay plot. Based on the data obtained by the overlay study, the final formulation batch was prepared and the observed value was found to be pretty much nearer as compared to predicted values. Drug-polymer interaction study included attenuated total reflectance, differential scanning calorimetry, and X-Ray diffraction study. CONCLUSION The principal of the study design was based on finding the prefixed set parameter values utilizing the concept of in-silico screening technique and optimization with a minimal number of trials and study expenses. It concluded that Poloxamer-188 (0.94%), chitosan (2.38%), swelling time (1.81 h), and parts of chitosan (78.51%) in a formulation batch would fulfill the predetermined parameter with specific values.
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Affiliation(s)
- Harekrishna Roy
- Institute of Pharmacy and Technology, Salipur, Cuttack 754202, Odisha, India
| | - Bhabani S Nayak
- Institute of Pharmacy and Technology, Salipur, Cuttack 754202, Odisha, India
| | - Sisir Nandi
- Department of Pharmaceutical Chemistry, Global Institute of Pharmaceutical Education and Research, Affiliated to Uttarakhand Technical University, Kashipur 244713, India
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MUHAMMED MT, AKI-YALCIN E. Pharmacophore Modeling in Drug Discovery: Methodology and Current Status. JOURNAL OF THE TURKISH CHEMICAL SOCIETY, SECTION A: CHEMISTRY 2021. [DOI: 10.18596/jotcsa.927426] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
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137
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Nichols PL. Automated and enabling technologies for medicinal chemistry. PROGRESS IN MEDICINAL CHEMISTRY 2021; 60:191-272. [PMID: 34147203 DOI: 10.1016/bs.pmch.2021.01.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Having always been driven by the need to get new treatments to patients as quickly as possible, drug discovery is a constantly evolving process. This chapter will review how medicinal chemistry was established, how it has changed over the years due to the emergence of new enabling technologies, and how early advances in synthesis, purification and analysis, have provided the foundations upon which the current automated and enabling technologies are built. Looking beyond the established technologies, this chapter will also consider technologies that are now emerging, and their impact on the future of drug discovery and the role of medicinal chemists.
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Affiliation(s)
- Paula L Nichols
- Synple Chem AG, Kemptthal, Switzerland; ETH, Zurich, Switzerland.
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138
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Dembitsky VM, Gloriozova TA, Poroikov VV. Antitumor Profile of Carbon-Bridged Steroids (CBS) and Triterpenoids. Mar Drugs 2021; 19:324. [PMID: 34205074 PMCID: PMC8228860 DOI: 10.3390/md19060324] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 06/01/2021] [Accepted: 06/01/2021] [Indexed: 12/12/2022] Open
Abstract
This review focuses on the rare group of carbon-bridged steroids (CBS) and triterpenoids found in various natural sources such as green, yellow-green, and red algae, marine sponges, soft corals, ascidians, starfish, and other marine invertebrates. In addition, this group of rare lipids is found in amoebas, fungi, fungal endophytes, and plants. For convenience, the presented CBS and triterpenoids are divided into four groups, which include: (a) CBS and triterpenoids containing a cyclopropane group; (b) CBS and triterpenoids with cyclopropane ring in the side chain; (c) CBS and triterpenoids containing a cyclobutane group; (d) CBS and triterpenoids containing cyclopentane, cyclohexane or cycloheptane moieties. For the comparative characterization of the antitumor profile, we have added several semi- and synthetic CBS and triterpenoids, with various additional rings, to identify possible promising sources for pharmacologists and the pharmaceutical industry. About 300 CBS and triterpenoids are presented in this review, which demonstrate a wide range of biological activities, but the most pronounced antitumor profile. The review summarizes biological activities both determined experimentally and estimated using the well-known PASS software. According to the data obtained, two-thirds of CBS and triterpenoids show moderate activity levels with a confidence level of 70 to 90%; however, one third of these lipids demonstrate strong antitumor activity with a confidence level exceeding 90%. Several CBS and triterpenoids, from different lipid groups, demonstrate selective action on different types of tumor cells such as renal cancer, sarcoma, pancreatic cancer, prostate cancer, lymphocytic leukemia, myeloid leukemia, liver cancer, and genitourinary cancer with varying degrees of confidence. In addition, the review presents graphical images of the antitumor profile of both individual CBS and triterpenoids groups and individual compounds.
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Affiliation(s)
- Valery M. Dembitsky
- Centre for Applied Research, Innovation and Entrepreneurship, Lethbridge College, 3000 College Drive South, Lethbridge, AB T1K 1L6, Canada
| | - Tatyana A. Gloriozova
- Institute of Biomedical Chemistry, Bldg. 8, 10 Pogodinskaya Str., 119121 Moscow, Russia; (T.A.G.); (V.V.P.)
| | - Vladimir V. Poroikov
- Institute of Biomedical Chemistry, Bldg. 8, 10 Pogodinskaya Str., 119121 Moscow, Russia; (T.A.G.); (V.V.P.)
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139
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Halder P, Pal U, Paladhi P, Dutta S, Paul P, Pal S, Das D, Ganguly A, IshitaDutta, SayarneelMandal, Ray A, Ghosh S. Evaluation of potency of the selected bioactive molecules from Indian medicinal plants with M Pro of SARS-CoV-2 through in silico analysis. J Ayurveda Integr Med 2021; 13:100449. [PMID: 34054246 PMCID: PMC8139275 DOI: 10.1016/j.jaim.2021.05.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 04/12/2021] [Accepted: 05/05/2021] [Indexed: 12/12/2022] Open
Abstract
Background The recent outbreak of novel SARs CoVid-2 across the globe and absence of specific drug against this virus lead the scientific community to look into some alternative indigenous treatments. India as a hub of ayurvedic and medicinal plants can shed light on its treatment using specific active bio-molecules from these plants. Objectives Keeping our herbal resources in mind we were interested to inquire whether some phytochemicals from Indian spices and medicinal plants can be used as alternative therapeutic agents in contrast to synthetic drugs. Materials and methods We used in-silico molecular docking approach to test whether bioactive molecules of herbal origin such as Hyperoside, Nimbaflavone, Ursolic acid, 6-gingerol, 6-shogaol& 6-paradol, Curcumin, Catechins&Epigallocatechin, α-Hederin, Piperine could bind and potentially block theMproenzyme of Sars-CoV-2 virus. Results Ursolic acid showed the highest docking score (-8.7 kcal/mol) followed by Hyperoside (-8.6kcal/mol), α-Hederin (-8.5 kcal/mol) and Nimbaflavone (-8.0kcal/mol). Epigallocatechin, Catechins, and Curcumin also exhibited high binding affinity (Docking score -7.3, -7.1 and -7.1 kcal/mol) with the Mpro. Rest of the tested phytochemicals exhibited moderate binding and inhibitory effects. Conclusion This finding provides a basis for biochemical assay on Sars-CoV-2 virus.
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Affiliation(s)
- Pinku Halder
- Cytogenetics& Genomics Research Unit, Department of Zoology; University of Calcutta, Taraknath-Palit-Siksha-Prangan (Ballygunge Science College Campus), 35 Ballygunge Circular Road, Kolkata, WestBengal, India,Pincode: 700019
| | - Upamanyu Pal
- Cytogenetics& Genomics Research Unit, Department of Zoology; University of Calcutta, Taraknath-Palit-Siksha-Prangan (Ballygunge Science College Campus), 35 Ballygunge Circular Road, Kolkata, WestBengal, India,Pincode: 700019
| | - Pranab Paladhi
- Cytogenetics& Genomics Research Unit, Department of Zoology; University of Calcutta, Taraknath-Palit-Siksha-Prangan (Ballygunge Science College Campus), 35 Ballygunge Circular Road, Kolkata, WestBengal, India,Pincode: 700019
| | - Saurav Dutta
- Cytogenetics& Genomics Research Unit, Department of Zoology; University of Calcutta, Taraknath-Palit-Siksha-Prangan (Ballygunge Science College Campus), 35 Ballygunge Circular Road, Kolkata, WestBengal, India,Pincode: 700019
| | - Pallab Paul
- Cytogenetics& Genomics Research Unit, Department of Zoology; University of Calcutta, Taraknath-Palit-Siksha-Prangan (Ballygunge Science College Campus), 35 Ballygunge Circular Road, Kolkata, WestBengal, India,Pincode: 700019
| | - Samudra Pal
- Cytogenetics& Genomics Research Unit, Department of Zoology; University of Calcutta, Taraknath-Palit-Siksha-Prangan (Ballygunge Science College Campus), 35 Ballygunge Circular Road, Kolkata, WestBengal, India,Pincode: 700019
| | - Debasmita Das
- Cytogenetics& Genomics Research Unit, Department of Zoology; University of Calcutta, Taraknath-Palit-Siksha-Prangan (Ballygunge Science College Campus), 35 Ballygunge Circular Road, Kolkata, WestBengal, India,Pincode: 700019
| | - Agnish Ganguly
- Cytogenetics& Genomics Research Unit, Department of Zoology; University of Calcutta, Taraknath-Palit-Siksha-Prangan (Ballygunge Science College Campus), 35 Ballygunge Circular Road, Kolkata, WestBengal, India,Pincode: 700019
| | - IshitaDutta
- Cytogenetics& Genomics Research Unit, Department of Zoology; University of Calcutta, Taraknath-Palit-Siksha-Prangan (Ballygunge Science College Campus), 35 Ballygunge Circular Road, Kolkata, WestBengal, India,Pincode: 700019
| | - SayarneelMandal
- Cytogenetics& Genomics Research Unit, Department of Zoology; University of Calcutta, Taraknath-Palit-Siksha-Prangan (Ballygunge Science College Campus), 35 Ballygunge Circular Road, Kolkata, WestBengal, India,Pincode: 700019
| | - Anirban Ray
- Department of Zoology, Bangabasi Morning College (affiliated to University of Calcutta), Kolkata, West Bengal, India, Pincode: 700009
| | - Sujay Ghosh
- Cytogenetics& Genomics Research Unit, Department of Zoology; University of Calcutta, Taraknath-Palit-Siksha-Prangan (Ballygunge Science College Campus), 35 Ballygunge Circular Road, Kolkata, WestBengal, India,Pincode: 700019
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Seffernick JT, Canfield SM, Harvey SR, Wysocki VH, Lindert S. Prediction of Protein Complex Structure Using Surface-Induced Dissociation and Cryo-Electron Microscopy. Anal Chem 2021; 93:7596-7605. [PMID: 33999617 DOI: 10.1021/acs.analchem.0c05468] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
A variety of techniques involving the use of mass spectrometry (MS) have been developed to obtain structural information on proteins and protein complexes. One example of these techniques, surface-induced dissociation (SID), has been used to study the oligomeric state and connectivity of protein complexes. Recently, we demonstrated that appearance energies (AE) could be extracted from SID experiments and that they correlate with structural features of specific protein-protein interfaces. While SID AE provides some structural information, the AE data alone are not sufficient to determine the structures of the complexes. For this reason, we sought to supplement the data with computational modeling, through protein-protein docking. In a previous study, we demonstrated that the scoring of structures generated from protein-protein docking could be improved with the inclusion of SID data; however, this work relied on knowledge of the correct tertiary structure and only built full complexes for a few cases. Here, we performed docking using input structures that require less prior knowledge, using homology models, unbound crystal structures, and bound+perturbed crystal structures. Using flexible ensemble docking (to build primarily subcomplexes from an ensemble of backbone structures), the RMSD100 of all (15/15) predicted structures using the combined Rosetta, cryo-electron microscopy (cryo-EM), and SID score was less than 4 Å, compared to only 7/15 without SID and cryo-EM. Symmetric docking (which used symmetry to build full complexes) resulted in predicted structures with RMSD100 less than 4 Å for 14/15 cases with experimental data, compared to only 5/15 without SID and cryo-EM. Finally, we also developed a confidence metric for which all (26/26) proteins flagged as high confidence were accurately predicted.
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Affiliation(s)
- Justin T Seffernick
- Department of Chemistry and Biochemistry, Ohio State University, 2114 Newman & Wolfrom Laboratory, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Shane M Canfield
- Department of Chemistry, Kenyon College, Gambier, Ohio 43022, United States
| | - Sophie R Harvey
- Department of Chemistry and Biochemistry, Ohio State University, 2114 Newman & Wolfrom Laboratory, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Vicki H Wysocki
- Department of Chemistry and Biochemistry, Ohio State University, 2114 Newman & Wolfrom Laboratory, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Steffen Lindert
- Department of Chemistry and Biochemistry, Ohio State University, 2114 Newman & Wolfrom Laboratory, 100 West 18th Avenue, Columbus, Ohio 43210, United States
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Zhu S, Wu M, Huang Z, An J. Trends in application of advancing computational approaches in GPCR ligand discovery. Exp Biol Med (Maywood) 2021; 246:1011-1024. [PMID: 33641446 PMCID: PMC8113737 DOI: 10.1177/1535370221993422] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
G protein-coupled receptors (GPCRs) comprise the most important superfamily of protein targets in current ligand discovery and drug development. GPCRs are integral membrane proteins that play key roles in various cellular signaling processes. Therefore, GPCR signaling pathways are closely associated with numerous diseases, including cancer and several neurological, immunological, and hematological disorders. Computer-aided drug design (CADD) can expedite the process of GPCR drug discovery and potentially reduce the actual cost of research and development. Increasing knowledge of biological structures, as well as improvements on computer power and algorithms, have led to unprecedented use of CADD for the discovery of novel GPCR modulators. Similarly, machine learning approaches are now widely applied in various fields of drug target research. This review briefly summarizes the application of rising CADD methodologies, as well as novel machine learning techniques, in GPCR structural studies and bioligand discovery in the past few years. Recent novel computational strategies and feasible workflows are updated, and representative cases addressing challenging issues on olfactory receptors, biased agonism, and drug-induced cardiotoxic effects are highlighted to provide insights into future GPCR drug discovery.
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Affiliation(s)
- Siyu Zhu
- Division of Infectious Diseases and Global Public Health, Department of Medicine, School of Medicine, University of California at San Diego, La Jolla, CA 92093, USA
- Ciechanover Institute of Precision and Regenerative Medicine, School of Life and Health Sciences, Chinese University of Hong Kong, Shenzhen 518172, China
| | - Meixian Wu
- Division of Infectious Diseases and Global Public Health, Department of Medicine, School of Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - Ziwei Huang
- Division of Infectious Diseases and Global Public Health, Department of Medicine, School of Medicine, University of California at San Diego, La Jolla, CA 92093, USA
- Ciechanover Institute of Precision and Regenerative Medicine, School of Life and Health Sciences, Chinese University of Hong Kong, Shenzhen 518172, China
- School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jing An
- Division of Infectious Diseases and Global Public Health, Department of Medicine, School of Medicine, University of California at San Diego, La Jolla, CA 92093, USA
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Ring C, Sipes NS, Hsieh JH, Carberry C, Koval LE, Klaren WD, Harris MA, Auerbach SS, Rager JE. Predictive modeling of biological responses in the rat liver using in vitro Tox21 bioactivity: Benefits from high-throughput toxicokinetics. COMPUTATIONAL TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2021; 18:100166. [PMID: 34013136 PMCID: PMC8130852 DOI: 10.1016/j.comtox.2021.100166] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Computational methods are needed to more efficiently leverage data from in vitro cell-based models to predict what occurs within whole body systems after chemical insults. This study set out to test the hypothesis that in vitro high-throughput screening (HTS) data can more effectively predict in vivo biological responses when chemical disposition and toxicokinetic (TK) modeling are employed. In vitro HTS data from the Tox21 consortium were analyzed in concert with chemical disposition modeling to derive nominal, aqueous, and intracellular estimates of concentrations eliciting 50% maximal activity. In vivo biological responses were captured using rat liver transcriptomic data from the DrugMatrix and TG-Gates databases and evaluated for pathway enrichment. In vivo dosing data were translated to equivalent body concentrations using HTTK modeling. Random forest models were then trained and tested to predict in vivo pathway-level activity across 221 chemicals using in vitro bioactivity data and physicochemical properties as predictor variables, incorporating methods to address imbalanced training data resulting from high instances of inactivity. Model performance was quantified using the area under the receiver operator characteristic curve (AUC-ROC) and compared across pathways for different combinations of predictor variables. All models that included toxicokinetics were found to outperform those that excluded toxicokinetics. Biological interpretation of the model features revealed that rather than a direct mapping of in vitro assays to in vivo pathways, unexpected combinations of multiple in vitro assays predicted in vivo pathway-level activities. To demonstrate the utility of these findings, the highest-performing model was leveraged to make new predictions of in vivo biological responses across all biological pathways for remaining chemicals tested in Tox21 with adequate data coverage (n = 6617). These results demonstrate that, when chemical disposition and toxicokinetics are carefully considered, in vitro HT screening data can be used to effectively predict in vivo biological responses to chemicals.
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Affiliation(s)
- Caroline Ring
- ToxStrategies, Inc., Austin, TX 78751, United States
| | - Nisha S. Sipes
- Division of the National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, United States
| | - Jui-Hua Hsieh
- Kelly Government Solutions, Durham, NC 27709, United States
| | - Celeste Carberry
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States
- The Institute for Environmental Health Solutions, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States
| | - Lauren E. Koval
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States
- The Institute for Environmental Health Solutions, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States
| | - William D. Klaren
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77840, United States
| | | | - Scott S. Auerbach
- Division of the National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, United States
| | - Julia E. Rager
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States
- The Institute for Environmental Health Solutions, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States
- Curriculum in Toxicology and Environmental Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States
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PharmaNet: Pharmaceutical discovery with deep recurrent neural networks. PLoS One 2021; 16:e0241728. [PMID: 33901196 PMCID: PMC8075191 DOI: 10.1371/journal.pone.0241728] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 04/01/2021] [Indexed: 12/23/2022] Open
Abstract
The discovery and development of novel pharmaceuticals is an area of active research mainly due to the large investments required and long payback times. As of 2016, the development of a novel drug candidate required up to $ USD 2.6 billion in investment for only 10% rate of approval by the FDA. To help decreasing the costs associated with the process, a number of in silico approaches have been developed with relatively low success due to limited predicting performance. Here, we introduced a machine learning-based algorithm as an alternative for a more accurate search of new pharmacological candidates, which takes advantage of Recurrent Neural Networks (RNN) for active molecule prediction within large databases. Our approach, termed PharmaNet was implemented here to search for ligands against specific cell receptors within 102 targets of the DUD-E database, which contains 22886 active molecules. PharmaNet comprises three main phases. First, a SMILES representation of the molecule is converted into a raw molecular image. Second, a convolutional encoder processes the data to obtain a fingerprint molecular image that is finally analyzed by a Recurrent Neural Network (RNN). This approach enables precise predictions of the molecules' target on the basis of the feature extraction, the sequence analysis and the relevant information filtered out throughout the process. Molecule Target prediction is a highly unbalanced detection problem and therefore, we propose that an adequate evaluation metric of performance is the area under the Normalized Average Precision (NAP) curve. PharmaNet largely surpasses the previous state-of-the-art method with 97.7% in the Receiver Operating Characteristic curve (ROC-AUC) and 65.5% in the NAP curve. We obtained a perfect performance for human farnesyl pyrophosphate synthase (FPPS), which is a potential target for antimicrobial and anticancer treatments. We decided to test PharmaNet for activity prediction against FPPS by searching in the CHEMBL data set. We obtained three (3) potential inhibitors that were further validated through both molecular docking and in silico toxicity prediction. Most importantly, one of this candidates, CHEMBL2007613, was predicted as a potential antiviral due to its involvement on the PCDH17 pathway, which has been reported to be related to viral infections.
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144
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Gupta SS, Kumar A, Shankar R, Sharma U. In silico approach for identifying natural lead molecules against SARS-COV-2. J Mol Graph Model 2021; 106:107916. [PMID: 33892297 PMCID: PMC8042570 DOI: 10.1016/j.jmgm.2021.107916] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 03/24/2021] [Accepted: 03/29/2021] [Indexed: 11/30/2022]
Abstract
The life challenging COVID-19 disease caused by the SARS-CoV-2 virus has greatly impacted smooth survival worldwide since its discovery in December 2019. Currently, it is one of the major threats to humanity. Moreover, any specific drug or vaccine unavailability against COVID-19 forces to discover a new drug on an urgent basis. Viral cycle inhibition could be one possible way to prevent the further genesis of this viral disease, which can be contributed by drug repurposing techniques or screening of small bioactive natural molecules against already validated targets of COVID-19. The main protease (Mpro) responsible for producing functional proteins from polyprotein is an important key step for SARS-CoV-2 virion replication. Natural product or herbal based formulations are an important platform for potential therapeutics and lead compounds in the drug discovery process. Therefore, here we have screened >53,500 bioactive natural molecules from six different natural product databases against Mpro (PDB ID: 6LU7) of COVID-19 through computational study. Further, the top three molecules were subjected to pharmacokinetics evaluation, which is an important factor that reduces the drug failure rate. Moreover, the top three screened molecules (C00014803, C00006660, ANLT0001) were further validated by a molecular dynamics study under a condition similar to the physiological one. Relative binding energy analysis of three lead molecules indicated that C00014803 possess highest binding affinity among all three hits. These extensive studies can be a significant foundation for developing a therapeutic agent against COVID-19 through vet lab studies.
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Affiliation(s)
- Shiv Shankar Gupta
- Chemical Technology Division, CSIR-IHBT, Palampur, HP, 176 061, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Ashwani Kumar
- Biotechnology Division, CSIR-IHBT, Palampur, HP, 176 061, India
| | - Ravi Shankar
- Biotechnology Division, CSIR-IHBT, Palampur, HP, 176 061, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
| | - Upendra Sharma
- Chemical Technology Division, CSIR-IHBT, Palampur, HP, 176 061, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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Andrianov AM, Nikolaev GI, Shuldov NA, Bosko IP, Anischenko AI, Tuzikov AV. Application of deep learning and molecular modeling to identify small drug-like compounds as potential HIV-1 entry inhibitors. J Biomol Struct Dyn 2021; 40:7555-7573. [PMID: 33855929 DOI: 10.1080/07391102.2021.1905559] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
A generative adversarial autoencoder for the rational design of potential HIV-1 entry inhibitors able to block CD4-binding site of the viral envelope protein gp120 was developed. To do this, the following studies were carried out: (i) an autoencoder architecture was constructed; (ii) a virtual compound library of potential anti-HIV-1 agents for training the neural network was formed by the concept of click chemistry allowing one to generate a large number of drug candidates by their assembly from small modular units; (iii) molecular docking of all compounds from this library with gp120 was made and calculations of the values of binding free energy were performed; (iv) molecular fingerprints of chemical compounds from the training dataset were generated; (v) training of the developed autoencoder was implemented followed by the validation of this neural network using more than 21 million molecules from the ZINC15 database. As a result, three small drug-like compounds that exhibited the high-affinity binding to gp120 were identified. According to the data from molecular docking, machine learning, quantum chemical calculations, and molecular dynamics simulations, these compounds show the low values of binding free energy in the complexes with gp120 similar to those calculated using the same computational protocols for the HIV-1 entry inhibitors NBD-11021 and NBD-14010, highly potent and broad anti-HIV-1 agents presenting a new generation of the viral CD4 antagonists. The identified CD4-mimetic candidates are suggested to present good scaffolds for the design of novel antiviral drugs inhibiting the early stages of HIV-1 infection.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Alexander M Andrianov
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, Minsk, Republic of Belarus
| | - Grigory I Nikolaev
- United Institute of Informatics Problems, National Academy of Sciences of Belarus, Minsk, Republic of Belarus
| | - Nikita A Shuldov
- Faculty of Applied Mathematics & Computer Science, Belarusian State University, Minsk, Republic of Belarus
| | - Ivan P Bosko
- United Institute of Informatics Problems, National Academy of Sciences of Belarus, Minsk, Republic of Belarus
| | - Arseny I Anischenko
- Faculty of Applied Mathematics & Computer Science, Belarusian State University, Minsk, Republic of Belarus
| | - Alexander V Tuzikov
- United Institute of Informatics Problems, National Academy of Sciences of Belarus, Minsk, Republic of Belarus
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146
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Souza PCT, Limongelli V, Wu S, Marrink SJ, Monticelli L. Perspectives on High-Throughput Ligand/Protein Docking With Martini MD Simulations. Front Mol Biosci 2021; 8:657222. [PMID: 33855050 PMCID: PMC8039319 DOI: 10.3389/fmolb.2021.657222] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 03/05/2021] [Indexed: 01/12/2023] Open
Abstract
Molecular docking is central to rational drug design. Current docking techniques suffer, however, from limitations in protein flexibility and solvation models and by the use of simplified scoring functions. All-atom molecular dynamics simulations, on the other hand, feature a realistic representation of protein flexibility and solvent, but require knowledge of the binding site. Recently we showed that coarse-grained molecular dynamics simulations, based on the most recent version of the Martini force field, can be used to predict protein/ligand binding sites and pathways, without requiring any a priori information, and offer a level of accuracy approaching all-atom simulations. Given the excellent computational efficiency of Martini, this opens the way to high-throughput drug screening based on dynamic docking pipelines. In this opinion article, we sketch the roadmap to achieve this goal.
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Affiliation(s)
- Paulo C. T. Souza
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Groningen, Netherlands
- PharmCADD, Busan, South Korea
- Molecular Microbiology and Structural Biochemistry (MMSB, UMR 5086), CNRS, University of Lyon, Lyon, France
| | - Vittorio Limongelli
- Faculty of Biomedical Sciences, Institute of Computational Science, Università della Svizzera Italiana (USI), Lugano, Switzerland
- Department of Pharmacy, University of Naples “Federico II”, Naples, Italy
| | - Sangwook Wu
- PharmCADD, Busan, South Korea
- Department of Physics, Pukyong National University, Busan, South Korea
| | - Siewert J. Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Groningen, Netherlands
| | - Luca Monticelli
- Molecular Microbiology and Structural Biochemistry (MMSB, UMR 5086), CNRS, University of Lyon, Lyon, France
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147
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Lobine D, Pairyanen B, Zengin G, Yılmaz MA, Ouelbani R, Bensari S, Ak G, Abdallah HH, Imran M, Mahomoodally MF. Chemical Composition and Pharmacological Evaluation and of Toddalia asiatica (Rutaceae) Extracts and Essential Oil by in Vitro and in Silico Approaches. Chem Biodivers 2021; 18:e2000999. [PMID: 33738900 DOI: 10.1002/cbdv.202000999] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Accepted: 02/15/2021] [Indexed: 12/24/2022]
Abstract
Toddalia asiatica (L.) Lam. is extensively used in traditional medicinal systems by various cultures. Despite its frequent use in traditional medicine, there is still a paucity of scientific information on T. asiatica growing on the tropical island of Mauritius. Therefore, the present study was designed to appraise the pharmacological and phytochemical profile of extracts (methanol, ethyl acetate and water) and essential oil obtained from aerial parts of T. asiatica. Biological investigation involved the evaluation of in vitro antioxidant and enzyme inhibitory potentials. The chemical profile of the EO was determined using gas chromatography coupled to mass spectrometry (GC/MS) analysis, while for the extracts, the total phenolic (TPC) and flavonoid content were quantified as well as their individual phenolic compounds by LC/MS/MS. Quinic acid, fumaric acid, chlorogenic acid, quercitrin and isoquercitrin were the main compounds in the extracts. Highest total phenolic (82.5±0.94 mg gallic acid equivalent (GAE/g)) and flavonoid (43.8±0.31 mg rutin equivalent (RE/g)) content were observed for the methanol extract. The GC/MS analysis has shown the presence of 26 compounds with linalool (30.9 %), linalyl acetate (20.9 %) and β-phellandrene (7.9 %) being most abundant components in the EO. The extracts and EO showed notable antioxidant properties, with the methanol extract proved to be superior source of antioxidant compounds. Noteworthy anti-acetylcholinesterase (AChE) and anti-butyrylcholinesterase (BChE) effects were recorded for the tested samples, while only the methanol and ethyl acetate extracts were active against tyrosinase. With respect to antidiabetic effects, the extracts and EO were potent inhibitors of α-glucosidase, while modest activity was recorded against α-amylase. Docking results showed that linalyl acetate has the highest affinity to interact with the active site of BChE with docking score of -6.25 kcal/mol. The findings amassed herein act as a stimulus for further investigations of this plant as a potential source of bioactive compounds which can be exploited as phyto-therapeutics.
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Affiliation(s)
- Devina Lobine
- Department of Health Sciences, Faculty of Medicine and Health Sciences, University of Mauritius, Moka, Réduit, 80837, Mauritius
| | - Bryan Pairyanen
- Department of Health Sciences, Faculty of Medicine and Health Sciences, University of Mauritius, Moka, Réduit, 80837, Mauritius.,Department of Agricultural and Food Sciences, Faculty of Agriculture, University of Mauritius, Moka, Réduit, 80837, Mauritius
| | - Gokhan Zengin
- Physiology and Biochemistry Research Laboratory, Department of Biology, Faculty of Science, Selcuk University, Konya, 42130, Turkey
| | - Mustafa Abdullah Yılmaz
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Dicle University, Diyarbakır, 21280, Turkey
| | - Rayene Ouelbani
- Laboratoire de Génétique, Biochimie et Biotechnologies Végétales GBBV, Faculté des Sciences de la nature et de la vie, Université Frères Mentouri Constantine1, Route d'Aïn El Bey, 25017, Constantine, Algérie
| | - Souheir Bensari
- Laboratoire de Génétique, Biochimie et Biotechnologies Végétales GBBV, Faculté des Sciences de la nature et de la vie, Université Frères Mentouri Constantine1, Route d'Aïn El Bey, 25017, Constantine, Algérie
| | - Gunes Ak
- Physiology and Biochemistry Research Laboratory, Department of Biology, Faculty of Science, Selcuk University, Konya, 42130, Turkey
| | - Hassan H Abdallah
- Chemistry Department, College of Education, Salahaddin University-Erbril, 44002, Erbil, Iraq
| | - Muhammad Imran
- University Institute of Diet and Nutritional Sciences, Faculty of Allied Health Sciences, The University of Lahore, Lahore, 54590, Pakistan
| | - Mohamad Fawzi Mahomoodally
- Department of Health Sciences, Faculty of Medicine and Health Sciences, University of Mauritius, Moka, Réduit, 80837, Mauritius
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148
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Tinivella A, Pinzi L, Rastelli G. Prediction of activity and selectivity profiles of human Carbonic Anhydrase inhibitors using machine learning classification models. J Cheminform 2021; 13:18. [PMID: 33676550 PMCID: PMC7937250 DOI: 10.1186/s13321-021-00499-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 02/22/2021] [Indexed: 11/23/2022] Open
Abstract
The development of selective inhibitors of the clinically relevant human Carbonic Anhydrase (hCA) isoforms IX and XII has become a major topic in drug research, due to their deregulation in several types of cancer. Indeed, the selective inhibition of these two isoforms, especially with respect to the homeostatic isoform II, holds great promise to develop anticancer drugs with limited side effects. Therefore, the development of in silico models able to predict the activity and selectivity against the desired isoform(s) is of central interest. In this work, we have developed a series of machine learning classification models, trained on high confidence data extracted from ChEMBL, able to predict the activity and selectivity profiles of ligands for human Carbonic Anhydrase isoforms II, IX and XII. The training datasets were built with a procedure that made use of flexible bioactivity thresholds to obtain well-balanced active and inactive classes. We used multiple algorithms and sampling sizes to finally select activity models able to classify active or inactive molecules with excellent performances. Remarkably, the results herein reported turned out to be better than those obtained by models built with the classic approach of selecting an a priori activity threshold. The sequential application of such validated models enables virtual screening to be performed in a fast and more reliable way to predict the activity and selectivity profiles against the investigated isoforms.
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Affiliation(s)
- Annachiara Tinivella
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Giuseppe Campi 103, 41125, Modena, Italy.,Clinical and Experimental Medicine PhD Program, University of Modena and Reggio Emilia, Modena, Italy
| | - Luca Pinzi
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Giuseppe Campi 103, 41125, Modena, Italy
| | - Giulio Rastelli
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Giuseppe Campi 103, 41125, Modena, Italy.
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149
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Sahoo BM, Ravi Kumar BVV, Sruti J, Mahapatra MK, Banik BK, Borah P. Drug Repurposing Strategy (DRS): Emerging Approach to Identify Potential Therapeutics for Treatment of Novel Coronavirus Infection. Front Mol Biosci 2021; 8:628144. [PMID: 33718434 PMCID: PMC7953054 DOI: 10.3389/fmolb.2021.628144] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 01/14/2021] [Indexed: 12/13/2022] Open
Abstract
Drug repurposing is also termed as drug repositioning or therapeutic switching. This method is applied to identify the novel therapeutic agents from the existing FDA approved clinically used drug molecules. It is considered as an efficient approach to develop drug candidates with new pharmacological activities or therapeutic properties. As the drug discovery is a costly, time-consuming, laborious, and highly risk process, the novel approach of drug repositioning is employed to increases the success rate of drug development. This strategy is more advantageous over traditional drug discovery process in terms of reducing duration of drug development, low-cost, highly efficient and minimum risk of failure. In addition to this, World health organization declared Coronavirus disease (COVID-19) as pandemic globally on February 11, 2020. Currently, there is an urgent need to develop suitable therapeutic agents for the prevention of the outbreak of COVID-19. So, various investigations were carried out to design novel drug molecules by utilizing different approaches of drug repurposing to identify drug substances for treatment of COVID-19, which can act as significant inhibitors against viral proteins. It has been reported that COVID-19 can infect human respiratory system by entering into the alveoli of lung via respiratory tract. So, the infection occurs due to specific interaction or binding of spike protein with angiotensin converting enzyme-2 (ACE-2) receptor. Hence, drug repurposing strategy is utilized to identify suitable drugs by virtual screening of drug libraries. This approach helps to determine the binding interaction of drug candidates with target protein of coronavirus by using computational tools such as molecular similarity and homology modeling etc. For predicting the drug-receptor interactions and binding affinity, molecular docking study and binding free energy calculations are also performed. The methodologies involved in drug repurposing can be categorized into three groups such as drug-oriented, target-oriented and disease or therapy-oriented depending on the information available related to quality and quantity of the physico-chemical, biological, pharmacological, toxicological and pharmacokinetic property of drug molecules. This review focuses on drug repurposing strategy applied for existing drugs including Remdesivir, Favipiravir, Ribavirin, Baraticinib, Tocilizumab, Chloroquine, Hydroxychloroquine, Prulifloxacin, Carfilzomib, Bictegravir, Nelfinavir, Tegobuvir and Glucocorticoids etc to determine their effectiveness toward the treatment of COVID-19.
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Affiliation(s)
- Biswa Mohan Sahoo
- Roland Institute of Pharmaceutical Sciences (Biju Patnaik University of Technology Nodal Centre of Research), Berhampur, India
| | - B V V Ravi Kumar
- Roland Institute of Pharmaceutical Sciences (Biju Patnaik University of Technology Nodal Centre of Research), Berhampur, India
| | - J Sruti
- Roland Institute of Pharmaceutical Sciences (Biju Patnaik University of Technology Nodal Centre of Research), Berhampur, India
| | | | - Bimal K Banik
- Department of Mathematics and Natural Sciences, College of Sciences and Human Studies, Prince Mohammad Bin Fahd University, Al Khobar, Saudi Arabia
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150
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Kim SS, Alves MJ, Gygli P, Otero J, Lindert S. Identification of Novel Cyclin A2 Binding Site and Nanomolar Inhibitors of Cyclin A2-CDK2 Complex. Curr Comput Aided Drug Des 2021; 17:57-68. [PMID: 31889491 DOI: 10.2174/1573409916666191231113055] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 11/25/2019] [Accepted: 12/09/2019] [Indexed: 01/10/2023]
Abstract
BACKGROUND Given the diverse roles of cyclin A2 both in cell cycle regulation and in DNA damage response, identifying small molecule regulators of cyclin A2 activity carries significant potential to regulate diverse cellular processes in both ageing/neurodegeneration and in cancer. OBJECTIVE Based on cyclin A2's recently discovered role in DNA repair, we hypothesized that small molecule inhibitors that were predicted to bind to both cyclin A2 and CDK2 will be useful as a radiosensitizer of cancer cells. In this study, we used structure-based drug discovery to find inhibitors that target both cyclin A2 and CDK2. METHODS Molecular dynamics simulations were used to generate diverse binding pocket conformations for application of the relaxed complex scheme. We then used structure-based virtual screening to find potential dual cyclin A2 and CDK2 inhibitors. Based on a consensus score of docked poses from Glide and AutoDock Vina, we identified about 40 promising hit compounds, where all PAINS scaffolds were removed from consideration. A biochemical luminescence assay of cyclin A2-CDK2 function was used for experimental verification. RESULTS Four lead inhibitors of cyclin A2-CDK2 complex have been identified using a relaxed complex scheme virtual screen have been verified in a biochemical luminescence assay of cyclin A2- CDK2 function. Two of the four lead inhibitors had inhibitory concentrations in the nanomolar range. CONCLUSION The four cyclin A2-CDK2 complex inhibitors are the first reported inhibitors that were specifically designed not to target the cyclin A2-CDK2 protein-protein interface. Overall, our results highlight the potential of combined advanced computational tools and biochemical verification to discover novel binding scaffolds.
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Affiliation(s)
- Stephanie S Kim
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH, 43210, United States
| | - Michele J Alves
- Departments of Neuroscience, Pathology and Neuropathology, Ohio State University, Columbus, OH, 43210, United States
| | - Patrick Gygli
- Departments of Neuroscience, Pathology and Neuropathology, Ohio State University, Columbus, OH, 43210, United States
| | - Jose Otero
- Departments of Neuroscience, Pathology and Neuropathology, Ohio State University, Columbus, OH, 43210, United States
| | - Steffen Lindert
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH, 43210, United States
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