1
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Maeda I, Tamura S, Ogura Y, Serizawa T, Shimada T, Kunimoto R, Miyao T. Scaffold-Hopped Compound Identification by Ligand-Based Approaches with a Prospective Affinity Test. J Chem Inf Model 2024; 64:5557-5569. [PMID: 38950192 PMCID: PMC11267578 DOI: 10.1021/acs.jcim.4c00342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 06/05/2024] [Accepted: 06/18/2024] [Indexed: 07/03/2024]
Abstract
Scaffold-hopped (SH) compounds are bioactive compounds structurally different from known active compounds. Identifying SH compounds in the ligand-based approaches has been a central issue in medicinal chemistry, and various molecular representations of scaffold hopping have been proposed. However, appropriate representations for SH compound identification remain unclear. Herein, the ability of SH compound identification among several representations was fairly evaluated based on retrospective validation and prospective demonstration. In the retrospective validation, the combinations of two screening algorithms and four two- and three-dimensional molecular representations were compared using controlled data sets for the early identification of SH compounds. We found that the combination of the support vector machine and extended connectivity fingerprint with bond diameter 4 (SVM-ECFP4) and SVM and the rapid overlay of chemical structures (SVM-ROCS) showed a relatively high performance. The compounds that were highly ranked by SVM-ROCS did not share substructures with the active training compounds, while those ranked by SVM-ECFP4 were mostly recombinant. In the prospective demonstration, 93 SH compounds were prepared by screening the Namiki database using SVM-ROCS, targeting ABL1 inhibitors. The primary screening using surface plasmon resonance suggested five active compounds; however, in the competitive binding assays with adenosine triphosphate, no hits were found.
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Affiliation(s)
- Itsuki Maeda
- Graduate
School of Science and Technology, Nara Institute
of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan
| | - Shunsuke Tamura
- Graduate
School of Science and Technology, Nara Institute
of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan
| | - Yoshihiro Ogura
- Medicinal
Chemistry Research Laboratories, R&D Division, Daiichi Sankyo Co., Ltd., 1-2-58 Hiromachi, Shinagawa-ku, Tokyo 140-8710, Japan
| | - Takayuki Serizawa
- Medicinal
Chemistry Research Laboratories, R&D Division, Daiichi Sankyo Co., Ltd., 1-2-58 Hiromachi, Shinagawa-ku, Tokyo 140-8710, Japan
| | - Takashi Shimada
- Structure-Based
Drug Design Group, Organic & Biomolecular Chemistry Department, Daiichi Sankyo RD Novare Co., Ltd., 1-16-13 Kitakasai, Edogawa-ku, Tokyo 134-8630, Japan
| | - Ryo Kunimoto
- Discovery
Intelligence Research Laboratories, R&D Division, Daiichi Sankyo Co., Ltd., 1-2-58 Hiromachi, Shinagawa-ku, Tokyo 140-8710, Japan
| | - Tomoyuki Miyao
- Graduate
School of Science and Technology, Nara Institute
of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan
- Data
Science Center, Nara Institute of Science
and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan
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2
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Atz K, Cotos L, Isert C, Håkansson M, Focht D, Hilleke M, Nippa DF, Iff M, Ledergerber J, Schiebroek CCG, Romeo V, Hiss JA, Merk D, Schneider P, Kuhn B, Grether U, Schneider G. Prospective de novo drug design with deep interactome learning. Nat Commun 2024; 15:3408. [PMID: 38649351 PMCID: PMC11035696 DOI: 10.1038/s41467-024-47613-w] [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: 09/13/2023] [Accepted: 04/02/2024] [Indexed: 04/25/2024] Open
Abstract
De novo drug design aims to generate molecules from scratch that possess specific chemical and pharmacological properties. We present a computational approach utilizing interactome-based deep learning for ligand- and structure-based generation of drug-like molecules. This method capitalizes on the unique strengths of both graph neural networks and chemical language models, offering an alternative to the need for application-specific reinforcement, transfer, or few-shot learning. It enables the "zero-shot" construction of compound libraries tailored to possess specific bioactivity, synthesizability, and structural novelty. In order to proactively evaluate the deep interactome learning framework for protein structure-based drug design, potential new ligands targeting the binding site of the human peroxisome proliferator-activated receptor (PPAR) subtype gamma are generated. The top-ranking designs are chemically synthesized and computationally, biophysically, and biochemically characterized. Potent PPAR partial agonists are identified, demonstrating favorable activity and the desired selectivity profiles for both nuclear receptors and off-target interactions. Crystal structure determination of the ligand-receptor complex confirms the anticipated binding mode. This successful outcome positively advocates interactome-based de novo design for application in bioorganic and medicinal chemistry, enabling the creation of innovative bioactive molecules.
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Affiliation(s)
- Kenneth Atz
- ETH Zurich, Department of Chemistry and Applied Biosciences, Vladimir-Prelog-Weg 4, 8093, Zurich, Switzerland
| | - Leandro Cotos
- ETH Zurich, Department of Chemistry and Applied Biosciences, Vladimir-Prelog-Weg 4, 8093, Zurich, Switzerland
| | - Clemens Isert
- ETH Zurich, Department of Chemistry and Applied Biosciences, Vladimir-Prelog-Weg 4, 8093, Zurich, Switzerland
| | - Maria Håkansson
- SARomics Biostructures AB, Medicon Village, SE-223 81, Lund, Sweden
| | - Dorota Focht
- SARomics Biostructures AB, Medicon Village, SE-223 81, Lund, Sweden
| | - Mattis Hilleke
- ETH Zurich, Department of Chemistry and Applied Biosciences, Vladimir-Prelog-Weg 4, 8093, Zurich, Switzerland
| | - David F Nippa
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, CH-4070, Basel, Switzerland
- Department of Pharmacy, Ludwig-Maximilians-Universität München, Butenandtstrasse 5, 81377, Munich, Germany
| | - Michael Iff
- ETH Zurich, Department of Chemistry and Applied Biosciences, Vladimir-Prelog-Weg 4, 8093, Zurich, Switzerland
| | - Jann Ledergerber
- ETH Zurich, Department of Chemistry and Applied Biosciences, Vladimir-Prelog-Weg 4, 8093, Zurich, Switzerland
| | - Carl C G Schiebroek
- ETH Zurich, Department of Chemistry and Applied Biosciences, Vladimir-Prelog-Weg 4, 8093, Zurich, Switzerland
| | - Valentina Romeo
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, CH-4070, Basel, Switzerland
| | - Jan A Hiss
- ETH Zurich, Department of Chemistry and Applied Biosciences, Vladimir-Prelog-Weg 4, 8093, Zurich, Switzerland
| | - Daniel Merk
- Department of Pharmacy, Ludwig-Maximilians-Universität München, Butenandtstrasse 5, 81377, Munich, Germany
| | - Petra Schneider
- ETH Zurich, Department of Chemistry and Applied Biosciences, Vladimir-Prelog-Weg 4, 8093, Zurich, Switzerland
| | - Bernd Kuhn
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, CH-4070, Basel, Switzerland
| | - Uwe Grether
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, CH-4070, Basel, Switzerland
| | - Gisbert Schneider
- ETH Zurich, Department of Chemistry and Applied Biosciences, Vladimir-Prelog-Weg 4, 8093, Zurich, Switzerland.
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3
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Song B, Nie L, Bozorov K, Kuryazov R, Zhao J, Aisa HA. Design, combinatorial synthesis and cytotoxic activity of 2-substituted furo[2,3-d]pyrimidinone and pyrrolo[2,3-d]pyrimidinone library. Mol Divers 2023; 27:1767-1783. [PMID: 36197552 DOI: 10.1007/s11030-022-10529-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Accepted: 09/11/2022] [Indexed: 11/28/2022]
Abstract
A facile protocol was developed for the combinatorial synthesis of furo[2,3-d]pyrimidinone and pyrrolo[2,3-d]pyrimidinone library via a one-pot condensation, from 2-amino furans/pyrroles. Herein reported process required a similar reaction condition, providing mild access to two diverse series of natural product-like heterocycles. Both furo[2,3-d]pyrimidinones and pyrrolo[2,3-d]pyrimidinones were evaluated in vitro against a panel of human cancer cell lines including against human cancer HeLa (cervical), MCF-7 (breast) and HT-29 (colon) cell lines. Derivative 12n ((2-(4-chlorophenyl)-1-methyl-6,7,8,9-tetrahydropyrido[1,2-a]pyrrolo[2,3-d]pyrimidin-4(1H)-one)) showed high activity (IC50 = 6.55 ± 0.31 µM) against the HeLa cell line. These products could be subjected to a various modification and therefore represent important skeletons for the anticancer drug discovery.
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Affiliation(s)
- Buer Song
- State Key Laboratory Basis of Xinjiang Indigenous Medicinal Plants Resource Utilization, Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, South Beijing Rd 40-1, Urumqi, 830011, People's Republic of China
- University of Chinese Academy of Sciences, 19 A Yuquan Rd, Beijing, 100049, People's Republic of China
| | - Lifei Nie
- State Key Laboratory Basis of Xinjiang Indigenous Medicinal Plants Resource Utilization, Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, South Beijing Rd 40-1, Urumqi, 830011, People's Republic of China
| | - Khurshed Bozorov
- State Key Laboratory Basis of Xinjiang Indigenous Medicinal Plants Resource Utilization, Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, South Beijing Rd 40-1, Urumqi, 830011, People's Republic of China
- Faculty of Chemistry, Samarkand State University, University blv. 15, Samarkand, Uzbekistan, 140104
| | - Rustamkhon Kuryazov
- Faculty of Chemistry, Samarkand State University, University blv. 15, Samarkand, Uzbekistan, 140104
- Urgench State University, Kh. Olimjon st. 14, Urgench, Uzbekistan, 220100
| | - Jiangyu Zhao
- State Key Laboratory Basis of Xinjiang Indigenous Medicinal Plants Resource Utilization, Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, South Beijing Rd 40-1, Urumqi, 830011, People's Republic of China.
| | - Haji Akber Aisa
- State Key Laboratory Basis of Xinjiang Indigenous Medicinal Plants Resource Utilization, Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, South Beijing Rd 40-1, Urumqi, 830011, People's Republic of China.
- University of Chinese Academy of Sciences, 19 A Yuquan Rd, Beijing, 100049, People's Republic of China.
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4
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Nakano H, Miyao T. Visualization of Topological Pharmacophore Space with Graph Edit Distance. ACS OMEGA 2022; 7:14057-14068. [PMID: 35559135 PMCID: PMC9088954 DOI: 10.1021/acsomega.2c00173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 03/25/2022] [Indexed: 06/15/2023]
Abstract
A topological pharmacophore (TP) is a chemical graph-based pharmacophore representation, where nodes are pharmacophoric features (PF) and edges are topological distances between PFs. Previously proposed sparse pharmacophore graphs (SPhGs) for TPs were shown to be effective in identifying structurally different active compounds while maintaining the interpretability of the graphs. However, one limitation of using SPhGs as queries is that many structurally similar SPhGs can be identified from a set of active compounds, requiring the classification and visualization of SPhGs, followed by an understanding of the pharmacophore hypotheses. In this study, we propose a scheme for SPhG analysis based on dimensionality reduction techniques with the graph edit distance (GED) metric. This metric enables measuring similarities among SPhGs in a quantitative manner. The visualization of SPhGs, which themselves are the graphs shared by active compounds, can help us understand the pharmacophore hypotheses as well as the data set. As a proof-of-concept study, we generated two-dimensional SPhG-maps using three dimensionality reduction techniques for six biological targets. A comparison with other pharmacophore representations was also conducted. We demonstrated knowledge extraction (interpretation of the data set) from the generated maps. Our findings include a suitable mapping algorithm as well as a pharmacophore hypothesis analysis procedure using an SPhG-map.
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Affiliation(s)
- Hiroshi Nakano
- Graduate
School of Science and Technology, Nara Institute
of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan
| | - Tomoyuki Miyao
- Graduate
School of Science and Technology, Nara Institute
of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan
- Data
Science Center, Nara Institute of Science
and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan
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5
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Joon S, Singla RK, Shen B. In Silico Drug Discovery for Treatment of Virus Diseases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1368:73-93. [DOI: 10.1007/978-981-16-8969-7_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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6
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Zheng S, Lei Z, Ai H, Chen H, Deng D, Yang Y. Deep scaffold hopping with multimodal transformer neural networks. J Cheminform 2021; 13:87. [PMID: 34774103 PMCID: PMC8590293 DOI: 10.1186/s13321-021-00565-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 10/31/2021] [Indexed: 11/10/2022] Open
Abstract
Scaffold hopping is a central task of modern medicinal chemistry for rational drug design, which aims to design molecules of novel scaffolds sharing similar target biological activities toward known hit molecules. Traditionally, scaffolding hopping depends on searching databases of available compounds that can't exploit vast chemical space. In this study, we have re-formulated this task as a supervised molecule-to-molecule translation to generate hopped molecules novel in 2D structure but similar in 3D structure, as inspired by the fact that candidate compounds bind with their targets through 3D conformations. To efficiently train the model, we curated over 50 thousand pairs of molecules with increased bioactivity, similar 3D structure, but different 2D structure from public bioactivity database, which spanned 40 kinases commonly investigated by medicinal chemists. Moreover, we have designed a multimodal molecular transformer architecture by integrating molecular 3D conformer through a spatial graph neural network and protein sequence information through Transformer. The trained DeepHop model was shown able to generate around 70% molecules having improved bioactivity together with high 3D similarity but low 2D scaffold similarity to the template molecules. This ratio was 1.9 times higher than other state-of-the-art deep learning methods and rule- and virtual screening-based methods. Furthermore, we demonstrated that the model could generalize to new target proteins through fine-tuning with a small set of active compounds. Case studies have also shown the advantages and usefulness of DeepHop in practical scaffold hopping scenarios.
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Affiliation(s)
- Shuangjia Zheng
- School of Data and Computer Science, Sun Yat-Sen University, China, 132 East Circle at University City, Guangzhou, 510006, China
| | - Zengrong Lei
- Fermion Technology Co., Ltd, 1088 Newport East Road, Guangzhou, 510335, China
| | - Haitao Ai
- Fermion Technology Co., Ltd, 1088 Newport East Road, Guangzhou, 510335, China
| | - Hongming Chen
- Centre of Chemistry and Chemical Biology, Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510530, China
| | - Daiguo Deng
- Fermion Technology Co., Ltd, 1088 Newport East Road, Guangzhou, 510335, China.
| | - Yuedong Yang
- School of Data and Computer Science, Sun Yat-Sen University, China, 132 East Circle at University City, Guangzhou, 510006, China.
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7
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Nakano H, Miyao T, Swarit J, Funatsu K. Sparse Topological Pharmacophore Graphs for Interpretable Scaffold Hopping. J Chem Inf Model 2021; 61:3348-3360. [PMID: 34264667 DOI: 10.1021/acs.jcim.1c00409] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The aim of scaffold hopping (SH) is to find compounds consisting of different scaffolds from those in already known active compounds, giving an opportunity for unexplored regions of chemical space. We previously demonstrated the usefulness of pharmacophore graphs (PhGs) for this purpose through proof-of-concept virtual screening experiments. PhGs consist of nodes and edges corresponding to pharmacophoric features (PFs) and their topological distances. Although PhGs were effective in SH, they are hard to interpret as they are complete graphs. Herein, we introduce an intuitive representation of a molecule, termed as sparse pharmacophore graphs (SPhG) by keeping the topological distances among PFs as much as possible while reducing the number of edges in the graphs. Several benchmark calculations quantitatively confirmed the sparseness of the graphs and the preservation of topological distances among pharmacophoric points. As proof-of-concept applications, virtual screening (VS) trials for SH were conducted using active and inactive compounds from ChEMBL and PubChem databases for three biological targets: thrombin, tyrosine kinase ABL1, and κ-opioid receptor. The performances of VS were comparable with using fully connected PhGs. Furthermore, highly ranked SPhGs were interpretable for the three biological targets, in particular for thrombin, for which selected SPhGs were in agreement with the structure-based interpretation.
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Affiliation(s)
- Hiroshi Nakano
- Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan
| | - Tomoyuki Miyao
- Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan.,Data Science Center, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan
| | - Jasial Swarit
- Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan.,Data Science Center, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan
| | - Kimito Funatsu
- Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan.,Data Science Center, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan.,Department of Chemical System Engineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
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8
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R S, Mk K. Lead optimization of 4-(thio)-chromenone 6- O-sulfamate analogs using QSAR, molecular docking and DFT - a combined approach as steroidal sulfatase inhibitors. J Recept Signal Transduct Res 2020; 41:123-137. [PMID: 32705921 DOI: 10.1080/10799893.2020.1794004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Aromatase and steroidal sulfatase (STS) are steroidogenic enzyme that increases the concentration of estrogens in circulation, a primary factor leading to breast cancer. At molecular level, 87% of STS is expressed and an inhibitor targeting STS could decrease the level of estrogens. In an attempt to identify the chemical structural requirement targeting placental STS inhibition, 26 compounds with pIC50 ranging from 4.61 to 9.46 were subjected to computational studies including Quantitative Structural-Activity Relationship (QSAR), MolecularDocking followed by Density Functional Theory (DFT) studies. A robust and predictable model were developed with good R2 (0.834) and cross-validated correlation coefficient value Q2 LOO (0.786) explaining the relationship quantitatively. The regression graphs suggests that the STS inhibition was greatly dependent on the electro topological state of an atom, sum of the atom type E-state (SdssC), maximum E-states for strong hydrogen bond acceptors (maxHBa) and basic group count descriptor (BCUTp-1h). Furthermore, docking results showed favorable interactions of sulfamate analogs with catalytically important amino acid residues such as LEU74, VAL101, and VAL486. The interactions of the best active compound 3j when compared with standard Irosustat show similar binding energies. DFT studies further confirm the presence of HOMO orbital centered on chromenone ring further highlighting its importance for receptor ligand hydrophobic interaction. The study reveals that substitution of thio in chromenone nucleus and introduction of adamantyl substitution at second position are favorable in inhibiting the enzyme STS.
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Affiliation(s)
- Srimathi R
- Department of Pharmaceutical Chemistry, SRM College of Pharmacy, SRMIST, Kattankulathur, TamilNadu, India
| | - Kathiravan Mk
- Department of Pharmaceutical Chemistry, SRM College of Pharmacy, SRMIST, Kattankulathur, TamilNadu, India.,Dr. APJ Abdul Kalam Research Lab, SRM College of Pharmacy, SRM IST, Kattankulathur, Tamil Nadu, India
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9
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Nakano H, Miyao T, Funatsu K. Exploring Topological Pharmacophore Graphs for Scaffold Hopping. J Chem Inf Model 2020; 60:2073-2081. [DOI: 10.1021/acs.jcim.0c00098] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Hiroshi Nakano
- Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan
| | - Tomoyuki Miyao
- Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan
- Data Science Center, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan
| | - Kimito Funatsu
- Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan
- Data Science Center, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan
- Department of Chemical System Engineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
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10
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Athanasiou C, Cournia Z. From Computers to Bedside: Computational Chemistry Contributing to FDA Approval. BIOMOLECULAR SIMULATIONS IN STRUCTURE-BASED DRUG DISCOVERY 2018. [DOI: 10.1002/9783527806836.ch7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Christina Athanasiou
- Biomedical Research Foundation; Academy of Athens; 4 Soranou Ephessiou 11527 Athens Greece
| | - Zoe Cournia
- Biomedical Research Foundation; Academy of Athens; 4 Soranou Ephessiou 11527 Athens Greece
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11
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Merk D, Grisoni F, Friedrich L, Gelzinyte E, Schneider G. Scaffold hopping from synthetic RXR modulators by virtual screening and de novo design. MEDCHEMCOMM 2018; 9:1289-1292. [PMID: 30151082 PMCID: PMC6096356 DOI: 10.1039/c8md00134k] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2018] [Accepted: 04/15/2018] [Indexed: 01/03/2023]
Abstract
The lack of potent subtype-selective modulators of retinoid X receptors (RXRs) has hindered their full exploitation as promising drug targets. Using computational similarity searching, target prediction and automated de novo design, we identified novel RXR ligands exhibiting innovative molecular frameworks, pronounced receptor-subtype preference and suitable properties for hit-to-lead expansion.
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Affiliation(s)
- Daniel Merk
- Department of Chemistry and Applied Biosciences , Swiss Federal Institute of Technology (ETH) , Vladimir-Prelog-Weg 4 , CH-8093 Zurich , Switzerland .
| | - Francesca Grisoni
- Department of Chemistry and Applied Biosciences , Swiss Federal Institute of Technology (ETH) , Vladimir-Prelog-Weg 4 , CH-8093 Zurich , Switzerland .
- Department of Earth and Environmental Sciences , University of Milano-Bicocca , P.za della Scienza, 1 , IT-20126 Milan , Italy
| | - Lukas Friedrich
- Department of Chemistry and Applied Biosciences , Swiss Federal Institute of Technology (ETH) , Vladimir-Prelog-Weg 4 , CH-8093 Zurich , Switzerland .
| | - Elena Gelzinyte
- Department of Chemistry and Applied Biosciences , Swiss Federal Institute of Technology (ETH) , Vladimir-Prelog-Weg 4 , CH-8093 Zurich , Switzerland .
| | - Gisbert Schneider
- Department of Chemistry and Applied Biosciences , Swiss Federal Institute of Technology (ETH) , Vladimir-Prelog-Weg 4 , CH-8093 Zurich , Switzerland .
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12
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Kumar A, Zhang KYJ. Advances in the Development of Shape Similarity Methods and Their Application in Drug Discovery. Front Chem 2018; 6:315. [PMID: 30090808 PMCID: PMC6068280 DOI: 10.3389/fchem.2018.00315] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 07/09/2018] [Indexed: 12/21/2022] Open
Abstract
Molecular similarity is a key concept in drug discovery. It is based on the assumption that structurally similar molecules frequently have similar properties. Assessment of similarity between small molecules has been highly effective in the discovery and development of various drugs. Especially, two-dimensional (2D) similarity approaches have been quite popular due to their simplicity, accuracy and efficiency. Recently, the focus has been shifted toward the development of methods involving the representation and comparison of three-dimensional (3D) conformation of small molecules. Among the 3D similarity methods, evaluation of shape similarity is now gaining attention for its application not only in virtual screening but also in molecular target prediction, drug repurposing and scaffold hopping. A wide range of methods have been developed to describe molecular shape and to determine the shape similarity between small molecules. The most widely used methods include atom distance-based methods, surface-based approaches such as spherical harmonics and 3D Zernike descriptors, atom-centered Gaussian overlay based representations. Several of these methods demonstrated excellent virtual screening performance not only retrospectively but also prospectively. In addition to methods assessing the similarity between small molecules, shape similarity approaches have been developed to compare shapes of protein structures and binding pockets. Additionally, shape comparisons between atomic models and 3D density maps allowed the fitting of atomic models into cryo-electron microscopy maps. This review aims to summarize the methodological advances in shape similarity assessment highlighting advantages, disadvantages and their application in drug discovery.
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Affiliation(s)
| | - Kam Y. J. Zhang
- Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, Yokohama, Japan
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13
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Abstract
Fragment-based drug design strategies have been used in drug discovery since it was first demonstrated using experimental structural biology techniques such as nuclear magnetic resonance (NMR) and X-ray crystallography. The underlying idea is that existing or new chemical entities with known desirable properties may serve both as tool compounds and as starting points for hit-to-lead expansion. Despite the recent advancements, there remain challenges to overcome, such as assembly of the synthetically feasible structures, development of scoring functions to correlate structure and their activities, and fine tuning of the promising molecules. This chapter first covers the theoretical background needed to understand the concepts and the challenges related to the field of study, followed by the description of important protocols and related software. Case studies are presented to demonstrate practical applications.
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14
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Stepniewska-Dziubinska MM, Zielenkiewicz P, Siedlecki P. DeCAF-Discrimination, Comparison, Alignment Tool for 2D PHarmacophores. Molecules 2017; 22:E1128. [PMID: 28684712 PMCID: PMC6152008 DOI: 10.3390/molecules22071128] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Revised: 06/30/2017] [Accepted: 07/04/2017] [Indexed: 01/24/2023] Open
Abstract
Comparison of small molecules is a common component of many cheminformatics workflows, including the design of new compounds and libraries as well as side-effect predictions and drug repurposing. Currently, large-scale comparison methods rely mostly on simple fingerprint representation of molecules, which take into account the structural similarities of compounds. Methods that utilize 3D information depend on multiple conformer generation steps, which are computationally expensive and can greatly influence their results. The aim of this study was to augment molecule representation with spatial and physicochemical properties while simultaneously avoiding conformer generation. To achieve this goal, we describe a molecule as an undirected graph in which the nodes correspond to atoms with pharmacophoric properties and the edges of the graph represent the distances between features. This approach combines the benefits of a conformation-free representation of a molecule with additional spatial information. We implemented our approach as an open-source Python module called DeCAF (Discrimination, Comparison, Alignment tool for 2D PHarmacophores), freely available at http://bitbucket.org/marta-sd/decaf. We show DeCAF's strengths and weaknesses with usage examples and thorough statistical evaluation. Additionally, we show that our method can be manually tweaked to further improve the results for specific tasks. The full dataset on which DeCAF was evaluated and all scripts used to calculate and analyze the results are also provided.
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Affiliation(s)
| | - Piotr Zielenkiewicz
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland.
- Department of Systems Biology, Institute of Experimental Plant Biology and Biotechnology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland.
| | - Pawel Siedlecki
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland.
- Department of Systems Biology, Institute of Experimental Plant Biology and Biotechnology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland.
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O'Hagan S, Kell DB. Analysis of drug-endogenous human metabolite similarities in terms of their maximum common substructures. J Cheminform 2017; 9:18. [PMID: 28316656 PMCID: PMC5344883 DOI: 10.1186/s13321-017-0198-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 02/09/2017] [Indexed: 12/21/2022] Open
Abstract
In previous work, we have assessed the structural similarities between marketed drugs (‘drugs’) and endogenous natural human metabolites (‘metabolites’ or ‘endogenites’), using ‘fingerprint’ methods in common use, and the Tanimoto and Tversky similarity metrics, finding that the fingerprint encoding used had a dramatic effect on the apparent similarities observed. By contrast, the maximal common substructure (MCS), when the means of determining it is fixed, is a means of determining similarities that is largely independent of the fingerprints, and also has a clear chemical meaning. We here explored the utility of the MCS and metrics derived therefrom. In many cases, a shared scaffold helps cluster drugs and endogenites, and gives insight into enzymes (in particular transporters) that they both share. Tanimoto and Tversky similarities based on the MCS tend to be smaller than those based on the MACCS fingerprint-type encoding, though the converse is also true for a significant fraction of the comparisons. While no single molecular descriptor can account for these differences, a machine learning-based analysis of the nature of the differences (MACCS_Tanimoto vs MCS_Tversky) shows that they are indeed deterministic, although the features that are used in the model to account for this vary greatly with each individual drug. The extent of its utility and interpretability vary with the drug of interest, implying that while MCS is neither ‘better’ nor ‘worse’ for every drug–endogenite comparison, it is sufficiently different to be of value. The overall conclusion is thus that the use of the MCS provides an additional and valuable strategy for understanding the structural basis for similarities between synthetic, marketed drugs and natural intermediary metabolites.
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Affiliation(s)
- Steve O'Hagan
- School of Chemistry, The University of Manchester, 131 Princess St, Manchester, M1 7DN UK.,Manchester Institute of Biotechnology, The University of Manchester, 131 Princess St, Manchester, M1 7DN UK
| | - Douglas B Kell
- School of Chemistry, The University of Manchester, 131 Princess St, Manchester, M1 7DN UK.,Manchester Institute of Biotechnology, The University of Manchester, 131 Princess St, Manchester, M1 7DN UK.,Centre for the Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), The University of Manchester, 131 Princess St, Manchester, M1 7DN UK
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16
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Naderi M, Alvin C, Ding Y, Mukhopadhyay S, Brylinski M. A graph-based approach to construct target-focused libraries for virtual screening. J Cheminform 2016; 8:14. [PMID: 26981157 PMCID: PMC4791927 DOI: 10.1186/s13321-016-0126-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 03/03/2016] [Indexed: 01/21/2023] Open
Abstract
Background Due to exorbitant costs of high-throughput screening, many drug discovery projects commonly employ inexpensive virtual screening to support experimental efforts. However, the vast majority of compounds in widely used screening libraries, such as the ZINC database, will have a very low probability to exhibit the desired bioactivity for a given protein. Although combinatorial chemistry methods can be used to augment existing compound libraries with novel drug-like compounds, the broad chemical space is often too large to be explored. Consequently, the trend in library design has shifted to produce screening collections specifically tailored to modulate the function of a particular target or a protein family.
Methods Assuming that organic compounds are composed of sets of rigid fragments connected by flexible linkers, a molecule can be decomposed into its building blocks tracking their atomic connectivity. On this account, we developed eSynth, an exhaustive graph-based search algorithm to computationally synthesize new compounds by reconnecting these building blocks following their connectivity patterns. Results We conducted a series of benchmarking calculations against the Directory of Useful Decoys, Enhanced database. First, in a self-benchmarking test, the correctness of the algorithm is validated with the objective to recover a molecule from its building blocks. Encouragingly, eSynth can efficiently rebuild more than 80 % of active molecules from their fragment components. Next, the capability to discover novel scaffolds is assessed in a cross-benchmarking test, where eSynth successfully reconstructed 40 % of the target molecules using fragments extracted from chemically distinct compounds. Despite an enormous chemical space to be explored, eSynth is computationally efficient; half of the molecules are rebuilt in less than a second, whereas 90 % take only about a minute to be generated. Conclusions eSynth can successfully reconstruct chemically feasible molecules from molecular fragments.
Furthermore, in a procedure mimicking the real application, where one expects to discover novel compounds based on a small set of already developed bioactives, eSynth is capable of generating diverse collections of molecules with the desired activity profiles. Thus, we are very optimistic that our effort will contribute to targeted drug discovery. eSynth is freely available to the academic community at www.brylinski.org/content/molecular-synthesis.Assuming that organic compounds are composed of sets of rigid fragments connected by flexible linkers, a molecule can be decomposed into its building blocks tracking their atomic connectivity. Here, we developed eSynth, an automated method to synthesize new compounds by reconnecting these building blocks following the connectivity patterns via an exhaustive graph-based search algorithm. eSynth opens up a possibility to rapidly construct virtual screening libraries for targeted drug discovery ![]()
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Affiliation(s)
- Misagh Naderi
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA USA
| | - Chris Alvin
- Department of Computer Science and Information Systems, Bradley University, Peoria, IL USA
| | - Yun Ding
- Department of Physics and Astronomy, Louisiana State University, Baton Rouge, LA USA
| | - Supratik Mukhopadhyay
- Department of Computer Science and Engineering, Louisiana State University, Baton Rouge, LA USA
| | - Michal Brylinski
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA USA ; Center for Computation and Technology, Louisiana State University, Baton Rouge, LA USA
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17
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Systematic assessment of scaffold hopping versus activity cliff formation across bioactive compound classes following a molecular hierarchy. Bioorg Med Chem 2015; 23:3183-91. [DOI: 10.1016/j.bmc.2015.04.067] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Revised: 04/21/2015] [Accepted: 04/24/2015] [Indexed: 11/22/2022]
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18
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Sukumar N, Krein MP, Prabhu G, Bhattacharya S, Sen S. Network measures for chemical library design. Drug Dev Res 2015; 75:402-11. [PMID: 25195584 DOI: 10.1002/ddr.21218] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
In this overview, we examine recent developments in network approaches to drug design. A brief overview of networks is followed by a discussion of how chemical similarity networks and their properties address challenges in drug design. Multiple methods used to assess or enhance chemical diversity for early-stage drug discovery are discussed, as well as methods that can be used for drug repositioning and ligand polypharmacology.
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Affiliation(s)
- Nagamani Sukumar
- Department of Chemistry, Shiv Nadar University, Dadri, Gautam Budh Nagar, U.P., 201314, India; Center for Informatics, Shiv Nadar University, Dadri, Gautam Budh Nagar, U.P., 201314, India
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19
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Schultes S, Kooistra AJ, Vischer HF, Nijmeijer S, Haaksma EEJ, Leurs R, de Esch IJP, de Graaf C. Combinatorial Consensus Scoring for Ligand-Based Virtual Fragment Screening: A Comparative Case Study for Serotonin 5-HT(3)A, Histamine H(1), and Histamine H(4) Receptors. J Chem Inf Model 2015; 55:1030-44. [PMID: 25815783 DOI: 10.1021/ci500694c] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
In the current study we have evaluated the applicability of ligand-based virtual screening (LBVS) methods for the identification of small fragment-like biologically active molecules using different similarity descriptors and different consensus scoring approaches. For this purpose, we have evaluated the performance of 14 chemical similarity descriptors in retrospective virtual screening studies to discriminate fragment-like ligands of three membrane-bound receptors from fragments that are experimentally determined to have no affinity for these proteins (true inactives). We used a complete fragment affinity data set of experimentally determined ligands and inactives for two G protein-coupled receptors (GPCRs), the histamine H1 receptor (H1R) and the histamine H4 receptor (H4R), and one ligand-gated ion channel (LGIC), the serotonin receptor (5-HT3AR), to validate our retrospective virtual screening studies. We have exhaustively tested consensus scoring strategies that combine the results of multiple actives (group fusion) or combine different similarity descriptors (similarity fusion), and for the first time systematically evaluated different combinations of group fusion and similarity fusion approaches. Our studies show that for these three case study protein targets both consensus scoring approaches can increase virtual screening enrichments compared to single chemical similarity search methods. Our cheminformatics analyses recommend to use a combination of both group fusion and similarity fusion for prospective ligand-based virtual fragment screening.
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Affiliation(s)
- Sabine Schultes
- †Division of Medicinal Chemistry, Faculty of Sciences, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Albert J Kooistra
- †Division of Medicinal Chemistry, Faculty of Sciences, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Henry F Vischer
- †Division of Medicinal Chemistry, Faculty of Sciences, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Saskia Nijmeijer
- †Division of Medicinal Chemistry, Faculty of Sciences, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Eric E J Haaksma
- †Division of Medicinal Chemistry, Faculty of Sciences, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Rob Leurs
- †Division of Medicinal Chemistry, Faculty of Sciences, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Iwan J P de Esch
- †Division of Medicinal Chemistry, Faculty of Sciences, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Chris de Graaf
- †Division of Medicinal Chemistry, Faculty of Sciences, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
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Roy A, Skolnick J. LIGSIFT: an open-source tool for ligand structural alignment and virtual screening. Bioinformatics 2014; 31:539-44. [PMID: 25336501 DOI: 10.1093/bioinformatics/btu692] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION Shape-based alignment of small molecules is a widely used approach in computer-aided drug discovery. Most shape-based ligand structure alignment applications, both commercial and freely available ones, use the Tanimoto coefficient or similar functions for evaluating molecular similarity. Major drawbacks of using such functions are the size dependence of the score and the fact that the statistical significance of the molecular match using such metrics is not reported. RESULTS We describe a new open-source ligand structure alignment and virtual screening (VS) algorithm, LIGSIFT, that uses Gaussian molecular shape overlay for fast small molecule alignment and a size-independent scoring function for efficient VS based on the statistical significance of the score. LIGSIFT was tested against the compounds for 40 protein targets available in the Directory of Useful Decoys and the performance was evaluated using the area under the ROC curve (AUC), the Enrichment Factor (EF) and Hit Rate (HR). LIGSIFT-based VS shows an average AUC of 0.79, average EF values of 20.8 and a HR of 59% in the top 1% of the screened library. AVAILABILITY AND IMPLEMENTATION LIGSIFT software, including the source code, is freely available to academic users at http://cssb.biology.gatech.edu/LIGSIFT. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online. CONTACT skolnick@gatech.edu.
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Affiliation(s)
- Ambrish Roy
- Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, Atlanta, GA 30076, USA
| | - Jeffrey Skolnick
- Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, Atlanta, GA 30076, USA
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21
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Willett P. The Calculation of Molecular Structural Similarity: Principles and Practice. Mol Inform 2014; 33:403-13. [DOI: 10.1002/minf.201400024] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Accepted: 03/14/2014] [Indexed: 01/28/2023]
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22
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Maggiora G, Vogt M, Stumpfe D, Bajorath J. Molecular similarity in medicinal chemistry. J Med Chem 2013; 57:3186-204. [PMID: 24151987 DOI: 10.1021/jm401411z] [Citation(s) in RCA: 352] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Similarity is a subjective and multifaceted concept, regardless of whether compounds or any other objects are considered. Despite its intrinsically subjective nature, attempts to quantify the similarity of compounds have a long history in chemical informatics and drug discovery. Many computational methods employ similarity measures to identify new compounds for pharmaceutical research. However, chemoinformaticians and medicinal chemists typically perceive similarity in different ways. Similarity methods and numerical readouts of similarity calculations are probably among the most misunderstood computational approaches in medicinal chemistry. Herein, we evaluate different similarity concepts, highlight key aspects of molecular similarity analysis, and address some potential misunderstandings. In addition, a number of practical aspects concerning similarity calculations are discussed.
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Affiliation(s)
- Gerald Maggiora
- College of Pharmacy and BIO5 Institute, University of Arizona , 1295 North Martin, P.O. Box 210202, Tucson, Arizona 85721, United States
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23
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Gfeller D, Michielin O, Zoete V. Shaping the interaction landscape of bioactive molecules. ACTA ACUST UNITED AC 2013; 29:3073-9. [PMID: 24048355 DOI: 10.1093/bioinformatics/btt540] [Citation(s) in RCA: 279] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
MOTIVATION Most bioactive molecules perform their action by interacting with proteins or other macromolecules. However, for a significant fraction of them, the primary target remains unknown. In addition, the majority of bioactive molecules have more than one target, many of which are poorly characterized. Computational predictions of bioactive molecule targets based on similarity with known ligands are powerful to narrow down the number of potential targets and to rationalize side effects of known molecules. RESULTS Using a reference set of 224 412 molecules active on 1700 human proteins, we show that accurate target prediction can be achieved by combining different measures of chemical similarity based on both chemical structure and molecular shape. Our results indicate that the combined approach is especially efficient when no ligand with the same scaffold or from the same chemical series has yet been discovered. We also observe that different combinations of similarity measures are optimal for different molecular properties, such as the number of heavy atoms. This further highlights the importance of considering different classes of similarity measures between new molecules and known ligands to accurately predict their targets.
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Affiliation(s)
- David Gfeller
- Swiss Institute of Bioinformatics (SIB), Quartier Sorge, Bâtiment Génopode, CH-1015 Lausanne, Switzerland, Ludwig Institute for Cancer Research and Pluridisciplinary Center for Clinical Oncology, Centre Hospitalier Universitaire Vaudois, CH-1015 Lausanne, Switzerland
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24
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Westermaier Y, Veurink M, Riis-Johannessen T, Guinchard S, Gurny R, Scapozza L. Identification of aggregation breakers for bevacizumab (Avastin®) self-association through similarity searching and interaction studies. Eur J Pharm Biopharm 2013; 85:773-80. [PMID: 23665445 DOI: 10.1016/j.ejpb.2013.04.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Revised: 04/16/2013] [Accepted: 04/19/2013] [Indexed: 10/26/2022]
Abstract
Aggregation is a common challenge in the optimization of therapeutic antibody formulations. Since initial self-association of two monomers is typically a reversible process, the aim of this study is to identify different excipients that are able to shift this equilibrium to the monomeric state. The hypothesis is that a specific interaction between excipient and antibody may hinder two monomers from approaching each other, based on previous work in which dexamethasone phosphate showed the ability to partially reverse formed aggregates of the monoclonal IgG1 antibody bevacizumab back into monomers. The current study focuses on the selection of therapeutically inactive compounds with similar properties. Adenosine monophosphate, adenosine triphosphate, sucrose-6-phosphate and guanosine monophosphate were selected in silico through similarity searching and docking. All four compounds were predicted to bind to a protein-protein interaction hotspot on the Fc region of bevacizumab and thereby breaking dimer formation. The predictions were supported in vitro: An interaction between AMP and bevacizumab with a dissociation constant of 9.59±0.15 mM was observed by microscale thermophoresis. The stability of the antibody at elevated temperature (40 °C) in a 51 mM phosphate buffer pH 7 was investigated in presence and absence of the excipients. Quantification of the different aggregation species by asymmetrical flow field-flow fractionation and size exclusion chromatography demonstrates that all four excipients are able to partially overcome the initial self-association of bevacizumab monomers.
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Affiliation(s)
- Y Westermaier
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Geneva 4, Switzerland
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25
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Reutlinger M, Koch CP, Reker D, Todoroff N, Schneider P, Rodrigues T, Schneider G. Chemically Advanced Template Search (CATS) for Scaffold-Hopping and Prospective Target Prediction for 'Orphan' Molecules. Mol Inform 2013; 32:133-138. [PMID: 23956801 PMCID: PMC3743170 DOI: 10.1002/minf.201200141] [Citation(s) in RCA: 117] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Accepted: 01/18/2013] [Indexed: 02/04/2023]
Affiliation(s)
- Michael Reutlinger
- ETH, Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences Wolfgang-Pauli-Str. 10, CH-8093 Zurich, Switzerland fax: +41 44 633 13 79, tel: +41 44 633 74 38
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Aparoy P, Reddy KK, Reddanna P. Structure and ligand based drug design strategies in the development of novel 5- LOX inhibitors. Curr Med Chem 2012; 19:3763-78. [PMID: 22680930 PMCID: PMC3480706 DOI: 10.2174/092986712801661112] [Citation(s) in RCA: 88] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2011] [Revised: 01/30/2012] [Accepted: 02/07/2012] [Indexed: 12/26/2022]
Abstract
Lipoxygenases (LOXs) are non-heme iron containing dioxygenases involved in the oxygenation of polyunsaturated fatty acids (PUFAs) such as arachidonic acid (AA). Depending on the position of insertion of oxygen, LOXs are classified into 5-, 8-, 9-, 12- and 15-LOX. Among these, 5-LOX is the most predominant isoform associated with the formation of 5-hydroperoxyeicosatetraenoic acid (5-HpETE), the precursor of non-peptido (LTB4) and peptido (LTC4, LTD4, and LTE4) leukotrienes. LTs are involved in inflammatory and allergic diseases like asthma, ulcerative colitis, rhinitis and also in cancer. Consequently 5-LOX has become target for the development of therapeutic molecules for treatment of various inflammatory disorders. Zileuton is one such inhibitor of 5-LOX approved for the treatment of asthma. In the recent times, computer aided drug design (CADD) strategies have been applied successfully in drug development processes. A comprehensive review on structure based drug design strategies in the development of novel 5-LOX inhibitors is presented in this article. Since the crystal structure of 5-LOX has been recently solved, efforts to develop 5-LOX inhibitors have mostly relied on ligand based rational approaches. The present review provides a comprehensive survey on these strategies in the development of 5-LOX inhibitors.
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Sun H, Tawa G, Wallqvist A. Classification of scaffold-hopping approaches. Drug Discov Today 2012; 17:310-24. [PMID: 22056715 PMCID: PMC3328312 DOI: 10.1016/j.drudis.2011.10.024] [Citation(s) in RCA: 247] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2011] [Revised: 10/17/2011] [Accepted: 10/19/2011] [Indexed: 10/15/2022]
Abstract
The general goal of drug discovery is to identify novel compounds that are active against a preselected biological target with acceptable pharmacological properties defined by marketed drugs. Scaffold hopping has been widely applied by medicinal chemists to discover equipotent compounds with novel backbones that have improved properties. In this article we classify scaffold hopping into four major categories, namely heterocycle replacements, ring opening or closure, peptidomimetics and topology-based hopping. We review the structural diversity of original and final scaffolds with respect to each category. We discuss the advantages and limitations of small, medium and large-step scaffold hopping. Finally, we summarize software that is frequently used to facilitate different kinds of scaffold-hopping methods.
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Affiliation(s)
- Hongmao Sun
- Biotechnology HPC Software Applications Institute, Telemedicine and Advanced Technology Research Center, US Army Medical Research and Materiel Command, Fort Frederick, MD 21702, USA.
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Investigation of imatinib and other approved drugs as starting points for antidiabetic drug discovery with FXR modulating activity. Biochem Pharmacol 2012; 83:1674-81. [PMID: 22414727 DOI: 10.1016/j.bcp.2012.02.027] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2012] [Revised: 02/25/2012] [Accepted: 02/28/2012] [Indexed: 12/11/2022]
Abstract
A self-organizing map (SOM) is a virtual screening method used for correlation of molecular structure and potential biological activity on a certain target and offers a way to represent multi-dimensional data of large databases in a two-dimensional space. Large databases, for example the DrugBank database, provide information about biological activity and chemical structure of small molecules and are widely used in drug development for identification of new lead structures. The farnesoid X receptor (FXR) is a ligand activated transcription factor involved in key regulation mechanisms within glucose and lipid homeostasis. Although FXR became an established target in drug development for diseases associated with lipid, glucose or hepatic disorders during the last decade, none of the developed compounds have reached later phases of clinical development so far. We used a SOM trained with known FXR ligands to screen the DrugBank database for potential ligands for FXR. In this article, we report the successful identification of six approved drugs out of the Drugbank as FXR modulators (ketoconazole, pentamidine, dobutamine, imatinib, papaverine and montelukast) by using a SOM for screening of the DrugBank database. We show FXR modulation by selected compounds in a full length FXR transactivation assay and modulation of a FXR target gene by imatinib.
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Pencheva T, Lagorce D, Pajeva I, Villoutreix BO, Miteva MA. AMMOS software: method and application. Methods Mol Biol 2012; 819:127-141. [PMID: 22183534 DOI: 10.1007/978-1-61779-465-0_9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Recent advances in computational sciences enabled extensive use of in silico methods in projects at the interface between chemistry and biology. Among them virtual ligand screening, a modern set of approaches, facilitates hit identification and lead optimization in drug discovery programs. Most of these approaches require the preparation of the libraries containing small organic molecules to be screened or a refinement of the virtual screening results. Here we present an overview of the open source AMMOS software, which is a platform performing an automatic procedure that allows for a structural generation and optimization of drug-like molecules in compound collections, as well as a structural refinement of protein-ligand complexes to assist in silico screening exercises.
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Affiliation(s)
- T Pencheva
- Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, Sofia, Bulgaria
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Harris CJ, Hill RD, Sheppard DW, Slater MJ, Stouten PFW. The design and application of target-focused compound libraries. Comb Chem High Throughput Screen 2011; 14:521-31. [PMID: 21521154 PMCID: PMC3182092 DOI: 10.2174/138620711795767802] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2010] [Accepted: 04/09/2011] [Indexed: 11/22/2022]
Abstract
Target-focused compound libraries are collections of compounds which are designed to interact with an individual protein target or, frequently, a family of related targets (such as kinases, voltage-gated ion channels, serine/cysteine proteases). They are used for screening against therapeutic targets in order to find hit compounds that might be further developed into drugs. The design of such libraries generally utilizes structural information about the target or family of interest. In the absence of such structural information, a chemogenomic model that incorporates sequence and mutagenesis data to predict the properties of the binding site can be employed. A third option, usually pursued when no structural data are available, utilizes knowledge of the ligands of the target from which focused libraries can be developed via scaffold hopping. Consequently, the methods used for the design of target-focused libraries vary according to the quantity and quality of structural or ligand data that is available for each target family. This article describes examples of each of these design approaches and illustrates them with case studies, which highlight some of the issues and successes observed when screening target-focused libraries.
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Smith VC, Cleghorn LAT, Woodland A, Spinks D, Hallyburton I, Collie IT, Mok NY, Norval S, Brenk R, Fairlamb AH, Frearson JA, Read KD, Gilbert IH, Wyatt PG. Optimisation of the anti-Trypanosoma brucei activity of the opioid agonist U50488. ChemMedChem 2011; 6:1832-40. [PMID: 21834094 PMCID: PMC3229842 DOI: 10.1002/cmdc.201100278] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2011] [Revised: 07/18/2011] [Indexed: 11/13/2022]
Abstract
Screening of the Sigma–Aldrich Library of Pharmacologically Active Compounds (LOPAC) against cultured Trypanosoma brucei, the causative agent of African sleeping sickness, resulted in the identification of a number of compounds with selective antiproliferative activity over mammalian cells. These included (+)-(1R,2R)-U50488, a weak opioid agonist with an EC50 value of 59 nm as determined in our T. brucei in vitro assay reported previously. This paper describes the modification of key structural elements of U50488 to investigate structure–activity relationships (SAR) and to optimise the antiproliferative activity and pharmacokinetic properties of this compound.
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Affiliation(s)
- Victoria C Smith
- Drug Discovery Unit, College of Life Sciences, James Black Centre, University of Dundee, Dundee, DD1 5EH, Scotland, UK
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32
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Koeppen H, Kriegl J, Lessel U, Tautermann CS, Wellenzohn B. Ligand-Based Virtual Screening. METHODS AND PRINCIPLES IN MEDICINAL CHEMISTRY 2011. [DOI: 10.1002/9783527633326.ch3] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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33
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Zhan P, Chen X, Li D, Fang Z, De Clercq E, Liu X. HIV-1 NNRTIs: structural diversity, pharmacophore similarity, and implications for drug design. Med Res Rev 2011; 33 Suppl 1:E1-72. [PMID: 21523792 DOI: 10.1002/med.20241] [Citation(s) in RCA: 153] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Nonnucleoside reverse transcriptase inhibitors (NNRTIs) nowadays represent very potent and most promising anti-AIDS agents that specifically target the HIV-1 reverse transcriptase (RT). However, the effectiveness of NNRTI drugs can be hampered by rapid emergence of drug-resistant viruses and severe side effects upon long-term use. Therefore, there is an urgent need to develop novel, highly potent NNRTIs with broad spectrum antiviral activity and improved pharmacokinetic properties, and more efficient strategies that facilitate and shorten the drug discovery process would be extremely beneficial. Fortunately, the structural diversity of NNRTIs provided a wide space for novel lead discovery, and the pharmacophore similarity of NNRTIs gave valuable hints for lead discovery and optimization. More importantly, with the continued efforts in the development of computational tools and increased crystallographic information on RT/NNRTI complexes, structure-based approaches using a combination of traditional medicinal chemistry, structural biology, and computational chemistry are being used increasingly in the design of NNRTIs. First, this review covers two decades of research and development for various NNRTI families based on their chemical scaffolds, and then describes the structural similarity of NNRTIs. We have attempted to assemble a comprehensive overview of the general approaches in NNRTI lead discovery and optimization reported in the literature during the last decade. The successful applications of medicinal chemistry strategies, crystallography, and computational tools for designing novel NNRTIs are highlighted. Future directions for research are also outlined.
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Affiliation(s)
- Peng Zhan
- Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Shandong University, Jinan, Shandong, PR China
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34
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Rödl CB, Tanrikulu Y, Wisniewska JM, Proschak E, Schneider G, Steinhilber D, Hofmann B. Potent Inhibitors of 5-Lipoxygenase Identified using Pseudoreceptors. ChemMedChem 2011; 6:1001-5. [DOI: 10.1002/cmdc.201100059] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2011] [Indexed: 01/19/2023]
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35
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Recent trends and observations in the design of high-quality screening collections. Future Med Chem 2011; 3:751-66. [DOI: 10.4155/fmc.11.15] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The design of a high-quality screening collection is of utmost importance for the early drug-discovery process and provides, in combination with high-quality assay systems, the foundation of future discoveries. Herein, we review recent trends and observations to successfully expand the access to bioactive chemical space, including the feedback from hit assessment interviews of high-throughput screening campaigns; recent successes with chemogenomics target family approaches, the identification of new relevant target/domain families, diversity-oriented synthesis and new emerging compound classes, and non-classical approaches, such as fragment-based screening and DNA-encoded chemical libraries. The role of in silico library design approaches are emphasized.
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36
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Warr WA. Representation of chemical structures. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2011. [DOI: 10.1002/wcms.36] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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37
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Abstract
Background: It has been suggested that similarity searching using 2D fingerprints may not be suitable for scaffold hopping. Methods: This article reports a detailed evaluation of the effectiveness of six common types of 2D fingerprints when they are used for scaffold-hopping similarity searches of the Molecular Design Limited Drug Data Report database, World of Molecular Bioactivity database and Maximum Unbiased Validation database. Results: The results demonstrate that 2D fingerprints can be used for scaffold hopping, with novel scaffolds being identified in nearly every search that was carried out. The degree of enrichment depends on the structural diversity of the actives that are being sought, with the greatest enrichments often being obtained using the extended connectivity fingerprint encoding a circular substructure of diameter four bonds (ECFP4) fingerprint. Conclusion: 2D fingerprints provide a simple and computationally efficient way of identifying novel chemotypes in lead-discovery programs.
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38
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Horvath D, Koch C, Schneider G, Marcou G, Varnek A. Local neighborhood behavior in a combinatorial library context. J Comput Aided Mol Des 2011; 25:237-52. [PMID: 21318427 DOI: 10.1007/s10822-011-9416-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2010] [Accepted: 01/31/2011] [Indexed: 11/30/2022]
Abstract
This article revisits a particular aspect of the molecular similarity principle-the Neighborhood Behavior (NB) concept. Earlier, the NB optimality criterion was introduced to select descriptor spaces, combining a given descriptor set and a similarity metric, which optimally comply with the similarity principle. Here, we focus on a "local" analysis based on the neighborhood of individual bioactive compounds. The defined NB-score measures similarity-based virtual screening success when using individual actives as queries. Systematic studies of local NB have been performed on a large combinatorial library of compounds with reported IC (50) values for five proteases, involving more than 140 descriptor/metric combinations of various fragment- and pharmacophore-based descriptors and different similarity metrics. Although, for each descriptor/metrics combination, the NB-score heavily depends on the query compound, on the average, 2D pharmacophore-based descriptors outperformed their 3D counterparts.
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Affiliation(s)
- Dragos Horvath
- Laboratoire d'InfoChime, UMR 7177 Université de Strasbourg-CNRS, Institut de Chimie, 4, rue Blaise Pascal, 67000 Strasbourg, France.
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39
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Nasonov AF. Computational methods and software in computer-aided combinatorial library design. RUSS J GEN CHEM+ 2011. [DOI: 10.1134/s1070363210120248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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40
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Classification of Aurora-A Kinase Inhibitors Using Self-Organizing Map (SOM) and Support Vector Machine (SVM). Mol Inform 2011; 30:35-44. [DOI: 10.1002/minf.201000106] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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41
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Synthetic conjugates of genistein affecting proliferation and mitosis of cancer cells. Bioorg Med Chem 2011; 19:295-305. [DOI: 10.1016/j.bmc.2010.11.024] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2010] [Revised: 11/04/2010] [Accepted: 11/08/2010] [Indexed: 12/30/2022]
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42
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Abstract
Molecular similarity is a pervasive concept in chemistry. It is essential to many aspects of chemical reasoning and analysis and is perhaps the fundamental assumption underlying medicinal chemistry. Dissimilarity, the complement of similarity, also plays a major role in a growing number of applications of molecular diversity in combinatorial chemistry, high-throughput screening, and related fields. How molecular information is represented, called the representation problem, is important to the type of molecular similarity analysis (MSA) that can be carried out in any given situation. In this work, four types of mathematical structure are used to represent molecular information: sets, graphs, vectors, and functions. Molecular similarity is a pairwise relationship that induces structure into sets of molecules, giving rise to the concept of chemical space. Although all three concepts - molecular similarity, molecular representation, and chemical space - are treated in this chapter, the emphasis is on molecular similarity measures. Similarity measures, also called similarity coefficients or indices, are functions that map pairs of compatible molecular representations that are of the same mathematical form into real numbers usually, but not always, lying on the unit interval. This chapter presents a somewhat pedagogical discussion of many types of molecular similarity measures, their strengths and limitations, and their relationship to one another. An expanded account of the material on chemical spaces presented in the first edition of this book is also provided. It includes a discussion of the topography of activity landscapes and the role that activity cliffs in these landscapes play in structure-activity studies.
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Ripphausen P, Nisius B, Peltason L, Bajorath J. Quo Vadis, Virtual Screening? A Comprehensive Survey of Prospective Applications. J Med Chem 2010; 53:8461-7. [DOI: 10.1021/jm101020z] [Citation(s) in RCA: 186] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Peter Ripphausen
- B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Department of Life Science Informatics, Rheinische Friedrich-Wilhelms-Universität, Dahlmannstrasse 2, D-53113 Bonn, Germany
| | - Britta Nisius
- B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Department of Life Science Informatics, Rheinische Friedrich-Wilhelms-Universität, Dahlmannstrasse 2, D-53113 Bonn, Germany
| | - Lisa Peltason
- B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Department of Life Science Informatics, Rheinische Friedrich-Wilhelms-Universität, Dahlmannstrasse 2, D-53113 Bonn, Germany
| | - Jürgen Bajorath
- B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Department of Life Science Informatics, Rheinische Friedrich-Wilhelms-Universität, Dahlmannstrasse 2, D-53113 Bonn, Germany
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44
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Hu Y, Bajorath J. Structural and Potency Relationships between Scaffolds of Compounds Active against Human Targets. ChemMedChem 2010; 5:1681-5. [DOI: 10.1002/cmdc.201000272] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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45
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Vogt M, Stumpfe D, Geppert H, Bajorath J. Scaffold Hopping Using Two-Dimensional Fingerprints: True Potential, Black Magic, or a Hopeless Endeavor? Guidelines for Virtual Screening. J Med Chem 2010; 53:5707-15. [DOI: 10.1021/jm100492z] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Martin Vogt
- Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Dahlmannstrasse 2, D-53113 Bonn, Germany
| | - Dagmar Stumpfe
- Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Dahlmannstrasse 2, D-53113 Bonn, Germany
| | - Hanna Geppert
- Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Dahlmannstrasse 2, D-53113 Bonn, Germany
| | - Jürgen Bajorath
- Department of Life Science Informatics, B-IT, LIMES Program Unit Chemical Biology and Medicinal Chemistry, Rheinische Friedrich-Wilhelms-Universität, Dahlmannstrasse 2, D-53113 Bonn, Germany
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46
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Lead generation and optimization based on protein-ligand complementarity. Molecules 2010; 15:4382-400. [PMID: 20657448 PMCID: PMC6264460 DOI: 10.3390/molecules15064382] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2010] [Accepted: 06/07/2010] [Indexed: 01/16/2023] Open
Abstract
This work proposes a computational procedure for structure-based lead generation and optimization, which relies on the complementarity of the protein-ligand interactions. This procedure takes as input the known structure of a protein-ligand complex. Retaining the positions of the ligand heavy atoms in the protein binding site it designs structurally similar compounds considering all possible combinations of atomic species (N, C, O, CH3, NH, etc). Compounds are ranked based on a score which incorporates energetic contributions evaluated using molecular mechanics force fields. This procedure was used to design new inhibitor molecules for three serine/threonine protein kinases (p38 MAP kinase, p42 MAP kinase (ERK2), and c-Jun N-terminal kinase 3 (JNK3)). For each enzyme, the calculations produce a set of potential inhibitors whose scores are in agreement with IC50 data and Ki values. Furthermore, the native ligands for each protein target, scored within the five top-ranking compounds predicted by our method, one of the top-ranking compounds predicted to inhibit JNK3 was synthesized and his inhibitory activity confirmed against ATP hydrolysis. Our computational procedure is therefore deemed to be a useful tool for generating chemically diverse molecules active against known target proteins.
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47
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Langdon SR, Ertl P, Brown N. Bioisosteric Replacement and Scaffold Hopping in Lead Generation and Optimization. Mol Inform 2010; 29:366-85. [PMID: 27463193 DOI: 10.1002/minf.201000019] [Citation(s) in RCA: 145] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2010] [Accepted: 04/01/2010] [Indexed: 11/09/2022]
Abstract
Bioisosteric replacement and scaffold hopping are twin methods used in drug design to improve the synthetic accessibility, potency and drug like properties of a compound and to move into novel chemical space. Bioisosteric replacement involves swapping functional groups of a molecule with other functional groups that have similar biological properties. Scaffold hopping is the replacement of the core framework of a molecule with another scaffold that will improve the properties of the molecule or to find similar potent compounds that exist in novel chemical space. This review outlines the key concepts, importance and challenges of both methods using examples and comparisons of techniques available for finding bioisosteric replacements and scaffold hops. There are many methods available for bioisosteric replacement and scaffold hopping, all with their own advantages and disadvantages. Drug design projects would benefit from a combination of these methods to retrieve diverse and complimentary results. Continuing progress in these fields will allow further validation of both methods as well as the accumulation of knowledge on bioisosteres and possible scaffold replacements.
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Affiliation(s)
- Sarah R Langdon
- In Silico Medicinal Chemistry, Cancer Research UK Centre for Cancer Therapeutics, The Institute of Cancer Research, 15 Cotswold Road, Sutton, SM2 5NG, UK phone/fax: +44 (0) 20 8722 4033/+44 (0) 20 8722 4205
| | - Peter Ertl
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Nathan Brown
- In Silico Medicinal Chemistry, Cancer Research UK Centre for Cancer Therapeutics, The Institute of Cancer Research, 15 Cotswold Road, Sutton, SM2 5NG, UK phone/fax: +44 (0) 20 8722 4033/+44 (0) 20 8722 4205.
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48
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Das S, Krein MP, Breneman CM. Binding affinity prediction with property-encoded shape distribution signatures. J Chem Inf Model 2010; 50:298-308. [PMID: 20095526 PMCID: PMC2846646 DOI: 10.1021/ci9004139] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
We report the use of the molecular signatures known as "property-encoded shape distributions" (PESD) together with standard support vector machine (SVM) techniques to produce validated models that can predict the binding affinity of a large number of protein ligand complexes. This "PESD-SVM" method uses PESD signatures that encode molecular shapes and property distributions on protein and ligand surfaces as features to build SVM models that require no subjective feature selection. A simple protocol was employed for tuning the SVM models during their development, and the results were compared to SFCscore, a regression-based method that was previously shown to perform better than 14 other scoring functions. Although the PESD-SVM method is based on only two surface property maps, the overall results were comparable. For most complexes with a dominant enthalpic contribution to binding (DeltaH/-TDeltaS > 3), a good correlation between true and predicted affinities was observed. Entropy and solvent were not considered in the present approach, and further improvement in accuracy would require accounting for these components rigorously.
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Affiliation(s)
- Sourav Das
- Department of Chemistry & Chemical Biology, Rensselaer Polytechnic Institute, 110-8th Street, Troy, NY 12180
| | - Michael P. Krein
- Department of Chemistry & Chemical Biology, Rensselaer Polytechnic Institute, 110-8th Street, Troy, NY 12180
| | - Curt M. Breneman
- Department of Chemistry & Chemical Biology / RECCR Center Rensselaer Polytechnic Institute, 110-8th Street, Center for Biotechnology and Interdisciplinary Studies, Troy, NY 12180, Phone Number: 518-276-2678, Fax Number: 518-276-4887,
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49
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Hu Y, Bajorath J. Global assessment of scaffold hopping potential for current pharmaceutical targets. MEDCHEMCOMM 2010. [DOI: 10.1039/c0md00156b] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A scaffold-based target network is shown together with scaffold pairs having different scaffold hopping potential for a given target.
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Affiliation(s)
- Ye Hu
- Department of Life Science Informatics
- B-IT
- LIMES Program Unit Chemical Biology and Medicinal Chemistry
- Rheinische Friedrich-Wilhelms-Universität
- Germany
| | - Jürgen Bajorath
- Department of Life Science Informatics
- B-IT
- LIMES Program Unit Chemical Biology and Medicinal Chemistry
- Rheinische Friedrich-Wilhelms-Universität
- Germany
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50
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Consonni V, Todeschini R. Molecular Descriptors. CHALLENGES AND ADVANCES IN COMPUTATIONAL CHEMISTRY AND PHYSICS 2010. [DOI: 10.1007/978-1-4020-9783-6_3] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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