1
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Li GC, Castro MA, Ukwaththage T, Sanders CR. Optimizing NMR fragment-based drug screening for membrane protein targets. J Struct Biol X 2024; 9:100100. [PMID: 38883400 PMCID: PMC11176934 DOI: 10.1016/j.yjsbx.2024.100100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 05/05/2024] [Accepted: 05/20/2024] [Indexed: 06/18/2024] Open
Abstract
NMR spectroscopy has played a pivotal role in fragment-based drug discovery by coupling detection of weak ligand-target binding with structural mapping of the binding site. Fragment-based screening by NMR has been successfully applied to many soluble protein targets, but only to a limited number of membrane proteins, despite the fact that many drug targets are membrane proteins. This is partly because of difficulties preparing membrane proteins for NMR-especially human membrane proteins-and because of the inherent complexity associated with solution NMR spectroscopy on membrane protein samples, which require the inclusion of membrane-mimetic agents such as micelles, nanodiscs, or bicelles. Here, we developed a generalizable protocol for fragment-based screening of membrane proteins using NMR. We employed two human membrane protein targets, both in fully protonated detergent micelles: the single-pass C-terminal domain of the amyloid precursor protein, C99, and the tetraspan peripheral myelin protein 22 (PMP22). For both we determined the optimal NMR acquisition parameters, protein concentration, protein-to-micelle ratio, and upper limit to the concentration of D6-DMSO in screening samples. Furthermore, we conducted preliminary screens of a plate-format molecular fragment mixture library using our optimized conditions and were able to identify hit compounds that selectively bound to the respective target proteins. It is hoped that the approaches presented here will be useful in complementing existing methods for discovering lead compounds that target membrane proteins.
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Affiliation(s)
- Geoffrey C Li
- Department of Biochemistry and Center for Structural Biology, Vanderbilt University School of Medicine - Basic Sciences, Nashville, TN 37240, USA
| | - Manuel A Castro
- Department of Biochemistry and Center for Structural Biology, Vanderbilt University School of Medicine - Basic Sciences, Nashville, TN 37240, USA
| | - Thilini Ukwaththage
- Department of Biochemistry and Center for Structural Biology, Vanderbilt University School of Medicine - Basic Sciences, Nashville, TN 37240, USA
| | - Charles R Sanders
- Department of Biochemistry and Center for Structural Biology, Vanderbilt University School of Medicine - Basic Sciences, Nashville, TN 37240, USA
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2
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Doak BC, Whitehouse RL, Rimmer K, Williams M, Heras B, Caria S, Ilyichova O, Vazirani M, Mohanty B, Harper JB, Scanlon MJ, Simpson JS. Fluoromethylketone-Fragment Conjugates Designed as Covalent Modifiers of EcDsbA are Atypical Substrates. ChemMedChem 2024:e202300684. [PMID: 38742480 DOI: 10.1002/cmdc.202300684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 05/09/2024] [Accepted: 05/10/2024] [Indexed: 05/16/2024]
Abstract
Disulfide bond protein A (DsbA) is an oxidoreductase enzyme that catalyzes the formation of disulfide bonds in Gram-negative bacteria. In Escherichia coli, DsbA (EcDsbA) is essential for bacterial virulence, thus inhibitors have the potential to act as antivirulence agents. A fragment-based screen was conducted against EcDsbA and herein we describe the development of a series of compounds based on a phenylthiophene hit identified from the screen. A novel thiol reactive and "clickable" ethynylfluoromethylketone was designed for reaction with azide-functionalized fragments to enable rapid and versatile attachment to a range of fragments. The resulting fluoromethylketone conjugates showed selectivity for reaction with the active site thiol of EcDsbA, however unexpectedly, turnover of the covalent adduct was observed. A mechanism for this turnover was investigated and proposed which may have wider ramifications for covalent reactions with dithiol-disulfide oxidoreducatases.
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Affiliation(s)
- Bradley C Doak
- Medicinal Chemistry, ARC Centre for Fragment-Based Design, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC, 3052, Australia
| | - Rebecca L Whitehouse
- Medicinal Chemistry, ARC Centre for Fragment-Based Design, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC, 3052, Australia
| | - Kieran Rimmer
- Medicinal Chemistry, ARC Centre for Fragment-Based Design, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC, 3052, Australia
| | - Martin Williams
- Medicinal Chemistry, ARC Centre for Fragment-Based Design, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC, 3052, Australia
| | - Begoña Heras
- Department of Biochemistry and Genetics, La Trobe, La Trobe University, Kingsbury Drive, Bundoora, Vic, 3083, Australia
| | - Sofia Caria
- Medicinal Chemistry, ARC Centre for Fragment-Based Design, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC, 3052, Australia
| | - Olga Ilyichova
- Medicinal Chemistry, ARC Centre for Fragment-Based Design, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC, 3052, Australia
| | - Mansha Vazirani
- Medicinal Chemistry, ARC Centre for Fragment-Based Design, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC, 3052, Australia
| | - Biswaranjan Mohanty
- Medicinal Chemistry, ARC Centre for Fragment-Based Design, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC, 3052, Australia
- Sydney Analytical Core Research Facility, The University of Sydney, Sydney, New South Wales, 2006, Australia
| | - Jason B Harper
- School of Chemistry, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Martin J Scanlon
- Medicinal Chemistry, ARC Centre for Fragment-Based Design, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC, 3052, Australia
- Sydney Analytical Core Research Facility, The University of Sydney, Sydney, New South Wales, 2006, Australia
| | - Jamie S Simpson
- Medicinal Chemistry, ARC Centre for Fragment-Based Design, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC, 3052, Australia
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3
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Shen X, Zeng T, Chen N, Li J, Wu R. NIMO: A Natural Product-Inspired Molecular Generative Model Based on Conditional Transformer. Molecules 2024; 29:1867. [PMID: 38675687 PMCID: PMC11053988 DOI: 10.3390/molecules29081867] [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: 03/05/2024] [Revised: 04/11/2024] [Accepted: 04/13/2024] [Indexed: 04/28/2024] Open
Abstract
Natural products (NPs) have diverse biological activity and significant medicinal value. The structural diversity of NPs is the mainstay of drug discovery. Expanding the chemical space of NPs is an urgent need. Inspired by the concept of fragment-assembled pseudo-natural products, we developed a computational tool called NIMO, which is based on the transformer neural network model. NIMO employs two tailor-made motif extraction methods to map a molecular graph into a semantic motif sequence. All these generated motif sequences are used to train our molecular generative models. Various NIMO models were trained under different task scenarios by recognizing syntactic patterns and structure-property relationships. We further explored the performance of NIMO in structure-guided, activity-oriented, and pocket-based molecule generation tasks. Our results show that NIMO had excellent performance for molecule generation from scratch and structure optimization from a scaffold.
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Affiliation(s)
- Xiaojuan Shen
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China; (X.S.); (T.Z.); (N.C.)
| | - Tao Zeng
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China; (X.S.); (T.Z.); (N.C.)
| | - Nianhang Chen
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China; (X.S.); (T.Z.); (N.C.)
| | - Jiabo Li
- ChemXAI Inc., 53 Barry Lane, Syosset, NY 11791, USA
| | - Ruibo Wu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China; (X.S.); (T.Z.); (N.C.)
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4
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Jinsong S, Qifeng J, Xing C, Hao Y, Wang L. Molecular fragmentation as a crucial step in the AI-based drug development pathway. Commun Chem 2024; 7:20. [PMID: 38302655 PMCID: PMC10834946 DOI: 10.1038/s42004-024-01109-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 01/19/2024] [Indexed: 02/03/2024] Open
Abstract
The AI-based small molecule drug discovery has become a significant trend at the intersection of computer science and life sciences. In the pursuit of novel compounds, fragment-based drug discovery has emerged as a novel approach. The Generative Pre-trained Transformers (GPT) model has showcased remarkable prowess across various domains, rooted in its pre-training and representation learning of fundamental linguistic units. Analogous to natural language, molecular encoding, as a form of chemical language, necessitates fragmentation aligned with specific chemical logic for accurate molecular encoding. This review provides a comprehensive overview of the current state of the art in molecular fragmentation. We systematically summarize the approaches and applications of various molecular fragmentation techniques, with special emphasis on the characteristics and scope of applicability of each technique, and discuss their applications. We also provide an outlook on the current development trends of molecular fragmentation techniques, including some potential research directions and challenges.
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Affiliation(s)
- Shao Jinsong
- Nantong University, School of Information Science and Technology, Nantong, China
| | - Jia Qifeng
- Nantong University, School of Information Science and Technology, Nantong, China
| | - Chen Xing
- Nantong University, School of Information Science and Technology, Nantong, China
| | - Yajie Hao
- Nantong University, School of Information Science and Technology, Nantong, China
| | - Li Wang
- Nantong University, Research Center for Intelligence Information Technology, Nantong, China.
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5
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Liao Y. Using Photoreactive Probes to Identify Viable Drug Targets in Non-small Cell Lung Cancer. Methods Mol Biol 2024; 2823:47-53. [PMID: 39052213 DOI: 10.1007/978-1-0716-3922-1_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2024]
Abstract
Recent advancements in chemoproteomics have accelerated new chemical tools for exploring protein ligandability in native biological systems. However, a large fraction of ligandable proteome in cancer cells remains poorly studied. Here, we present a practical and efficient sample processing method for liquid chromatography high-resolution-tandem mass spectrometry (HPLC-MS/MS) analysis. This method uses fully functionalized photoreactive fragment-like probes for profiling protein-ligand interactions in live cancer cells. This method adopts "on-bead" digestion in conjunction with ZipTip desalting prior sample injection to MS. By using this protocol, fragment protein interactions can be visualized using fluorescent imaging, and fragment-associated proteins can be identified via HPLC-MS/MS analysis. Approximately 16 samples would generally expect to be processed within 3 days by following this protocol.
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Affiliation(s)
- Yi Liao
- Department of Drug Discovery, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA.
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6
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Banerjee S, Kejriwal S, Ghosh B, Lanka G, Jha T, Adhikari N. Fragment-based investigation of thiourea derivatives as VEGFR-2 inhibitors: a cross-validated approach of ligand-based and structure-based molecular modeling studies. J Biomol Struct Dyn 2024; 42:1047-1063. [PMID: 37029768 DOI: 10.1080/07391102.2023.2198039] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 03/26/2023] [Indexed: 04/09/2023]
Abstract
Angiogenesis is mediated by the vascular endothelial growth factor (VEGF) that plays a key role in the modulation of progression, invasion and metastasis, related to solid tumors and hematological malignancies. Several small-molecule VEGFR-2 inhibitors are marketed, but their usage is restricted to specific cancers due to severe toxicities. Therefore, cost-effective novel small molecule VEGFR-2 inhibitors may be an alternative to overcome these adverse effects. Here, a set of thiourea-based VEGFR-2 inhibitors were considered for a combined fragment-based QSAR technique, structure-based molecular docking followed by molecular dynamics simulation studies to acquire insights into the key structural attributes and the binding pattern of enzyme-ligand interactions. Noticeably, amine-substituted quinazoline phenyl ring and a higher number of nitrogen atoms, and the hydrazide function in the molecular structure are crucial for VEGFR-2 inhibition whereas methoxy groups are detrimental to VEGFR-2 inhibition. The MD simulation study of sorafenib and thiourea derivatives explored the significance of urea and thiourea moiety binding at VEGFR-2 active site that can be utilized further in the future to design molecules for greater binding stability and better VEGFR-2 selectivity. Therefore, such findings can be beneficial for the development of newer VEGFR-2 inhibitors for further refinement to acquire better therapeutic efficacy.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Suvankar Banerjee
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - Shristi Kejriwal
- Indian Institute of Science Education and Research (IISER) Kolkata, Nadia, West Bengal, India
| | - Balaram Ghosh
- Epigenetic Research Laboratory, Department of Pharmacy, Birla Institute of Technology and Science-Pilani, Hyderabad Campus, Shamirpet, Hyderabad, India
| | - Goverdhan Lanka
- Epigenetic Research Laboratory, Department of Pharmacy, Birla Institute of Technology and Science-Pilani, Hyderabad Campus, Shamirpet, Hyderabad, India
| | - Tarun Jha
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - Nilanjan Adhikari
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
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7
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Torres F, Stadler G, Kwiatkowski W, Orts J. A Benchmark Study of Protein-Fragment Complex Structure Calculations with NMR 2. Int J Mol Sci 2023; 24:14329. [PMID: 37762631 PMCID: PMC10531959 DOI: 10.3390/ijms241814329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 09/05/2023] [Accepted: 09/07/2023] [Indexed: 09/29/2023] Open
Abstract
Protein-fragment complex structures are particularly sought after in medicinal chemistry to rationally design lead molecules. These structures are usually derived using X-ray crystallography, but the failure rate is non-neglectable. NMR is a possible alternative for the calculation of weakly interacting complexes. Nevertheless, the time-consuming protein signal assignment step remains a barrier to its routine application. NMR Molecular Replacement (NMR2) is a versatile and rapid method that enables the elucidation of a protein-ligand complex structure. It has been successfully applied to peptides, drug-like molecules, and more recently to fragments. Due to the small size of the fragments, ca < 300 Da, solving the structures of the protein-fragment complexes is particularly challenging. Here, we present the expected performances of NMR2 when applied to protein-fragment complexes. The NMR2 approach has been benchmarked with the SERAPhic fragment library to identify the technical challenges in protein-fragment NMR structure calculation. A straightforward strategy is proposed to increase the method's success rate further. The presented work confirms that NMR2 is an alternative method to X-ray crystallography for solving protein-fragment complex structures.
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Affiliation(s)
- Felix Torres
- Institute of Molecular Physical Science, Swiss Federal Institute of Technology, ETH-Hönggerberg, 8093 Zurich, Switzerland (G.S.); (W.K.)
| | - Gabriela Stadler
- Institute of Molecular Physical Science, Swiss Federal Institute of Technology, ETH-Hönggerberg, 8093 Zurich, Switzerland (G.S.); (W.K.)
| | - Witek Kwiatkowski
- Institute of Molecular Physical Science, Swiss Federal Institute of Technology, ETH-Hönggerberg, 8093 Zurich, Switzerland (G.S.); (W.K.)
| | - Julien Orts
- Department of Pharmaceutical Sciences, Faculty of Life Sciences, University of Vienna, Josef-Holaubek-Platz 2, 1090 Vienna, Austria
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8
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Michaelides IN, Collie GW. E3 Ligases Meet Their Match: Fragment-Based Approaches to Discover New E3 Ligands and to Unravel E3 Biology. J Med Chem 2023; 66:3173-3194. [PMID: 36821822 PMCID: PMC10009759 DOI: 10.1021/acs.jmedchem.2c01882] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Indexed: 02/25/2023]
Abstract
Ubiquitination is a key post-translational modification of proteins, affecting the regulation of multiple cellular processes. Cells are equipped with over 600 ubiquitin orchestrators, called E3 ubiquitin ligases, responsible for directing the covalent attachment of ubiquitin to substrate proteins. Due to their regulatory role in cells, significant efforts have been made to discover ligands for E3 ligases. The recent emergence of the proteolysis targeting chimera (PROTAC) and molecular glue degrader (MGD) modalities has further increased interest in E3 ligases as drug targets. This perspective focuses on how fragment based lead discovery (FBLD) methods have been used to discover new ligands for this important target class. In some cases these efforts have led to clinical candidates; in others, they have provided tools for deepening our understanding of E3 ligase biology. Recently, FBLD-derived ligands have inspired the design of PROTACs that are able to artificially modulate protein levels in cells.
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Affiliation(s)
- Iacovos N. Michaelides
- Discovery Sciences, BioPharmaceuticals
R&D, AstraZeneca, Cambridge, CB4 0WG, United
Kingdom
| | - Gavin W. Collie
- Discovery Sciences, BioPharmaceuticals
R&D, AstraZeneca, Cambridge, CB4 0WG, United
Kingdom
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9
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Szwabowski GL, Baker DL, Parrill AL. Application of computational methods for class A GPCR Ligand discovery. J Mol Graph Model 2023; 121:108434. [PMID: 36841204 DOI: 10.1016/j.jmgm.2023.108434] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 02/11/2023] [Accepted: 02/13/2023] [Indexed: 02/22/2023]
Abstract
G protein-coupled receptors (GPCR) are integral membrane proteins of considerable interest as targets for drug development due to their role in transmitting cellular signals in a multitude of biological processes. Of the six classes categorizing GPCR (A, B, C, D, E, and F), class A contains the largest number of therapeutically relevant GPCR. Despite their importance as drug targets, many challenges exist for the discovery of novel class A GPCR ligands serving as drug precursors. Though knowledge of the structural and functional characteristics of GPCR has grown significantly over the past 20 years, a large portion of GPCR lack reported, experimentally determined structures. Furthermore, many GPCR have no known endogenous and/or synthetic ligands, limiting further exploration of their biochemical, cellular, and physiological roles. While many successes in GPCR ligand discovery have resulted from experimental high-throughput screening, computational methods have played an increasingly important role in GPCR ligand identification in the past decade. Here we discuss computational techniques applied to GPCR ligand discovery. This review summarizes class A GPCR structure/function and provides an overview of many obstacles currently faced in GPCR ligand discovery. Furthermore, we discuss applications and recent successes of computational techniques used to predict GPCR structure as well as present a summary of ligand- and structure-based methods used to identify potential GPCR ligands. Finally, we discuss computational hit list generation and refinement and provide comprehensive workflows for GPCR ligand identification.
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Affiliation(s)
| | - Daniel L Baker
- Department of Chemistry, The University of Memphis, Memphis, TN, 38152, USA
| | - Abby L Parrill
- Department of Chemistry, The University of Memphis, Memphis, TN, 38152, USA.
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10
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Henriquez-Figuereo A, Morán-Serradilla C, Angulo-Elizari E, Sanmartín C, Plano D. Small molecules containing chalcogen elements (S, Se, Te) as new warhead to fight neglected tropical diseases. Eur J Med Chem 2023; 246:115002. [PMID: 36493616 DOI: 10.1016/j.ejmech.2022.115002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 11/21/2022] [Accepted: 12/01/2022] [Indexed: 12/13/2022]
Abstract
Neglected tropical diseases (NTDs) encompass a group of infectious diseases with a protozoan etiology, high incidence, and prevalence in developing countries. As a result, economic factors constitute one of the main obstacles to their management. Endemic countries have high levels of poverty, deprivation and marginalization which affect patients and limit their access to proper medical care. As a matter of fact, statistics remain uncollected in some affected areas due to non-reporting cases. World Health Organization and other organizations proposed a plan for the eradication and control of the vector, although many of these plans were halted by the COVID-19 pandemic. Despite of the available drugs to treat these pathologies, it exists a lack of effectiveness against several parasite strains. Treatment protocols for diseases such as American trypanosomiasis (Chagas disease), leishmaniasis, and human African trypanosomiasis (HAT) have not achieved the desired results. Unfortunately, these drugs present limitations such as side effects, toxicity, teratogenicity, renal, and hepatic impairment, as well as high costs that have hindered the control and eradication of these diseases. This review focuses on the analysis of a collection of scientific shreds of evidence with the aim of identifying novel chalcogen-derived molecules with biological activity against Chagas disease, leishmaniasis and HAT. Compounds illustrated in each figure share the distinction of containing at least one chalcogen element. Sulfur (S), selenium (Se), and tellurium (Te) have been grouped and analyzed in accordance with their design strategy, chemical synthesis process and biological activity. After an exhaustive revision of the related literature on S, Se, and Te compounds, 183 compounds presenting excellent biological performance were gathered against the different causative agents of CD, leishmaniasis and HAT.
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Affiliation(s)
- Andreina Henriquez-Figuereo
- University of Navarra, School of Pharmacy and Nutrition, Department of Pharmaceutical Technology and Chemistry, Irunlarrea 1, 31008, Pamplona, Spain; Institute of Tropical Health, University of Navarra, Irunlarrea 1, 31008, Pamplona, Spain.
| | - Cristina Morán-Serradilla
- University of Navarra, School of Pharmacy and Nutrition, Department of Pharmaceutical Technology and Chemistry, Irunlarrea 1, 31008, Pamplona, Spain
| | - Eduardo Angulo-Elizari
- University of Navarra, School of Pharmacy and Nutrition, Department of Pharmaceutical Technology and Chemistry, Irunlarrea 1, 31008, Pamplona, Spain
| | - Carmen Sanmartín
- University of Navarra, School of Pharmacy and Nutrition, Department of Pharmaceutical Technology and Chemistry, Irunlarrea 1, 31008, Pamplona, Spain; Institute of Tropical Health, University of Navarra, Irunlarrea 1, 31008, Pamplona, Spain.
| | - Daniel Plano
- University of Navarra, School of Pharmacy and Nutrition, Department of Pharmaceutical Technology and Chemistry, Irunlarrea 1, 31008, Pamplona, Spain; Institute of Tropical Health, University of Navarra, Irunlarrea 1, 31008, Pamplona, Spain.
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11
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Moinul M, Khatun S, Amin SA, Jha T, Gayen S. Recent trends in fragment-based anticancer drug design strategies against different targets: A mini-review. Biochem Pharmacol 2022; 206:115301. [DOI: 10.1016/j.bcp.2022.115301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 10/07/2022] [Accepted: 10/10/2022] [Indexed: 11/02/2022]
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12
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Wang D, Deng H, Zhang T, Tian F, Wei D. Open access databases available for the pesticide lead discovery. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2022; 188:105267. [PMID: 36464372 DOI: 10.1016/j.pestbp.2022.105267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 10/04/2022] [Accepted: 10/11/2022] [Indexed: 06/17/2023]
Abstract
Pesticide research is a multi-disciplinary collaborative study, and big data analysis based on integrating information from databases benefits decision-making in pesticide research. In the last 40 years, dozens of pesticide-related databases have been built up to describe their biological activities, toxicity, modes of action, and environmental risks, etc. However, these data are scattered and overlapping in different databases in multiple inconsistent formats, which is not convenient for information analysis and comparison. In this study, the content of 26 open access databases related to pesticide research was illustrated according to the information provided for the ligand-based drug design (LBDD) and receptor-based (or structure-based drug design, SBDD), and was summarized into three categories:1) the correspondence between the chemical structures and functional properties (biological activity, resistance, toxicity, environmental adaptation); 2) action mode study (target identification, target structures, and biological pathways); 3) computational servers for pesticide design. To our knowledge, this is the first review about the open access databases for pesticide research. The data classification could facilitate the information accessibility for pesticide research, and speed up the decision-making process in pesticide discovery.
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Affiliation(s)
- Daozhong Wang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; Interdisciplinary Sciences Institute, Huazhong Agricultural University, Wuhan 430070, China; College of Veterinary Medicine, National Reference Laboratory of Veterinary Drug Residues (HZAU) and MAO Key Laboratory for Detection of Veterinary Drug Residues, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; Shenzhen Institute of Nutrition and Health,Huazhong Agricultural University, Shenzhen 518000, China; Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Hua Deng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China
| | - Tao Zhang
- College of Science, Huazhong Agricultural University, Wuhan 430070, China
| | - Fang Tian
- College of Informatics, Huazhong Agricultural University, Wuhan 430070, China.
| | - Dengguo Wei
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; Interdisciplinary Sciences Institute, Huazhong Agricultural University, Wuhan 430070, China; College of Veterinary Medicine, National Reference Laboratory of Veterinary Drug Residues (HZAU) and MAO Key Laboratory for Detection of Veterinary Drug Residues, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; Shenzhen Institute of Nutrition and Health,Huazhong Agricultural University, Shenzhen 518000, China; Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China.
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13
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Forces Driving a Magic Bullet to Its Target: Revisiting the Role of Thermodynamics in Drug Design, Development, and Optimization. Life (Basel) 2022; 12:life12091438. [PMID: 36143474 PMCID: PMC9504344 DOI: 10.3390/life12091438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 09/02/2022] [Accepted: 09/03/2022] [Indexed: 11/27/2022] Open
Abstract
Drug discovery strategies have advanced significantly towards prioritizing target selectivity to achieve the longstanding goal of identifying “magic bullets” amongst thousands of chemical molecules screened for therapeutic efficacy. A myriad of emerging and existing health threats, including the SARS-CoV-2 pandemic, alarming increase in bacterial resistance, and potentially fatal chronic ailments, such as cancer, cardiovascular disease, and neurodegeneration, have incentivized the discovery of novel therapeutics in treatment regimens. The design, development, and optimization of lead compounds represent an arduous and time-consuming process that necessitates the assessment of specific criteria and metrics derived via multidisciplinary approaches incorporating functional, structural, and energetic properties. The present review focuses on specific methodologies and technologies aimed at advancing drug development with particular emphasis on the role of thermodynamics in elucidating the underlying forces governing ligand–target interaction selectivity and specificity. In the pursuit of novel therapeutics, isothermal titration calorimetry (ITC) has been utilized extensively over the past two decades to bolster drug discovery efforts, yielding information-rich thermodynamic binding signatures. A wealth of studies recognizes the need for mining thermodynamic databases to critically examine and evaluate prospective drug candidates on the basis of available metrics. The ultimate power and utility of thermodynamics within drug discovery strategies reside in the characterization and comparison of intrinsic binding signatures that facilitate the elucidation of structural–energetic correlations which assist in lead compound identification and optimization to improve overall therapeutic efficacy.
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Togre NS, Vargas AM, Bhargavi G, Mallakuntla MK, Tiwari S. Fragment-Based Drug Discovery against Mycobacteria: The Success and Challenges. Int J Mol Sci 2022; 23:ijms231810669. [PMID: 36142582 PMCID: PMC9500838 DOI: 10.3390/ijms231810669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 09/10/2022] [Accepted: 09/10/2022] [Indexed: 11/29/2022] Open
Abstract
The emergence of drug-resistant mycobacteria, including Mycobacterium tuberculosis (Mtb) and non-tuberculous mycobacteria (NTM), poses an increasing global threat that urgently demands the development of new potent anti-mycobacterial drugs. One of the approaches toward the identification of new drugs is fragment-based drug discovery (FBDD), which is the most ingenious among other drug discovery models, such as structure-based drug design (SBDD) and high-throughput screening. Specialized techniques, such as X-ray crystallography, nuclear magnetic resonance spectroscopy, and many others, are part of the drug discovery approach to combat the Mtb and NTM global menaces. Moreover, the primary drawbacks of traditional methods, such as the limited measurement of biomolecular toxicity and uncertain bioavailability evaluation, are successfully overcome by the FBDD approach. The current review focuses on the recognition of fragment-based drug discovery as a popular approach using virtual, computational, and biophysical methods to identify potent fragment molecules. FBDD focuses on designing optimal inhibitors against potential therapeutic targets of NTM and Mtb (PurC, ArgB, MmpL3, and TrmD). Additionally, we have elaborated on the challenges associated with the FBDD approach in the identification and development of novel compounds. Insights into the applications and overcoming the challenges of FBDD approaches will aid in the identification of potential therapeutic compounds to treat drug-sensitive and drug-resistant NTMs and Mtb infections.
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15
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Martins V, Fazal L, Oganesian A, Shah A, Stow J, Walton H, Wilsher N. A commentary on the use of pharmacoenhancers in the pharmaceutical industry and the implication for DMPK drug discovery strategies. Xenobiotica 2022; 52:786-796. [PMID: 36537234 DOI: 10.1080/00498254.2022.2130838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Paxlovid, a drug combining nirmatrelvir and ritonavir, was designed for the treatment of COVID-19 and its rapid development has led to emergency use approval by the FDA to reduce the impact of COVID-19 infection on patients.In order to overcome potentially suboptimal therapeutic exposures, nirmatrelvir is dosed in combination with ritonavir to boost the pharmacokinetics of the active product.Here we consider examples of drugs co-administered with pharmacoenhancers.Pharmacoenhancers have been adopted for multiple purposes such as ensuring therapeutic exposure of the active product, reducing formation of toxic metabolites, changing the route of administration, and increasing the cost-effectiveness of a therapy.We weigh the benefits and risks of this approach, examining the impact of technology developments on drug design and how enhanced integration between cross-discipline teams can improve the outcome of drug discovery.
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16
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Wang ZZ, Wang MS, Wang F, Shi XX, Huang W, Hao GF, Yang GF. Exploring the kinase-inhibitor fragment interaction space facilitates the discovery of kinase inhibitor overcoming resistance by mutations. Brief Bioinform 2022; 23:6596988. [PMID: 35649390 DOI: 10.1093/bib/bbac203] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 04/07/2022] [Accepted: 05/03/2022] [Indexed: 11/13/2022] Open
Abstract
Protein kinases play crucial roles in many cellular signaling processes, making them become important targets for drug discovery. But drug resistance mediated by mutation puts a barrier to the therapeutic effect of kinase inhibitors. Fragment-based drug discovery has been successfully applied to overcome such resistance. However, the complicate kinase-inhibitor fragment interaction and fragment-to-lead process seriously limit the efficiency of kinase inhibitor discovery against resistance caused by mutation. Here, we constructed a comprehensive web platform KinaFrag for the fragment-based kinase inhibitor discovery to overcome resistance. The kinase-inhibitor fragment space was investigated from 7783 crystal kinase-inhibitor fragment complexes, and the structural requirements of kinase subpockets were analyzed. The core fragment-based virtual screening workflow towards specific subpockets was developed to generate new kinase inhibitors. A series of tropomyosin receptor kinase (TRK) inhibitors were designed, and the most potent compound YT9 exhibits up to 70-fold activity improvement than marketed drugs larotrectinib and selitrectinib against G595R, G667C and F589L mutations of TRKA. YT9 shows promising antiproliferative against tumor cells in vitro and effectively inhibits tumor growth in vivo for wild type TRK and TRK mutants. Our results illustrate the great potential of KinaFrag in the kinase inhibitor discovery to combat resistance mediated by mutation. KinaFrag is freely available at http://chemyang.ccnu.edu.cn/ccb/database/KinaFrag/.
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Affiliation(s)
- Zhi-Zheng Wang
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan, 430079, P. R. China
| | - Ming-Shu Wang
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan, 430079, P. R. China
| | - Fan Wang
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan, 430079, P. R. China
| | - Xing-Xing Shi
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan, 430079, P. R. China
| | - Wei Huang
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan, 430079, P. R. China
| | - Ge-Fei Hao
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan, 430079, P. R. China
| | - Guang-Fu Yang
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan, 430079, P. R. China
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17
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A fragment-based structural analysis of MMP-2 inhibitors in search of meaningful structural fragments. Comput Biol Med 2022; 144:105360. [DOI: 10.1016/j.compbiomed.2022.105360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 02/22/2022] [Accepted: 02/25/2022] [Indexed: 11/21/2022]
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18
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Farahani MD, França TCC, Alapour S, Shahout F, Boulon R, Iddir M, Maddalena M, Ayotte Y, Laplante SR. Jumping From Fragment To Drug Via Smart Scaffolds. ChemMedChem 2022; 17:e202200092. [PMID: 35298873 DOI: 10.1002/cmdc.202200092] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 03/16/2022] [Indexed: 11/08/2022]
Abstract
A focused drug repurposing approach is described where an FDA-approved drug is rationally selected for biological testing based on structural similarities to a fragment compound found to bind a target protein by an NMR screen. The approach is demonstrated by first screening a curated fragment library using 19F NMR to discover a quality binder to ACE2, the human receptor required for entry and infection by the SARS-CoV-2 virus. Based on this binder, a highly related scaffold was derived and used as a "smart scaffold" or template in a computer-aided finger-print search of a library of FDA-approved or marketed drugs. The most interesting structural match involved the drug vortioxetine which was then experimentally shown by NMR spectroscopy to bind directly to human ACE2. Also, an ELISA assay showed that the drug inhibits the interaction of human ACE2 to the SARS-CoV-2 receptor-binding-domain (RBD). Moreover, our cell-culture infectivity assay confirmed that vortioxetine is active against SARS-CoV-2 and inhibits viral replication. Thus, the use of "smart scaffolds" based on binders from fragment screens may have general utility for identifying candidates of FDA-approved or marketed drugs as a rapid repurposing strategy. Similar approaches can be envisioned for other fields involving small-molecule chemical applications.
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Affiliation(s)
- Majid D Farahani
- Institut national de la recherche scientifique, Armand-Frappier Santé Biotechnologie, 531 boulevard des Prairies, H7V1B7, Laval, CANADA
| | - Tanos C C França
- Institut national de la recherche scientifique, Armand-Frappier Santé Biotechnologie, 531 boulevard des Prairies, H7V1B7, Laval, CANADA
| | - Saba Alapour
- National Institute of Scientific Research: Institut national de la recherche scientifique, Armand-Frappier Santé Biotechnologie, 531 boulevard des Prairies, H7V1B7, Laval, CANADA
| | - Fatma Shahout
- National Institute of Scientific Research: Institut national de la recherche scientifique, Armand-Frappier Santé Biotechnologie, 531 boulevard des Prairies, H7V1B7, Laval, CANADA
| | - Richard Boulon
- National Institute of Scientific Research: Institut national de la recherche scientifique, Armand-Frappier Santé Biotechnologie, 531 boulevard des Prairies, H7V1B7, Laval, CANADA
| | - Mustapha Iddir
- National Institute of Scientific Research: Institut national de la recherche scientifique, Armand-Frappier Santé Biotechnologie, 531 boulevard des Prairies, H7V1B7, Laval, CANADA
| | - Michael Maddalena
- National Institute of Scientific Research: Institut national de la recherche scientifique, Armand-Frappier Santé Biotechnologie, 531 boulevard des Prairies, H7V1B7, Laval, CANADA
| | - Yann Ayotte
- National Institute of Scientific Research: Institut national de la recherche scientifique, Armand-Frappier Santé Biotechnologie, 531 boulevard des Prairies, H7V1B7, Laval, CANADA
| | - Steven R Laplante
- Institut national de la recherche scientifique, Armand-Frappier Santé Biotechnologie, 531, boulevard des Prairies, H7V 1B7, Canada, H7V1B7, Laval, CANADA
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19
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Brink A, Jacobs FJF, Helliwell JR. Trends in coordination of rhenium organometallic complexes in the Protein Data Bank. IUCRJ 2022; 9:180-193. [PMID: 35371500 PMCID: PMC8895017 DOI: 10.1107/s2052252522000665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 01/18/2022] [Indexed: 06/14/2023]
Abstract
Radiopharmaceutical development has similar overall characteristics to any biomedical drug development requiring a compound's stability, aqueous solubility and selectivity to a specific disease site. However, organometallic complexes containing 188/186Re or 99mTc involve a d-block transition-metal radioactive isotope and therefore bring additional factors such as metal oxidation states, isotope purity and half life into play. This topical review is focused on the development of radiopharmaceuticals containing the radioisotopes of rhenium and technetium and, therefore, on the occurrence of these organometallic complexes in protein structures in the Worldwide Protein Data Bank (wwPDB). The purpose of incorporating the group 7 transition metals of rhenium/technetium in the protein and the reasons for study by protein crystallography are described, as certain PDB studies were not aimed at drug development. Technetium is used as a medical diagnostic agent and involves the 99mTc isotope which decays to release gamma radiation, thereby employed for its use in gamma imaging. Due to the periodic relationship among group 7 transition metals, the coordination chemistry of rhenium is similar (but not identical) to that of technetium. The types of reactions the potential model radiopharmaceutical would prefer to partake in, and by extension knowing which proteins and biomolecules the compound would react with in vivo, are needed. Crystallography studies, both small molecule and macromolecular, are a key aspect in understanding chemical coordination. Analyses of bonding modes, coordination to particular residues and crystallization conditions are presented. In our Forward look as a concluding summary of this topical review, the question we ask is: what is the best way for this field to progress?
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Affiliation(s)
- Alice Brink
- Chemistry Department, University of the Free State, Nelson Mandela Drive, Bloemfontein, South Africa
- Department of Chemistry, The University of Manchester, Oxford Road, Manchester, United Kingdom
| | - Francois J. F. Jacobs
- Chemistry Department, University of the Free State, Nelson Mandela Drive, Bloemfontein, South Africa
| | - John R. Helliwell
- Department of Chemistry, The University of Manchester, Oxford Road, Manchester, United Kingdom
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20
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Sachdeo RA, Anthwal T, Nain S. Fragment based drug design. PHYSICAL SCIENCES REVIEWS 2022. [DOI: 10.1515/psr-2018-0162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
Rational approaches towards drug development have emerged as one of the most promising ways among the tedious conventional procedures with the aim of redefining the drug discovery process. The need of current medical system is demanding a much precise, faster and reliable approaches in parallel to faster growing technology for development of drugs with more intrinsic action and fewer side effects. Systematic and well-defined diagnostic studies have revealed the specific causes of disease and related targets for drug development. Designing a drug as per the specific target, studying it in-silico prior to its development has been proved as an added benefit to the studies. Many approaches like structure based drug design, fragment based drug design and ligand based drug design are been in practice for the drug discovery and development with the similar fundamental theory. Fragment based drug design utilizes a library of fragments designed specifically for the concerned target and these fragments are studied further before screening with virtual methods as well as with biophysical methods. The process follows a well-defined pathway which moulds a fragment into a perfect drug candidate. In this chapter we have tried to cover all the basic aspects of fragment based drug design and related technologies.
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Affiliation(s)
- Rahul Ashok Sachdeo
- Department of Pharmaceutical Chemistry , Government College of Pharmacy , Karad , Maharashtra , 415124 , India
| | - Tulika Anthwal
- Department of Pharmacy , Banasthali Vidyapith , Banasthali , Rajasthan , 304022 , India
| | - Sumitra Nain
- Department of Pharmacy , Banasthali Vidyapith , Banasthali , Rajasthan , 304022 , India
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21
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Jiang Y, Idikuda V, Chanda B. Preparation of Giant Escherichia coli spheroplasts for Electrophysiological Recordings. Bio Protoc 2021; 11:e4261. [PMID: 35087920 PMCID: PMC8720513 DOI: 10.21769/bioprotoc.4261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 09/27/2021] [Accepted: 10/05/2021] [Indexed: 07/07/2024] Open
Abstract
Prokaryotic ion channels have been instrumental in furthering our understanding of many fundamental aspects of ion channels' structure and function. However, characterizing the biophysical properties of a prokaryotic ion channel in a native membrane system using patch-clamp electrophysiology is technically challenging. Patch-clamp is regarded as a gold standard technique to study ion channel properties in both native and heterologous expression systems. The presence of a cell wall and the small size of bacterial cells makes it impossible to directly patch clamp using microelectrodes. Here, we describe a method for the preparation of giant E. coli spheroplasts in order to investigate the electrophysiological properties of bacterial cell membranes. Spheroplasts are formed by first inhibiting bacterial cell wall synthesis, followed by enzymatic digestion of the outer cell wall in the presence of a permeabilizing agent. This protocol can be used to characterize the function of any heterologous ion channels or ion transporters expressed in E. coli membranes.
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Affiliation(s)
- Yihao Jiang
- Department of Psychiatry of First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
- The MOE Frontier Research Center of Brain & Brain-machine Integration, Zhejiang University School of Brain Science and Brain Medicine, China
| | - Vinay Idikuda
- Department of Anesthesiology, Washington University School of Medicine, St. Louis, Missouri, USA
- Center for the Investigation of Membrane Excitability Diseases (CIMED)
| | - Baron Chanda
- Department of Anesthesiology, Washington University School of Medicine, St. Louis, Missouri, USA
- Center for the Investigation of Membrane Excitability Diseases (CIMED)
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22
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Adhikari N, Banerjee S, Baidya SK, Ghosh B, Jha T. Ligand-based quantitative structural assessments of SARS-CoV-2 3CL pro inhibitors: An analysis in light of structure-based multi-molecular modeling evidences. J Mol Struct 2021; 1251:132041. [PMID: 34866654 PMCID: PMC8627846 DOI: 10.1016/j.molstruc.2021.132041] [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: 10/02/2021] [Revised: 11/10/2021] [Accepted: 11/26/2021] [Indexed: 12/11/2022]
Abstract
Due to COVID-19, the whole world is undergoing a devastating situation, but treatment with no such drug candidates still has been established exclusively. In that context, 69 diverse chemicals with potential SARS-CoV-2 3CLpro inhibitory property were taken into consideration for building different internally and externally validated linear (SW-MLR and GA-MLR), non-linear (ANN and SVM) QSAR, and HQSAR models to identify important structural and physicochemical characters required for SARS-CoV-2 3CLpro inhibition. Importantly, 2-oxopyrrolidinyl methyl and benzylester functions, and methylene (hydroxy) sulphonic acid warhead group, were crucial for retaining higher SARS-CoV-2 3CLpro inhibition. These GA-MLR and HQSAR models were also applied to predict some already repurposed drugs. As per the GA-MLR model, curcumin, ribavirin, saquinavir, sepimostat, and remdesivir were found to be the potent ones, whereas according to the HQSAR model, lurasidone, saquinavir, lopinavir, elbasvir, and paritaprevir were the highly effective SARS-CoV-2 3CLpro inhibitors. The binding modes of those repurposed drugs were also justified by the molecular docking, molecular dynamics (MD) simulation, and binding energy calculations conducted by several groups of researchers. This current work, therefore, may be able to find out important structural parameters to accelerate the COVID-19 drug discovery processes in the future.
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Affiliation(s)
- Nilanjan Adhikari
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata 700032, India
| | - Suvankar Banerjee
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata 700032, India
| | - Sandip Kumar Baidya
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata 700032, India
| | - Balaram Ghosh
- Epigenetic Research Laboratory, Birla Institute of Technology and Science-Pilani Hyderabad Campus, Shamirpet, Hyderabad, India, 500078
| | - Tarun Jha
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata 700032, India
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23
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Li R, Yao L, Wang YB, Zhu JY, Zhang L, Fu JY, Zhang CB, Zhao L. Divergent Metal-Free [4 + 2] Cascade Reaction of 1-Indanylidenemalononitrile with 3-Benzylidenebenzofuran-2(3 H)-one: Access to Spiro-dihydrofluorene-benzofuranone and Axially Chiral Fluorenylamine-phenol Derivatives. Org Lett 2021; 23:5611-5615. [PMID: 34240601 DOI: 10.1021/acs.orglett.1c01510] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
An efficient cascade reaction of 1-indanylidenemalononitrile with 3-benzylidenebenzofuran-2(3H)-one divergently promoted by DABCO or chiral organocatalyst was developed under mild reaction conditions, and various spiro-dihydrofluorene-benzofuranones were produced in gratifying results, respectively. It is worth noting that both the spiro and axially chiral products can be obtained by tuning the reaction conditions. The mechanism of the transformation was also studied by quantum chemical calculations.
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Affiliation(s)
- Ran Li
- Institute of Functional Organic Molecular Engineering, College of Chemistry and Chemical Engineering, Henan University, Kaifeng 475004, China
| | - Lei Yao
- Institute of Advanced Synthesis, School of Chemistry and Molecular Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Yan-Bo Wang
- Institute of Functional Organic Molecular Engineering, College of Chemistry and Chemical Engineering, Henan University, Kaifeng 475004, China
| | - Jun-Yan Zhu
- Institute of Functional Organic Molecular Engineering, College of Chemistry and Chemical Engineering, Henan University, Kaifeng 475004, China
| | - Lixiong Zhang
- College of Chemical Engineering, State Key Laboratory of Materials-oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Ji-Ya Fu
- Institute of Functional Organic Molecular Engineering, College of Chemistry and Chemical Engineering, Henan University, Kaifeng 475004, China
| | - Chuan-Bao Zhang
- School of Pharmacy, Zhengzhou Railway Vocational & Technical College, Zhengzhou 450052, China
| | - Lili Zhao
- Institute of Advanced Synthesis, School of Chemistry and Molecular Engineering, Nanjing Tech University, Nanjing 211816, China
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24
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Chitsike L, Duerksen-Hughes PJ. PPI Modulators of E6 as Potential Targeted Therapeutics for Cervical Cancer: Progress and Challenges in Targeting E6. Molecules 2021; 26:molecules26103004. [PMID: 34070144 PMCID: PMC8158384 DOI: 10.3390/molecules26103004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 05/05/2021] [Accepted: 05/15/2021] [Indexed: 12/13/2022] Open
Abstract
Advanced cervical cancer is primarily managed using cytotoxic therapies, despite evidence of limited efficacy and known toxicity. There is a current lack of alternative therapeutics to treat the disease more effectively. As such, there have been more research endeavors to develop targeted therapies directed at oncogenic host cellular targets over the past 4 decades, but thus far, only marginal gains in survival have been realized. The E6 oncoprotein, a protein of human papillomavirus origin that functionally inactivates various cellular antitumor proteins through protein–protein interactions (PPIs), represents an alternative target and intriguing opportunity to identify novel and potentially effective therapies to treat cervical cancer. Published research has reported a number of peptide and small-molecule modulators targeting the PPIs of E6 in various cell-based models. However, the reported compounds have rarely been well characterized in animal or human subjects. This indicates that while notable progress has been made in targeting E6, more extensive research is needed to accelerate the optimization of leads. In this review, we summarize the current knowledge and understanding of specific E6 PPI inhibition, the progress and challenges being faced, and potential approaches that can be utilized to identify novel and potent PPI inhibitors for cervical cancer treatment.
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25
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Wang ZZ, Shi XX, Huang GY, Hao GF, Yang GF. Fragment-based drug design facilitates selective kinase inhibitor discovery. Trends Pharmacol Sci 2021; 42:551-565. [PMID: 33958239 DOI: 10.1016/j.tips.2021.04.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 03/30/2021] [Accepted: 04/07/2021] [Indexed: 12/16/2022]
Abstract
Protein kinases (PKs) are important drug targets, but kinases selectivity poses a challenge to protein kinase inhibitors (PKIs) design. Fragment-based drug discovery (FBDD) has achieved great success in the discovery of highly specific PKIs. It makes full use of kinase-fragment interaction in target kinase subpockets to obtain promising selectivity. However, it's difficult to understand the complicated kinase-fragment interaction space, and systemic discussion of these interactions is still lacking. Herein, we introduce the advantages of the FBDD strategy in PKIs design. Key features of the selectivity of kinase-fragment interactions are summarized and analyzed. Some promising PKIs are introduced as case studies to help understand the fragment-to-lead (F2L) optimization process. Novel strategies and technologies for FBDD in PKIs discovery are also outlooked.
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Affiliation(s)
- Zhi-Zheng Wang
- Key Laboratory of Pesticide and Chemical Biology, Ministry of Education, College of Chemistry, International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan, 430079, China; International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan 430079, China
| | - Xing-Xing Shi
- Key Laboratory of Pesticide and Chemical Biology, Ministry of Education, College of Chemistry, International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan, 430079, China; International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan 430079, China
| | - Guang-Yi Huang
- Key Laboratory of Pesticide and Chemical Biology, Ministry of Education, College of Chemistry, International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan, 430079, China; International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan 430079, China
| | - Ge-Fei Hao
- Key Laboratory of Pesticide and Chemical Biology, Ministry of Education, College of Chemistry, International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan, 430079, China; International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan 430079, China; State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for Research and Development of Fine Chemicals, Guizhou University, Guiyang 550025, China.
| | - Guang-Fu Yang
- Key Laboratory of Pesticide and Chemical Biology, Ministry of Education, College of Chemistry, International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan, 430079, China; International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan 430079, China
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26
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Amin SA, Banerjee S, Gayen S, Jha T. Protease targeted COVID-19 drug discovery: What we have learned from the past SARS-CoV inhibitors? Eur J Med Chem 2021; 215:113294. [PMID: 33618158 PMCID: PMC7880840 DOI: 10.1016/j.ejmech.2021.113294] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 02/06/2021] [Accepted: 02/08/2021] [Indexed: 12/25/2022]
Abstract
The fascinating similarity between the SARS-CoV and SARS-CoV-2, inspires scientific community to investigate deeper into the SARS-CoV proteases such as main protease (Mpro) and papain-like protease (PLpro) and their inhibitors for the discovery of SARS-CoV-2 protease inhibitors. Because of the similarity in the proteases of these two corona viruses, there is a greater chance for the previous SARS-CoV Mpro and PLpro inhibitors to provide effective results against SARS-CoV-2. In this context, the molecular fragments from the SARS-CoV protease inhibitors through the fragment-based drug design and discovery technique can be useful guidance for COVID-19 drug discovery. Here, we have focused on the structure-activity relationship studies of previous SARS-CoV protease inhibitors and discussed about crucial fragments generated from previous SARS-CoV protease inhibitors important for the lead optimization of SARS-CoV-2 protease inhibitors. This study surely offers different strategic options of lead optimization to the medicinal chemists to discover effective anti-viral agent against the devastating disease, COVID-19.
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Affiliation(s)
- Sk Abdul Amin
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, P. O. Box 17020, Jadavpur University, Kolkata, 700032, India
| | - Suvankar Banerjee
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, P. O. Box 17020, Jadavpur University, Kolkata, 700032, India
| | - Shovanlal Gayen
- Laboratory of Drug Design and Discovery, Department of Pharmaceutical Sciences, Dr. Harisingh Gour University, Sagar, MP, India.
| | - Tarun Jha
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, P. O. Box 17020, Jadavpur University, Kolkata, 700032, India.
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27
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Wakefield AE, Yueh C, Beglov D, Castilho MS, Kozakov D, Keserű GM, Whitty A, Vajda S. Benchmark Sets for Binding Hot Spot Identification in Fragment-Based Ligand Discovery. J Chem Inf Model 2020; 60:6612-6623. [PMID: 33291870 DOI: 10.1021/acs.jcim.0c00877] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Binding hot spots are regions of proteins that, due to their potentially high contribution to the binding free energy, have high propensity to bind small molecules. We present benchmark sets for testing computational methods for the identification of binding hot spots with emphasis on fragment-based ligand discovery. Each protein structure in the set binds a fragment, which is extended into larger ligands in other structures without substantial change in its binding mode. Structures of the same proteins without any bound ligand are also collected to form an unbound benchmark. We also discuss a set developed by Astex Pharmaceuticals for the validation of hot and warm spots for fragment binding. The set is based on the assumption that a fragment that occurs in diverse ligands in the same subpocket identifies a binding hot spot. Since this set includes only ligand-bound proteins, we added a set with unbound structures. All four sets were tested using FTMap, a computational analogue of fragment screening experiments to form a baseline for testing other prediction methods, and differences among the sets are discussed.
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Affiliation(s)
- Amanda E Wakefield
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States.,Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - Christine Yueh
- Acpharis Inc., Holliston, Massachusetts 01746, United States
| | - Dmitri Beglov
- Acpharis Inc., Holliston, Massachusetts 01746, United States
| | - Marcelo S Castilho
- Faculdade de Farmácia da Universidade Federal da Bahia, Bahia, Salvador, BA 40170-115, Brazil
| | - Dima Kozakov
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York 11794, United States.,Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York 11794, United States
| | - György M Keserű
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar tudósok krt. 2, 1117 Budapest, Hungary
| | - Adrian Whitty
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - Sandor Vajda
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States.,Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
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28
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St Denis JD, Hall RJ, Murray CW, Heightman TD, Rees DC. Fragment-based drug discovery: opportunities for organic synthesis. RSC Med Chem 2020; 12:321-329. [PMID: 34041484 PMCID: PMC8130625 DOI: 10.1039/d0md00375a] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 12/01/2020] [Indexed: 12/28/2022] Open
Abstract
This Review describes the increasing demand for organic synthesis to facilitate fragment-based drug discovery (FBDD), focusing on polar, unprotected fragments. In FBDD, X-ray crystal structures are used to design target molecules for synthesis with new groups added onto a fragment via specific growth vectors. This requires challenging synthesis which slows down drug discovery, and some fragments are not progressed into optimisation due to synthetic intractability. We have evaluated the output from Astex's fragment screenings for a number of programs, including urokinase-type plasminogen activator, hematopoietic prostaglandin D2 synthase, and hepatitis C virus NS3 protease-helicase, and identified fragments that were not elaborated due, in part, to a lack of commercially available analogues and/or suitable synthetic methodology. This represents an opportunity for the development of new synthetic research to enable rapid access to novel chemical space and fragment optimisation.
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Affiliation(s)
| | - Richard J Hall
- Astex Pharmaceuticals 436 Cambridge Science Park Cambridge CB4 0QA UK
| | | | - Tom D Heightman
- Astex Pharmaceuticals 436 Cambridge Science Park Cambridge CB4 0QA UK
| | - David C Rees
- Astex Pharmaceuticals 436 Cambridge Science Park Cambridge CB4 0QA UK
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29
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Jin CF, Wang ZZ, Chen KZ, Xu TF, Hao GF. Computational Fragment-Based Design Facilitates Discovery of Potent and Selective Monoamine Oxidase-B (MAO-B) Inhibitor. J Med Chem 2020; 63:15021-15036. [PMID: 33210537 DOI: 10.1021/acs.jmedchem.0c01663] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Parkinson's disease (PD) is one of the most common age-related neurodegenerative diseases. Inhibition of monoamine oxidase-B (MAO-B), which is mainly found in the glial cells of the brain, may lead to an elevated level of dopamine (DA) in patients. MAO-B inhibitors have been used extensively for patients with PD. However, the discovery of the selective MAO-B inhibitor is still a challenge. In this study, a computational strategy was designed for the rapid discovery of selective MAO-B inhibitors. A series of (S)-2-(benzylamino)propanamide derivatives were designed. In vitro biological evaluations revealed that (S)-1-(4-((3-fluorobenzyl)oxy)benzyl)azetidine-2-carboxamide (C3) was more potent and selective than safinamide, a promising drug for regulating MAO-B. Further studies revealed that the selectivity mechanism of C3 was due to the steric clash caused by the residue difference of Phe208 (MAO-A) and Ile199 (MAO-B). Animal studies showed that compound C3 could inhibit cerebral MAO-B activity and alleviate 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP)-induced dopaminergic neuronal loss.
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Affiliation(s)
- Chuan-Fei Jin
- Sunshine Lake Pharma Co. Ltd., Shenzhen 518000; HEC Pharm Group, HEC Research and Development Center, Dongguan 523871, P. R. China
| | - Zhi-Zheng Wang
- Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China
| | - Kang-Zhi Chen
- Sunshine Lake Pharma Co. Ltd., Shenzhen 518000; HEC Pharm Group, HEC Research and Development Center, Dongguan 523871, P. R. China
| | - Teng-Fei Xu
- Sunshine Lake Pharma Co. Ltd., Shenzhen 518000; HEC Pharm Group, HEC Research and Development Center, Dongguan 523871, P. R. China
| | - Ge-Fei Hao
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Research and Development Center for Fine Chemicals, Guizhou University, Guiyang 550025, P. R. China
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30
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An Y, Dong Y, Liu M, Han J, Zhao L, Sun B. Novel naphthylamide derivatives as dual-target antifungal inhibitors: Design, synthesis and biological evaluation. Eur J Med Chem 2020; 210:112991. [PMID: 33183866 DOI: 10.1016/j.ejmech.2020.112991] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 10/15/2020] [Accepted: 10/31/2020] [Indexed: 12/12/2022]
Abstract
Fungal infections have become a serious medical problem due to the high infection rate and the frequent emergence of drug resistance. Squalene epoxidase (SE) and 14α-demethylase (CYP51) are considered as the important antifungal targets, they can show the synergistic effect on antifungal therapy. In the study, a series of active fragments were screened through the method of De Novo Link, and these active fragments with the higher Ludi_Scores were selected, which can show the obvious binding ability with the dual targets (SE, CYP51). Subsequently, three series of target compounds with naphthyl amide scaffolds were constructed by connecting these core fragments, and their structures were synthesized. Most of compounds showed the antifungal activity in the treatment of pathogenic fungi. It was worth noting that compounds 10b-5 and 17a-2 with the excellent broad-spectrum antifungal properties also exhibited the obvious antifungal effects against drug-resistant fungi. Preliminary mechanism study has proved these target compounds can block the biosynthesis of ergosterol by inhibiting the activity of dual targets (SE, CYP51). Furthermore, target compounds 10-5 and 17a-2 with low toxicity side effects also demonstrated the excellent pharmacological effects in vivo. The molecular docking and ADMET prediction were performed, which can guide the optimization of subsequent lead compounds.
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Affiliation(s)
- Yunfei An
- Institute of BioPharmaceutical Research, Liaocheng University, 1 Hunan Road, Liaocheng, 252000, PR China
| | - Yue Dong
- Institute of BioPharmaceutical Research, Liaocheng University, 1 Hunan Road, Liaocheng, 252000, PR China
| | - Min Liu
- Institute of BioPharmaceutical Research, Liaocheng University, 1 Hunan Road, Liaocheng, 252000, PR China
| | - Jun Han
- Institute of BioPharmaceutical Research, Liaocheng University, 1 Hunan Road, Liaocheng, 252000, PR China
| | - Liyu Zhao
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenhe District, Shenyang, 110016, PR China
| | - Bin Sun
- Institute of BioPharmaceutical Research, Liaocheng University, 1 Hunan Road, Liaocheng, 252000, PR China.
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31
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Sun B, Dong Y, An Y, Liu M, Han J, Zhao L, Liu X. Design, synthesis and bioactivity evaluation of novel arylalkene-amide derivatives as dual-target antifungal inhibitors. Eur J Med Chem 2020; 205:112645. [DOI: 10.1016/j.ejmech.2020.112645] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 06/19/2020] [Accepted: 07/05/2020] [Indexed: 01/07/2023]
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32
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Agarwal S, Smith M, De La Rosa I, Verba KA, Swartz P, Segura-Totten M, Mattos C. Development of a structure-analysis pipeline using multiple-solvent crystal structures of barrier-to-autointegration factor. Acta Crystallogr D Struct Biol 2020; 76:1001-1014. [DOI: 10.1107/s2059798320011341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 08/18/2020] [Indexed: 11/10/2022] Open
Abstract
The multiple-solvent crystal structure (MSCS) approach uses high concentrations of organic solvents to characterize the interactions and effects of solvents on proteins. Here, the method has been further developed and an MSCS data-handling pipeline is presented that uses the Detection of Related Solvent Positions (DRoP) program to improve data quality. DRoP is used to selectively model conserved water molecules, so that an advanced stage of structural refinement is reached quickly. This allows the placement of organic molecules more accurately and convergence on high-quality maps and structures. This pipeline was applied to the chromatin-associated protein barrier-to-autointegration factor (BAF), resulting in structural models with better than average statistics. DRoP and Phenix Structure Comparison were used to characterize the data sets and to identify a binding site that overlaps with the interaction site of BAF with emerin. The conserved water-mediated networks identified by DRoP suggested a mechanism by which water molecules are used to drive the binding of DNA. Normalized and differential B-factor analysis is shown to be a valuable tool to characterize the effects of specific solvents on defined regions of BAF. Specific solvents are identified that cause stabilization of functionally important regions of the protein. This work presents tools and a standardized approach for the analysis and comprehension of MSCS data sets.
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33
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Ghosh K, Bhardwaj B, Amin SA, Jha T, Gayen S. Identification of structural fingerprints for ABCG2 inhibition by using Monte Carlo optimization, Bayesian classification, and structural and physicochemical interpretation (SPCI) analysis. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2020; 31:439-455. [PMID: 32539470 DOI: 10.1080/1062936x.2020.1771769] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 05/17/2020] [Indexed: 06/11/2023]
Abstract
The human breast cancer resistance protein (BCRP), one of the members of the large ATP binding cassette (ABC) transporter superfamily, is crucial for resistance against chemotherapeutic agents. Currently, it has been emerged as one of the best biological targets for the designing of small molecule drugs capable of eliminating multidrug resistance in breast cancer. In order to gain insights into the relationship between the molecular structure of compounds and the ABCG2 inhibition, a multi-QSAR approach using different methods was performed on a dataset of 294 ABCG2 inhibitors with diverse scaffolds. The best models obtained by different chemometric methods have the following statistical characteristics: Monte Carlo Optimization-based QSAR (sensitivity = 0.905, specificity = 0.6255, accuracy = 0.756, and MCC = 0.545), Bayesian classification model (sensitivity = 0.735, specificity = 0.775, and concordance = 0.757); structural and physicochemical interpretation analysis-random forest method (balance accuracy = 0.750, sensitivity = 0.810, and specificity = 0.700). Additionally, structural fingerprints modulating the ABCG2 inhibitory properties were identified from the best models of each method and also validated with each other. The current modelling study is an attempt to get a deep insight into the different important structural fingerprints modulating ABCG2 inhibition.
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Affiliation(s)
- K Ghosh
- Laboratory of Drug Design and Discovery, Department of Pharmaceutical Sciences, Dr. H. S. Gour University , Sagar, India
| | - B Bhardwaj
- Laboratory of Drug Design and Discovery, Department of Pharmaceutical Sciences, Dr. H. S. Gour University , Sagar, India
| | - S A Amin
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University , Kolkata, India
| | - T Jha
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University , Kolkata, India
| | - S Gayen
- Laboratory of Drug Design and Discovery, Department of Pharmaceutical Sciences, Dr. H. S. Gour University , Sagar, India
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34
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Lanzarotti E, Defelipe LA, Marti MA, Turjanski AG. Aromatic clusters in protein-protein and protein-drug complexes. J Cheminform 2020; 12:30. [PMID: 33431014 PMCID: PMC7206889 DOI: 10.1186/s13321-020-00437-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 04/30/2020] [Indexed: 11/10/2022] Open
Abstract
Aromatic rings are important residues for biological interactions and appear to a large extent as part of protein-drug and protein-protein interactions. They are relevant for both protein stability and molecular recognition processes due to their natural occurrence in aromatic aminoacids (Trp, Phe, Tyr and His) as well as in designed drugs since they are believed to contribute to optimizing both affinity and specificity of drug-like molecules. Despite the mentioned relevance, the impact of aromatic clusters on protein-protein and protein-drug complexes is still poorly characterized, especially in those that go beyond a dimer. In this work, we studied protein-drug and protein-protein complexes and systematically analyzed the presence and structure of their aromatic clusters. Our results show that aromatic clusters are highly prevalent in both protein-protein and protein-drug complexes, and suggest that protein-protein aromatic clusters have idealized interactions, probably because they were optimized by evolution, as compared to protein-drug clusters that were manually designed. Interestingly, the configuration, solvent accessibility and secondary structure of aromatic residues in protein-drug complexes shed light on the relation between these properties and compound affinity, allowing researchers to better design new molecules.
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Affiliation(s)
- Esteban Lanzarotti
- Departamento de Computación, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Lucas A Defelipe
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina.,IQUIBICEN/UBA-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina.,European Molecular Biology Laboratory Hamburg, Notkestraße 85, 22607, Hamburg, Germany
| | - Marcelo A Marti
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina.,IQUIBICEN/UBA-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Adrián G Turjanski
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina. .,IQUIBICEN/UBA-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina.
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35
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Coyle J, Walser R. Applied Biophysical Methods in Fragment-Based Drug Discovery. SLAS DISCOVERY 2020; 25:471-490. [PMID: 32345095 DOI: 10.1177/2472555220916168] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Fragment-based drug discovery (FBDD) has come of age in the last decade with the FDA approval of four fragment-derived drugs. Biophysical methods are at the heart of hit discovery and validation in FBDD campaigns. The three most commonly used methods, thermal shift, surface plasmon resonance, and nuclear magnetic resonance, can be daunting for the novice user. We aim here to provide the nonexpert user of these methods with a summary of problems and challenges that might be faced, but also highlight the potential gains that each method can contribute to an FBDD project. While our view on FBDD is slightly biased toward enabling structure-guided drug discovery, most of the points we address in this review are also valid for non-structure-focused FBDD.
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Affiliation(s)
- Joe Coyle
- Astex Pharmaceuticals, Cambridge, UK
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36
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Liang JW, Li SL, Wang S, Li WQ, Meng FH. Synthesis and biological evaluation of novel ( E)- N'-benzylidene hydrazides as novel c-Met inhibitors through fragment based virtual screening. J Enzyme Inhib Med Chem 2020; 35:468-477. [PMID: 31902266 PMCID: PMC6968643 DOI: 10.1080/14756366.2019.1702655] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
C-Met plays a crucial role in the development and progression of neoplastic disease. Type II c-Met inhibitors recognise the inactive DFG-out conformation of the kinase, result in better anti-tumour effects due to synergistic effect against the other kinases. According to our previous works, an (E)-N'-benzylidene group was selected as the initial fragment. Two series of (E)-N'-benzylidene hydrazides were designed by fragment growth method. The inhibitory activities were in vitro investigated against c-Met and VEGFR-2. Compound 10b exhibited the most potent inhibitory activity against the c-Met inhibitor (IC50 = 0.37 nM). Compound 11b exhibited multi-target c-Met kinase inhibitory activity as a potential type II c-Met inhibitor (IC50 = 3.41 nM against c-Met; 25.34 nM against VEGFR-2). The two compounds also demonstrate the feasibility of fragment-based virtual screening method for drug discovery.
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Affiliation(s)
- Jing-Wei Liang
- School of Pharmacy, China Medical University, Shen Yang, China
| | - Shi-Long Li
- School of Pharmacy, China Medical University, Shen Yang, China
| | - Shan Wang
- School of Pharmacy, China Medical University, Shen Yang, China
| | - Wan-Qiu Li
- School of Pharmacy, China Medical University, Shen Yang, China
| | - Fan-Hao Meng
- School of Pharmacy, China Medical University, Shen Yang, China
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37
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Hassaan E, Eriksson P, Geschwindner S, Heine A, Klebe G. Fragments as Novel Starting Points for tRNA-Guanine Transglycosylase Inhibitors Found by Alternative Screening Strategies. ChemMedChem 2020; 15:324-337. [PMID: 31808981 PMCID: PMC7687107 DOI: 10.1002/cmdc.201900604] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 12/02/2019] [Indexed: 12/02/2022]
Abstract
Crystallography provides structural information crucial for fragment optimization, however several criteria must be met to screen directly on protein crystals as soakable, well-diffracting specimen must be available. We screened a 96-fragment library against the tRNA-modifying enzyme TGT using crystallography. Eight hits, some with surprising binding poses, were detected. However, the amount of data collection, reduction and refinement is assumed substantial. Therefore, having a reliable cascade of fast and cost-efficient methods available for pre-screening before embarking to elaborate crystallographic screening appears beneficial. This allows filtering of compounds to the most promising hits, available to rapidly progress from hit-to-lead. But how to ensure that this workflow is reliable? To answer this question, we also applied SPR and NMR to the same screening sample to study whether identical hits are retrieved. Upon hit-list comparisons, crystallography shows with NMR and SPR, only one overlapping hit and all three methods shared no common hits. This questions a cascade-type screening protocol at least in the current example. Compared to crystallography, SPR and NMR detected higher percentages of non-active-site binders suggesting the importance of running reporter ligand-based competitive screens in SPR and NMR, a requirement not needed in crystallography. Although not specific, NMR proved a more sensitive method relative to SPR and crystallography, as it picked up the highest numbers of binders.
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Affiliation(s)
- Engi Hassaan
- Institute of Pharmaceutical ChemistryPhilipps University MarburgMarbacher Weg 635032MarburgGermany
| | - Per‐Olof Eriksson
- Structure, Biophysics and Fragment-based Lead GenerationDiscovery Sciences, R&D, AstraZeneca431 83GothenburgSweden
| | - Stefan Geschwindner
- Structure, Biophysics and Fragment-based Lead GenerationDiscovery Sciences, R&D, AstraZeneca431 83GothenburgSweden
| | - Andreas Heine
- Institute of Pharmaceutical ChemistryPhilipps University MarburgMarbacher Weg 635032MarburgGermany
| | - Gerhard Klebe
- Institute of Pharmaceutical ChemistryPhilipps University MarburgMarbacher Weg 635032MarburgGermany
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38
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Brink A, Helliwell JR. Why is interoperability between the two fields of chemical crystallography and protein crystallography so difficult? IUCRJ 2019; 6:788-793. [PMID: 31576212 PMCID: PMC6760442 DOI: 10.1107/s2052252519010972] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 08/06/2019] [Indexed: 05/06/2023]
Abstract
The interoperability of chemical and biological crystallographic data is a key challenge to research and its application to pharmaceutical design. Research attempting to combine data from the two disciplines, small-molecule or chemical crystallography (CX) and macromolecular crystallography (MX), will face unique challenges including variations in terminology, software development, file format and databases which differ significantly from CX to MX. This perspective overview spans the two disciplines and originated from the investigation of protein binding to model radiopharmaceuticals. The opportunities of interlinked research while utilizing the two databases of the CSD (Cambridge Structural Database) and the PDB (Protein Data Bank) will be highlighted. The advantages of software that can handle multiple file formats and the circuitous route to convert organometallic small-molecule structural data for use in protein refinement software will be discussed. In addition some pointers to avoid being shipwrecked will be shared, such as the care which must be taken when interpreting data precision involving small molecules versus proteins.
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Affiliation(s)
- Alice Brink
- Department of Chemistry, University of the Free State, Nelson Mandela Drive, Bloemfontein, Free State 9301, South Africa
- Department of Chemistry, University of Manchester, Brunswick Street, Manchester M13 9PL, UK
| | - John R. Helliwell
- Department of Chemistry, University of Manchester, Brunswick Street, Manchester M13 9PL, UK
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39
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Tsopelas F, Tsantili-Kakoulidou A. Advances with weak affinity chromatography for fragment screening. Expert Opin Drug Discov 2019; 14:1125-1135. [DOI: 10.1080/17460441.2019.1648425] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Fotios Tsopelas
- Laboratory of Inorganic and Analytical Chemistry, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
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40
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Brink A, Helliwell JR. Formation of a highly dense tetra-rhenium cluster in a protein crystal and its implications in medical imaging. IUCRJ 2019; 6:695-702. [PMID: 31316813 PMCID: PMC6608631 DOI: 10.1107/s2052252519006651] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 05/09/2019] [Indexed: 05/22/2023]
Abstract
The fact that a protein crystal can serve as a chemical reaction vessel is intrinsically fascinating. That it can produce an electron-dense tetranuclear rhenium cluster compound from a rhenium tri-carbonyl tri-bromo starting compound adds to the fascination. Such a cluster has been synthesized previously in vitro, where it formed under basic conditions. Therefore, its synthesis in a protein crystal grown at pH 4.5 is even more unexpected. The X-ray crystal structures presented here are for the protein hen egg-white lysozyme incubated with a rhenium tri-carbonyl tri-bromo compound for periods of one and two years. These reveal a completed, very well resolved, tetra-rhenium cluster after two years and an intermediate state, where the carbonyl ligands to the rhenium cluster are not yet clearly resolved, after one year. A dense tetranuclear rhenium cluster, and its technetium form, offer enhanced contrast in medical imaging. Stimulated by these crystallography results, the unusual formation of such a species directly in an in vivo situation has been considered. It offers a new option for medical imaging compounds, particularly when considering the application of the pre-formed tetranuclear cluster, suggesting that it may be suitable for medical diagnosis because of its stability, preference of formation and biological compatibility.
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Affiliation(s)
- Alice Brink
- Department of Chemistry, University of the Free State, Nelson Mandela Drive, Bloemfontein, 9301, South Africa
- School of Chemistry, University of Manchester, Brunswick Street, Manchester M13 9PL, UK
| | - John R. Helliwell
- School of Chemistry, University of Manchester, Brunswick Street, Manchester M13 9PL, UK
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41
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Thomas SE, Collins P, James RH, Mendes V, Charoensutthivarakul S, Radoux C, Abell C, Coyne AG, Floto RA, von Delft F, Blundell TL. Structure-guided fragment-based drug discovery at the synchrotron: screening binding sites and correlations with hotspot mapping. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2019; 377:20180422. [PMID: 31030650 PMCID: PMC6501894 DOI: 10.1098/rsta.2018.0422] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Structure-guided drug discovery emerged in the 1970s and 1980s, stimulated by the three-dimensional structures of protein targets that became available, mainly through X-ray crystal structure analysis, assisted by the development of synchrotron radiation sources. Structures of known drugs or inhibitors were used to guide the development of leads. The growth of high-throughput screening during the late 1980s and the early 1990s in the pharmaceutical industry of chemical libraries of hundreds of thousands of compounds of molecular weight of approximately 500 Da was impressive but still explored only a tiny fraction of the chemical space of the predicted 1040 drug-like compounds. The use of fragments with molecular weights less than 300 Da in drug discovery not only decreased the chemical space needing exploration but also increased promiscuity in binding targets. Here we discuss advances in X-ray fragment screening and the challenge of identifying sites where fragments not only bind but can be chemically elaborated while retaining their positions and binding modes. We first describe the analysis of fragment binding using conventional X-ray difference Fourier techniques, with Mycobacterium abscessus SAICAR synthetase (PurC) as an example. We observe that all fragments occupy positions predicted by computational hotspot mapping. We compare this with fragment screening at Diamond Synchrotron Light Source XChem facility using PanDDA software, which identifies many more fragment hits, only some of which bind to the predicted hotspots. Many low occupancy sites identified may not support elaboration to give adequate ligand affinity, although they will likely be useful in drug discovery as 'warm spots' for guiding elaboration of fragments bound at hotspots. We discuss implications of these observations for fragment screening at the synchrotron sources. This article is part of the theme issue 'Fifty years of synchrotron science: achievements and opportunities'.
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Affiliation(s)
- Sherine E. Thomas
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK
| | - Patrick Collins
- Diamond Light Source (DLS), Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - Rory Hennell James
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Vitor Mendes
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK
| | | | - Chris Radoux
- The European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge CB10 1SD, UK
| | - Chris Abell
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Anthony G. Coyne
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - R. Andres Floto
- Cambridge Centre for Lung Infection, Royal Papworth Hospital, Cambridge CB23 3RE, UK
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC-Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Frank von Delft
- Diamond Light Source (DLS), Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7DQ, UK
- Department of Biochemistry, University of Johannesburg, Auckland Park 2006, South Africa
| | - Tom L. Blundell
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK
- e-mail:
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42
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Machiraju PK, Yedla P, Gubbala SP, Bohari T, Abdul JK, Xu S, Patel R, Chittireddy VRR, Boppana K, Jagarlapudi SA, Neamati N, Syed R, Amanchy R. Identification, synthesis and evaluation of CSF1R inhibitors using fragment based drug design. Comput Biol Chem 2019; 80:374-383. [DOI: 10.1016/j.compbiolchem.2019.04.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 03/12/2019] [Accepted: 04/28/2019] [Indexed: 02/07/2023]
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43
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Sun B, Dong Y, Lei K, Wang J, Zhao L, Liu M. Design, synthesis and biological evaluation of amide-pyridine derivatives as novel dual-target (SE, CYP51) antifungal inhibitors. Bioorg Med Chem 2019; 27:2427-2437. [DOI: 10.1016/j.bmc.2019.02.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 01/28/2019] [Accepted: 02/02/2019] [Indexed: 10/27/2022]
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44
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Giordanetto F, Jin C, Willmore L, Feher M, Shaw DE. Fragment Hits: What do They Look Like and How do They Bind? J Med Chem 2019; 62:3381-3394. [PMID: 30875465 PMCID: PMC6466478 DOI: 10.1021/acs.jmedchem.8b01855] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
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A “fragment hit”, a
molecule of low molecular weight
that has been validated to bind to a target protein, can be an effective
chemical starting point for a drug discovery project. Our ability
to find and progress fragment hits could potentially be improved by
enhancing our understanding of their binding properties, which to
date has largely been based on tacit knowledge and reports from individual
projects. In the work reported here, we systematically analyzed the
molecular and binding properties of fragment hits using 489 published
protein–fragment complexes. We identified a number of notable
features that these hits tend to have in common, including preferences
in buried surface area upon binding, hydrogen bonding and other directional
interactions with the protein targets, structural topology, functional-group
occurrence, and degree of carbon saturation. In the future, taking
account of these preferences in designing and selecting fragments
to screen against protein targets may increase the chances of success
in fragment screening campaigns.
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Affiliation(s)
| | - Chentian Jin
- D. E. Shaw Research , New York , New York 10036 , United States
| | | | - Miklos Feher
- D. E. Shaw Research , New York , New York 10036 , United States
| | - David E Shaw
- D. E. Shaw Research , New York , New York 10036 , United States.,Department of Biochemistry and Molecular Biophysics , Columbia University , New York , New York 10032 , United States
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45
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Ozawa SI, Takahashi M, Yamaotsu N, Hirono S. Structure-based virtual screening for novel chymase inhibitors by in silico fragment mapping. J Mol Graph Model 2019; 89:102-108. [PMID: 30884446 DOI: 10.1016/j.jmgm.2019.03.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 03/06/2019] [Accepted: 03/07/2019] [Indexed: 01/22/2023]
Abstract
The term chymase refers to a family of chymotrypsin-like serine proteases stored within the secretory granules of mast cells. Recently, a variety of small molecule inhibitors for chymase have been developed with a primary focus on the treatment of cardiovascular diseases. Despite the expected therapeutic benefit of these chymase inhibitors, they have not been used clinically. Here, we attempted to identify new chymase inhibitors using a multistep structure-based virtual screening protocol combined with our knowledge-based in silico fragment mapping technique. The mapping procedure identified fragments with novel modes of interaction at the oxyanion hole of chymase. Next, we constructed a three-dimensional (3D) pharmacophore model and retrieved eight candidate chymase inhibitors from a commercial database that included approximately five million compounds. This selection was achieved using a multistep virtual screening protocol, which combined a 3D pharmacophore-based search, docking calculations, and analyses of binding free energy. One of the eight compounds exhibited concentration-dependent chymase inhibitory activity, which could be further optimized to develop more potent chymase inhibitors.
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Affiliation(s)
- Shin-Ichiro Ozawa
- Department of Pharmaceutical Sciences, School of Pharmacy, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo, 108-8641, Japan.
| | - Miki Takahashi
- Department of Pharmaceutical Sciences, School of Pharmacy, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo, 108-8641, Japan
| | - Noriyuki Yamaotsu
- Department of Pharmaceutical Sciences, School of Pharmacy, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo, 108-8641, Japan
| | - Shuichi Hirono
- Department of Pharmaceutical Sciences, School of Pharmacy, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo, 108-8641, Japan
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46
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Li ZR, Wang S, Yang L, Yuan XH, Suo FZ, Yu B, Liu HM. Experience-based discovery (EBD) of aryl hydrazines as new scaffolds for the development of LSD1/KDM1A inhibitors. Eur J Med Chem 2019; 166:432-444. [DOI: 10.1016/j.ejmech.2019.01.075] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 01/01/2019] [Accepted: 01/29/2019] [Indexed: 01/22/2023]
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47
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Robson-Tull J. Biophysical screening in fragment-based drug design: a brief overview. ACTA ACUST UNITED AC 2019. [DOI: 10.1093/biohorizons/hzy015] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Jacob Robson-Tull
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
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48
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van Hilten N, Chevillard F, Kolb P. Virtual Compound Libraries in Computer-Assisted Drug Discovery. J Chem Inf Model 2019; 59:644-651. [PMID: 30624918 DOI: 10.1021/acs.jcim.8b00737] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The use of virtual compound libraries in computer-assisted drug discovery has gained in popularity and has already lead to numerous successes. Here, we examine key static and dynamic virtual library concepts that have been developed over the past decade. To facilitate the search for new drugs in the vastness of chemical space, there are still several hurdles to overcome, including the current difficulties in screening and parsing efficiency and the need for more reliable vendors and accurate synthesis prediction tools. These challenges should be tackled by both the developers of virtual libraries and by their users, in order for the exploration of chemical space to live up to its potential.
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Affiliation(s)
- Niek van Hilten
- Department of Pharmaceutical Chemistry , Philipps-University Marburg , Marbacher Weg 6 , 35032 Marburg , Germany
| | - Florent Chevillard
- Department of Pharmaceutical Chemistry , Philipps-University Marburg , Marbacher Weg 6 , 35032 Marburg , Germany
| | - Peter Kolb
- Department of Pharmaceutical Chemistry , Philipps-University Marburg , Marbacher Weg 6 , 35032 Marburg , Germany
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49
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Erlanson DA, Davis BJ, Jahnke W. Fragment-Based Drug Discovery: Advancing Fragments in the Absence of Crystal Structures. Cell Chem Biol 2018; 26:9-15. [PMID: 30482678 DOI: 10.1016/j.chembiol.2018.10.001] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 07/12/2018] [Accepted: 09/28/2018] [Indexed: 01/08/2023]
Abstract
Fragment-based drug discovery typically requires an interplay between screening methods, structural methods, and medicinal chemistry. X-ray crystallography is generally the method of choice to obtain three-dimensional structures of the bound ligand/protein complex, but this can sometimes be difficult, particularly for early, low-affinity fragment hits. In this Perspective, we discuss strategies to advance and evolve fragments in the absence of crystal structures of protein-fragment complexes, although the structure of the unliganded protein may be available. The strategies can involve other structural techniques, such as NMR spectroscopy, molecular modeling, or a variety of chemical approaches. Often, these strategies are aimed at guiding evolution of initial fragment hits to a stage where crystal structures can be obtained for further structure-based optimization.
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Affiliation(s)
- Daniel A Erlanson
- Carmot Therapeutics, Inc., 740 Heinz Avenue, Berkeley, CA 94710, USA.
| | - Ben J Davis
- Vernalis (R&D) Ltd, Granta Park, Cambridge, UK.
| | - Wolfgang Jahnke
- Novartis Institutes for Biomedical Research, Chemical Biology and Therapeutics, Novartis Campus, Basel, Switzerland.
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50
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Najjar A, Platzer C, Luft A, Aßmann CA, Elghazawy NH, Erdmann F, Sippl W, Schmidt M. Computer-aided design, synthesis and biological characterization of novel inhibitors for PKMYT1. Eur J Med Chem 2018; 161:479-492. [PMID: 30388464 DOI: 10.1016/j.ejmech.2018.10.050] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 10/16/2018] [Accepted: 10/19/2018] [Indexed: 12/12/2022]
Abstract
In the current work, we applied computational methods to analyze the membrane-associated inhibitory kinase PKMYT1 and small molecule inhibitors. PKMYT1 regulates the cell cycle at G2/M transition and phosphorylates Thr14 and Tyr15 in the Cdk1-cyclin B complex. A combination of in silico and in vitro screening was applied to identify novel PKMYT1 inhibitors. The computational approach combined structural analysis, molecular docking, binding free energy calculations, and quantitative structure-activity relationship (QSAR) models. In addition, a computational fragment growing approach was applied to a set of previously identified diaminopyrimidines. Based on the derived computational models, several derivatives were synthesized and tested in vitro on PKMYT1. Novel inhibitors active in the sub-micromolar range were identified which provide the basis for further characterization of PKMYT1 as putative target for cancer therapy.
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Affiliation(s)
- Abdulkarim Najjar
- Institute of Pharmacy, Department of Medicinal Chemistry, Martin-Luther-University Halle-Wittenberg, W.-Langenbeck-Str. 4, 06120, Halle, Germany
| | - Charlott Platzer
- Institute of Pharmacy, Department of Medicinal Chemistry, Martin-Luther-University Halle-Wittenberg, W.-Langenbeck-Str. 4, 06120, Halle, Germany
| | - Anton Luft
- Institute of Pharmacy, Department of Medicinal Chemistry, Martin-Luther-University Halle-Wittenberg, W.-Langenbeck-Str. 4, 06120, Halle, Germany
| | - Chris Alexander Aßmann
- Institute of Pharmacy, Department of Medicinal Chemistry, Martin-Luther-University Halle-Wittenberg, W.-Langenbeck-Str. 4, 06120, Halle, Germany
| | - Nehal H Elghazawy
- Institute of Pharmacy, Department of Medicinal Chemistry, Martin-Luther-University Halle-Wittenberg, W.-Langenbeck-Str. 4, 06120, Halle, Germany
| | - Frank Erdmann
- Institute of Pharmacy, Department of Pharmacology, Martin-Luther-University Halle-Wittenberg, W.-Langenbeck-Str. 4, 06120, Halle, Germany
| | - Wolfgang Sippl
- Institute of Pharmacy, Department of Medicinal Chemistry, Martin-Luther-University Halle-Wittenberg, W.-Langenbeck-Str. 4, 06120, Halle, Germany
| | - Matthias Schmidt
- Institute of Pharmacy, Department of Medicinal Chemistry, Martin-Luther-University Halle-Wittenberg, W.-Langenbeck-Str. 4, 06120, Halle, Germany.
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