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Zhang L, Rao V, Cornell W. r-BRICS - A Revised BRICS Module That Breaks Ring Structures and Carbon Chains. ChemMedChem 2024; 19:e202300202. [PMID: 37574458 DOI: 10.1002/cmdc.202300202] [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: 04/13/2023] [Revised: 07/24/2023] [Accepted: 08/11/2023] [Indexed: 08/15/2023]
Abstract
Molecular fragmentation has been frequently used for machine learning, molecular modeling, and drug discovery studies. However, the current molecular fragmentation tools often lead to large fragments that are useful to limited tasks. Specifically, long aliphatic chains, certain connected ring structures, fused rings, as well as various nitrogen-containing molecular entities often remain intact when using BRICS. With no known methods to solve this issue, we find that the fragments taken from BRICS are inflexible for tasks such as fragment-based machine learning, coarse-graining, and ligand-protein interaction assessment. In this work, a revised BRICS (r-BRICS) module is developed to allow more flexible fragmentation on a wider variety of molecules. It is shown that r-BRICS generates smaller fragments than BRICS, allowing localized fragment assessments. Furthermore, r-BRICS generates a fragment database with significantly more unique small fragments than BRICS, which is potentially useful for fragment-based drug discovery.
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Affiliation(s)
- Leili Zhang
- IBM Thomas J. Watson Research Center, 1101 Kitchawan Road, Yorktown Heights, NY, 10598, USA
| | - Vasumitra Rao
- IBM Thomas J. Watson Research Center, 1101 Kitchawan Road, Yorktown Heights, NY, 10598, USA
| | - Wendy Cornell
- IBM Thomas J. Watson Research Center, 1101 Kitchawan Road, Yorktown Heights, NY, 10598, USA
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Bon M, Bilsland A, Bower J, McAulay K. Fragment-based drug discovery-the importance of high-quality molecule libraries. Mol Oncol 2022; 16:3761-3777. [PMID: 35749608 PMCID: PMC9627785 DOI: 10.1002/1878-0261.13277] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 05/16/2022] [Accepted: 06/23/2022] [Indexed: 12/24/2022] Open
Abstract
Fragment-based drug discovery (FBDD) is now established as a complementary approach to high-throughput screening (HTS). Contrary to HTS, where large libraries of drug-like molecules are screened, FBDD screens involve smaller and less complex molecules which, despite a low affinity to protein targets, display more 'atom-efficient' binding interactions than larger molecules. Fragment hits can, therefore, serve as a more efficient start point for subsequent optimisation, particularly for hard-to-drug targets. Since the number of possible molecules increases exponentially with molecular size, small fragment libraries allow for a proportionately greater coverage of their respective 'chemical space' compared with larger HTS libraries comprising larger molecules. However, good library design is essential to ensure optimal chemical and pharmacophore diversity, molecular complexity, and physicochemical characteristics. In this review, we describe our views on fragment library design, and on what constitutes a good fragment from a medicinal and computational chemistry perspective. We highlight emerging chemical and computational technologies in FBDD and discuss strategies for optimising fragment hits. The impact of novel FBDD approaches is already being felt, with the recent approval of the covalent KRASG12C inhibitor sotorasib highlighting the utility of FBDD against targets that were long considered undruggable.
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Affiliation(s)
- Marta Bon
- Cancer Research HorizonsCancer Research UK Beatson InstituteGlasgowUK
| | - Alan Bilsland
- Cancer Research HorizonsCancer Research UK Beatson InstituteGlasgowUK
| | - Justin Bower
- Cancer Research HorizonsCancer Research UK Beatson InstituteGlasgowUK
| | - Kirsten McAulay
- Cancer Research HorizonsCancer Research UK Beatson InstituteGlasgowUK
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Toti D, Macari G, Barbierato E, Polticelli F. FGDB: a comprehensive graph database of ligand fragments from the Protein Data Bank. Database (Oxford) 2022; 2022:6619197. [PMID: 35763362 PMCID: PMC9239314 DOI: 10.1093/database/baac044] [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: 02/14/2022] [Revised: 05/06/2022] [Accepted: 05/31/2022] [Indexed: 11/22/2022]
Abstract
This work presents Fragment Graph DataBase (FGDB), a graph database of ligand fragments extracted and generated from the protein entries available in the Protein Data Bank (PDB). FGDB is meant to support and elicit campaigns of fragment-based drug design, by enabling users to query it in order to construct ad hoc, target-specific libraries. In this regard, the database features more than 17 000 fragments, typically small, highly soluble and chemically stable molecules expressed via their canonical Simplified Molecular Input Line Entry System (SMILES) representation. For these fragments, the database provides information related to their contact frequencies with the amino acids, the ligands they are contained in and the proteins the latter bind to. The graph database can be queried via standard web forms and textual searches by a number of identifiers (SMILES, ligand and protein PDB ids) as well as via graphical queries that can be performed against the graph itself, providing users with an intuitive and effective view upon the underlying biological entities. Further search mechanisms via advanced conjunctive/disjunctive/negated textual queries are also possible, in order to allow scientists to look for specific relationships and export their results for further studies. This work also presents two sample use cases where maternal embryonic leucine zipper kinase and mesotrypsin are used as a target, being proteins of high biomedical relevance for the development of cancer therapies. Database URL: http://biochimica3.bio.uniroma3.it/fragments-web/
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Affiliation(s)
- Daniele Toti
- Department of Mathematics and Physics, Catholic University of the Sacred Heart, Faculty of Mathematical, Physical and Natural Sciences , via della Garzetta 48, Brescia 25133, Italy
| | - Gabriele Macari
- Department of Sciences, Roma Tre University , viale Marconi 446, Roma, Lazio 00146, Italy
| | - Enrico Barbierato
- Department of Mathematics and Physics, Catholic University of the Sacred Heart, Faculty of Mathematical, Physical and Natural Sciences , via della Garzetta 48, Brescia 25133, Italy
| | - Fabio Polticelli
- Department of Sciences, Roma Tre University , viale Marconi 446, Roma, Lazio 00146, Italy
- Roma Tre Section, National Institute of Nuclear Physics , via della Vasca Navale 84, Roma 00146, Italy
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Macari G, Toti D, Pasquadibisceglie A, Polticelli F. DockingApp RF: A State-of-the-Art Novel Scoring Function for Molecular Docking in a User-Friendly Interface to AutoDock Vina. Int J Mol Sci 2020; 21:ijms21249548. [PMID: 33333976 PMCID: PMC7765429 DOI: 10.3390/ijms21249548] [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: 11/26/2020] [Revised: 12/11/2020] [Accepted: 12/11/2020] [Indexed: 11/28/2022] Open
Abstract
Motivation: Bringing a new drug to the market is expensive and time-consuming. To cut the costs and time, computer-aided drug design (CADD) approaches have been increasingly included in the drug discovery pipeline. However, despite traditional docking tools show a good conformational space sampling ability, they are still unable to produce accurate binding affinity predictions. This work presents a novel scoring function for molecular docking seamlessly integrated into DockingApp, a user-friendly graphical interface for AutoDock Vina. The proposed function is based on a random forest model and a selection of specific features to overcome the existing limits of Vina’s original scoring mechanism. A novel version of DockingApp, named DockingApp RF, has been developed to host the proposed scoring function and to automatize the rescoring procedure of the output of AutoDock Vina, even to nonexpert users. Results: By coupling intermolecular interaction, solvent accessible surface area features and Vina’s energy terms, DockingApp RF’s new scoring function is able to improve the binding affinity prediction of AutoDock Vina. Furthermore, comparison tests carried out on the CASF-2013 and CASF-2016 datasets demonstrate that DockingApp RF’s performance is comparable to other state-of-the-art machine-learning- and deep-learning-based scoring functions. The new scoring function thus represents a significant advancement in terms of the reliability and effectiveness of docking compared to AutoDock Vina’s scoring function. At the same time, the characteristics that made DockingApp appealing to a wide range of users are retained in this new version and have been complemented with additional features.
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Affiliation(s)
- Gabriele Macari
- Department of Sciences, Roma Tre University, 00146 Rome, Italy; (G.M.); (A.P.)
| | - Daniele Toti
- Faculty of Mathematical, Physical and Natural Sciences, Catholic University of the Sacred Heart, 25121 Brescia, Italy;
| | | | - Fabio Polticelli
- Department of Sciences, Roma Tre University, 00146 Rome, Italy; (G.M.); (A.P.)
- National Institute of Nuclear Physics, Roma Tre Section, 00146 Rome, Italy
- Correspondence:
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Pratama MRF, Poerwono H, Siswodihardjo S. Molecular Docking of Novel 5-O-benzoylpinostrobin Derivatives as SARS-CoV-2 Main Protease Inhibitors. PHARMACEUTICAL SCIENCES 2020. [DOI: 10.34172/ps.2020.57] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Affiliation(s)
- Mohammad Rizki Fadhil Pratama
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Universitas Airlangga, Jl Dr Ir H Soekarno Mulyorejo, Surabaya, East Java, Indonesia
| | - Hadi Poerwono
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Universitas Airlangga, Jl Dr Ir H Soekarno Mulyorejo, Surabaya, East Java, Indonesia
| | - Siswandono Siswodihardjo
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Universitas Airlangga, Jl Dr Ir H Soekarno Mulyorejo, Surabaya, East Java, Indonesia
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Leboffe L, di Masi A, Trezza V, Pasquadibisceglie A, Macari G, Polticelli F, Ascenzi P. Neonicotinoid trapping by the FA1 site of human serum albumin. IUBMB Life 2019; 72:716-723. [PMID: 31614076 DOI: 10.1002/iub.2173] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 09/07/2019] [Indexed: 11/11/2022]
Abstract
Neonicotinoids are a widely used class of insecticides that target the acetylcholine recognition site of the nicotinic acetylcholine receptors in the central nervous system of insects. Although neonicotinoids display a high specificity for insects, their use has been recently debated since several studies led to the hypothesis that they may have adverse ecological effects and potential risks to mammals and even humans. Due to their hydrophobic nature, neonicotinoids need specific carriers to allow their distribution in body fluids. Human serum albumin (HSA), the most abundant plasma protein, is a key carrier of endogenous and exogenous compounds. The in silico docking and ligand binding properties of acetamiprid, clothianidin, dinotefuran, imidacloprid, nitenpyram, thiacloprid, and thiamethoxam to HSA are here reported. Neonicotinoids bind to multiple fatty acid (FA) binding sites, preferentially to the FA1 pocket, with high affinity. Values of the dissociation equilibrium constant for neonicotinoid binding FA1 of HSA (i.e., calc Kn ) derived from in silico docking simulations (ranging between 3.9 × 10-5 and 6.3 × 10-4 M) agree with those determined experimentally from competitive inhibition of heme-Fe(III) binding (i.e., exp Kn ; ranging between 2.1 × 10-5 and 6.9 × 10-5 M). Accounting for the HSA concentration in vivo (~7.5 10-4 M), values of Kn here determined suggest that the formation of the HSA:neonicotinoid complexes may occur in vivo. Therefore, HSA appears to be an important determinant for neonicotinoid transport and distribution to tissues and organs, particularly to the liver where they are metabolized.
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Affiliation(s)
- Loris Leboffe
- Department of Sciences, Roma Tre University, Rome, Italy
| | | | - Viviana Trezza
- Department of Sciences, Roma Tre University, Rome, Italy
| | | | | | - Fabio Polticelli
- Department of Sciences, Roma Tre University, Rome, Italy.,Roma Tre Section, National Institute of Nuclear Physics, Rome, Italy
| | - Paolo Ascenzi
- Interdepartmental Laboratory for Electron Microscopy, Roma Tre University, Rome, Italy
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