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Choung OH, Vianello R, Segler M, Stiefl N, Jiménez-Luna J. Extracting medicinal chemistry intuition via preference machine learning. Nat Commun 2023; 14:6651. [PMID: 37907461 PMCID: PMC10618272 DOI: 10.1038/s41467-023-42242-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 09/21/2023] [Indexed: 11/02/2023] Open
Abstract
The lead optimization process in drug discovery campaigns is an arduous endeavour where the input of many medicinal chemists is weighed in order to reach a desired molecular property profile. Building the expertise to successfully drive such projects collaboratively is a very time-consuming process that typically spans many years within a chemist's career. In this work we aim to replicate this process by applying artificial intelligence learning-to-rank techniques on feedback that was obtained from 35 chemists at Novartis over the course of several months. We exemplify the usefulness of the learned proxies in routine tasks such as compound prioritization, motif rationalization, and biased de novo drug design. Annotated response data is provided, and developed models and code made available through a permissive open-source license.
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Affiliation(s)
- Oh-Hyeon Choung
- Novartis Institutes for Biomedical Research, 4002, Basel, Switzerland
| | - Riccardo Vianello
- Novartis Institutes for Biomedical Research, 4002, Basel, Switzerland
| | - Marwin Segler
- Microsoft Research AI4Science, CB1 2FB, Cambridge, UK
| | - Nikolaus Stiefl
- Novartis Institutes for Biomedical Research, 4002, Basel, Switzerland.
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Alves FDM, Bellei JCB, Barbosa CDS, Duarte CL, da Fonseca AL, Pinto ACDS, Raimundo FO, Carpinter BA, Lemos ASDO, Coimbra ES, Taranto AG, Rocha VN, de Pilla Varotti F, Ribeiro Viana GH, Scopel KKG. Rational-Based Discovery of Novel β-Carboline Derivatives as Potential Antimalarials: From In Silico Identification of Novel Targets to Inhibition of Experimental Cerebral Malaria. Pathogens 2022; 11:pathogens11121529. [PMID: 36558863 PMCID: PMC9781199 DOI: 10.3390/pathogens11121529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 12/08/2022] [Accepted: 12/11/2022] [Indexed: 12/15/2022] Open
Abstract
Malaria is an infectious disease widespread in underdeveloped tropical regions. The most severe form of infection is caused by Plasmodium falciparum, which can lead to development of cerebral malaria (CM) and is responsible for deaths and significant neurocognitive sequelae throughout life. In this context and considering the emergence and spread of drug-resistant P. falciparum isolates, the search for new antimalarial candidates becomes urgent. β-carbolines alkaloids are good candidates since a wide range of biological activity for these compounds has been reported. Herein, we designed 20 chemical entities and performed an in silico virtual screening against a pool of P. falciparum molecular targets, the Brazilian Malaria Molecular Targets (BRAMMT). Seven structures showed potential to interact with PfFNR, PfPK7, PfGrx1, and PfATP6, being synthesized and evaluated for in vitro antiplasmodial activity. Among them, compounds 3−6 and 10 inhibited the growth of the W2 strain at µM concentrations, with low cytotoxicity against the human cell line. In silico physicochemical and pharmacokinetic properties were found to be favorable for oral administration. The compound 10 provided the best results against CM, with important values of parasite growth inhibition on the 5th day post-infection for both curative (67.9%) and suppressive (82%) assays. Furthermore, this compound was able to elongate mice survival and protect them against the development of the experimental model of CM (>65%). Compound 10 also induced reduction of the NO level, possibly by interaction with iNOS. Therefore, this alkaloid showed promising activity for the treatment of malaria and was able to prevent the development of experimental cerebral malaria (ECM), probably by reducing NO synthesis.
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Affiliation(s)
- Fernanda de Moura Alves
- Research Center on Biological Chemistry (NQBio), Federal University of São João Del Rei, Divinópolis 35501-296, Brazil
| | - Jessica Correa Bezerra Bellei
- Research Center Parasitology, Departament of Parasitology, Microbiology and Immunology, Federal University of Juiz de Fora, Juiz de Fora 36036-900, Brazil
| | - Camila de Souza Barbosa
- Research Center on Biological Chemistry (NQBio), Federal University of São João Del Rei, Divinópolis 35501-296, Brazil
| | - Caíque Lopes Duarte
- Research Center on Biological Chemistry (NQBio), Federal University of São João Del Rei, Divinópolis 35501-296, Brazil
| | - Amanda Luisa da Fonseca
- Research Center on Biological Chemistry (NQBio), Federal University of São João Del Rei, Divinópolis 35501-296, Brazil
| | - Ana Claudia de Souza Pinto
- Research Center on Biological Chemistry (NQBio), Federal University of São João Del Rei, Divinópolis 35501-296, Brazil
| | - Felipe Oliveira Raimundo
- Research Center Parasitology, Departament of Parasitology, Microbiology and Immunology, Federal University of Juiz de Fora, Juiz de Fora 36036-900, Brazil
| | - Bárbara Albuquerque Carpinter
- Research Center Parasitology, Departament of Parasitology, Microbiology and Immunology, Federal University of Juiz de Fora, Juiz de Fora 36036-900, Brazil
| | - Ari Sérgio de Oliveira Lemos
- Research Center Parasitology, Departament of Parasitology, Microbiology and Immunology, Federal University of Juiz de Fora, Juiz de Fora 36036-900, Brazil
| | - Elaine Soares Coimbra
- Research Center Parasitology, Departament of Parasitology, Microbiology and Immunology, Federal University of Juiz de Fora, Juiz de Fora 36036-900, Brazil
| | - Alex Gutterres Taranto
- Research Center on Biological Chemistry (NQBio), Federal University of São João Del Rei, Divinópolis 35501-296, Brazil
| | - Vinícius Novaes Rocha
- Research Center of Pathology and Veterinary Histology, Departament of Veterinary Medicine, Federal University of Juiz de Fora, Juiz de Fora 36036-900, Brazil
| | - Fernando de Pilla Varotti
- Research Center on Biological Chemistry (NQBio), Federal University of São João Del Rei, Divinópolis 35501-296, Brazil
- Correspondence: (F.d.P.V.); (K.K.G.S.)
| | | | - Kézia K. G. Scopel
- Research Center Parasitology, Departament of Parasitology, Microbiology and Immunology, Federal University of Juiz de Fora, Juiz de Fora 36036-900, Brazil
- Correspondence: (F.d.P.V.); (K.K.G.S.)
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Avila-Bonilla RG, López-Sandoval Á, Soto-Sánchez J, Marchat LA, Rivera G, Medina-Contreras O, Ramírez-Moreno E. Proteomic and Functional Analysis of the Effects of Quinoxaline Derivatives on Entamoeba histolytica. Front Cell Infect Microbiol 2022; 12:887647. [PMID: 35832378 PMCID: PMC9271875 DOI: 10.3389/fcimb.2022.887647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 05/23/2022] [Indexed: 11/13/2022] Open
Abstract
Quinoxalines are heterocyclic compounds that contain a benzene ring and a pyrazine ring. The oxidation of both nitrogen of the pyrazine ring results in quinoxaline derivatives (QdNO), which exhibit a variety of biological properties, including antiparasitic activity. However, its activity against Entamoeba histolytica, the protozoan that causes human amebiasis, is poorly understood. Recently, our group reported that various QdNOs produce morphological changes in E. histolytica trophozoites, increase reactive oxygen species, and inhibit thioredoxin reductase activity. Notably, T-001 and T-017 derivatives were among the QdNOs with the best activity. In order to contribute to the characterization of the antiamebic effect of QdNOs, in this work we analyzed the proteomic profile of E. histolytica trophozoites treated with the QdNOs T-001 and T-017, and the results were correlated with functional assays. A total number of 163 deregulated proteins were found in trophozoites treated with T-001, and 131 in those treated with T-017. A set of 21 overexpressed and 24 under-expressed proteins was identified, which were mainly related to cytoskeleton and intracellular traffic, nucleic acid transcription, translation and binding, and redox homeostasis. Furthermore, T-001 and T-017 modified the virulence of trophozoites, since they altered their erythrophagocytosis, migration, adhesion and cytolytic capacity. Our results show that in addition to alter reactive oxygen species, and thioredoxin reductase activity, T-001 and T-017 affect essential functions related to the actin cytoskeleton, which eventually affects E. histolytica virulence and survival.
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Affiliation(s)
- Rodolfo Gamaliel Avila-Bonilla
- Instituto Politécnico Nacional, Escuela Nacional de Medicina y Homeopatía, Laboratorio de Biomedicina Molecular 2, México City, Mexico
| | - Ángel López-Sandoval
- Instituto Politécnico Nacional, Escuela Nacional de Medicina y Homeopatía, Laboratorio de Biomedicina Molecular 2, México City, Mexico
| | - Jacqueline Soto-Sánchez
- Instituto Politécnico Nacional, Escuela Nacional de Medicina y Homeopatía, Laboratorio de Biomedicina Molecular 2, México City, Mexico
| | - Laurence A. Marchat
- Instituto Politécnico Nacional, Escuela Nacional de Medicina y Homeopatía, Laboratorio de Biomedicina Molecular 2, México City, Mexico
| | - Gildardo Rivera
- Instituto Politécnico Nacional, Centro de Biotecnología Genómica, Laboratorio de Biotecnología Farmacéutica, Reynosa, Mexico
| | - Oscar Medina-Contreras
- Hospital Infantil de México Federico Gómez, Unidad de Investigación Epidemiológica en Endocrinología y Nutrición (UIEEN), México City, Mexico
| | - Esther Ramírez-Moreno
- Instituto Politécnico Nacional, Escuela Nacional de Medicina y Homeopatía, Laboratorio de Biomedicina Molecular 2, México City, Mexico
- *Correspondence: Esther Ramírez-Moreno, ;
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Qamar M, Sultanat, Shafiullah, Khan AU, Ali A, Farhat N. One pot facile synthesis of flavanoidal oxadiazinanones: In vitro antibacterial activity, docking and MD simulation using DNA gyrase. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.131944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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Khan RA, Hossain R, Siyadatpanah A, Al-Khafaji K, Khalipha ABR, Dey D, Asha UH, Biswas P, Saikat ASM, Chenari HA, Wilairatana P, Islam MT. Diterpenes/Diterpenoids and Their Derivatives as Potential Bioactive Leads against Dengue Virus: A Computational and Network Pharmacology Study. Molecules 2021; 26:6821. [PMID: 34833913 PMCID: PMC8623982 DOI: 10.3390/molecules26226821] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 11/06/2021] [Accepted: 11/08/2021] [Indexed: 12/22/2022] Open
Abstract
Dengue fever is a dangerous infectious endemic disease that affects over 100 nations worldwide, from Africa to the Western Pacific, and is caused by the dengue virus, which is transmitted to humans by an insect bite of Aedes aegypti. Millions of citizens have died as a result of dengue fever and dengue hemorrhagic fever across the globe. Envelope (E), serine protease (NS3), RNA-directed RNA polymerase (NS5), and non-structural protein 1 (NS1) are mostly required for cell proliferation and survival. Some of the diterpenoids and their derivatives produced by nature possess anti-dengue viral properties. The goal of the computational study was to scrutinize the effectiveness of diterpenoids and their derivatives against dengue viral proteins through in silico study. Methods: molecular docking was performed to analyze the binding affinity of compounds against four viral proteins: the envelope (E) protein, the NS1 protein, the NS3 protein, and the NS5 protein. Results: among the selected drug candidates, triptolide, stevioside, alepterolic acid, sphaeropsidin A, methyl dodovisate A, andrographolide, caesalacetal, and pyrimethamine have demonstrated moderate to good binding affinities (-8.0 to -9.4 kcal/mol) toward the selected proteins: E protein, NS3, NS5, and NS1 whereas pyrimethamine exerts -7.5, -6.3, -7.8, and -6.6 kcal/mol with viral proteins, respectively. Interestingly, the binding affinities of these lead compounds were better than those of an FDA-approved anti-viral medication (pyrimethamine), which is underused in dengue fever. Conclusion: we can conclude that diterpenoids can be considered as a possible anti-dengue medication option. However, in vivo investigation is recommended to back up the conclusions of this study.
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Affiliation(s)
- Rasel Ahmed Khan
- Pharmacy Discipline, Life Science School, Khulna University, Khulna 9280, Bangladesh;
| | - Rajib Hossain
- Department of Pharmacy, Life Science Faculty, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, Dhaka 8100, Bangladesh; (A.B.R.K.); (U.H.A.)
| | - Abolghasem Siyadatpanah
- Ferdows School of Paramedical and Health, Birjand University of Medical Sciences, Birjand 9717853577, Iran; (A.S.); (H.A.C.)
| | - Khattab Al-Khafaji
- Department of Medical Laboratory Technology, Al-Nisour University College, Baghdad 10001, Iraq;
| | - Abul Bashar Ripon Khalipha
- Department of Pharmacy, Life Science Faculty, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, Dhaka 8100, Bangladesh; (A.B.R.K.); (U.H.A.)
| | - Dipta Dey
- Department of Biochemistry and Molecular Biology, Life Science Faculty, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, Dhaka 8100, Bangladesh; (D.D.); (A.S.M.S.)
| | - Umma Hafsa Asha
- Department of Pharmacy, Life Science Faculty, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, Dhaka 8100, Bangladesh; (A.B.R.K.); (U.H.A.)
| | - Partha Biswas
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Science and Technology, Jashore University of Science and Technology (JUST), Jashore 7408, Bangladesh;
| | - Abu Saim Mohammad Saikat
- Department of Biochemistry and Molecular Biology, Life Science Faculty, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, Dhaka 8100, Bangladesh; (D.D.); (A.S.M.S.)
| | - Hadi Ahmadi Chenari
- Ferdows School of Paramedical and Health, Birjand University of Medical Sciences, Birjand 9717853577, Iran; (A.S.); (H.A.C.)
| | - Polrat Wilairatana
- Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand
| | - Muhammad Torequl Islam
- Department of Pharmacy, Life Science Faculty, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, Dhaka 8100, Bangladesh; (A.B.R.K.); (U.H.A.)
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Raza MA, Fatima K. Molecular modeling approach for designing of amino‐derived anti‐Alzheimer agents: A computational study. J PHYS ORG CHEM 2020. [DOI: 10.1002/poc.4076] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Muhammad Asam Raza
- Department of Chemistry, Hafiz Hayat Campus University of Gujrat Gujrat Pakistan
| | - Kiran Fatima
- Department of Chemistry, Hafiz Hayat Campus University of Gujrat Gujrat Pakistan
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A review of ligand-based virtual screening web tools and screening algorithms in large molecular databases in the age of big data. Future Med Chem 2018; 10:2641-2658. [PMID: 30499744 DOI: 10.4155/fmc-2018-0076] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Virtual screening has become a widely used technique for helping in drug discovery processes. The key to this success is its ability to aid in the identification of novel bioactive compounds by screening large molecular databases. Several web servers have emerged in the last few years supplying platforms to guide users in screening publicly accessible chemical databases in a reasonable time. In this review, we discuss a representative set of online virtual screening servers and their underlying similarity algorithms. Other related topics, such as molecular representation or freely accessible databases are also treated. The most relevant contributions to this review arise from critical discussions concerning the pros and cons of servers and algorithms, and the challenges that future works must solve in a virtual screening framework.
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Ansari A, Ali A, Asif M, Rauf MA, Owais M. Facile one-pot multicomponent synthesis and molecular docking studies of steroidal oxazole/thiazole derivatives with effective antimicrobial, antibiofilm and hemolytic properties. Steroids 2018; 134:22-36. [PMID: 29653115 DOI: 10.1016/j.steroids.2018.04.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 03/17/2018] [Accepted: 04/06/2018] [Indexed: 10/17/2022]
Abstract
A series of steroidal oxazole and thiazole derivatives have been synthesized employing thiosemicarbazide/semicarbazide hydrochloride and ethyl 2-chloroacetoacetate with a simple and facile one-pot multicomponent reaction pathway. The antimicrobial activity of newly synthesized compounds were evaluated against four bacterial strains namely Gram-negative (Escherichia coliand Pseudomonas aeruginosa) and Gram-positive bacteria (Staphylococcus aureus and Listeria monocytogenes) in addition to pathogenic fungi (Candida albicans and Cryptococcus neoformans). Bioactivity assay manifested that most of the compounds exhibited good antimicrobial activity. To provide additional insight into antimicrobial activity, the compounds were also tested for their antibiofilm activity against S. aureus biofilm. Moreover, molecular docking study shows binding of compounds with amino acid residues of DNA gyrase and glucosamine-6-phosphate synthase (promising antimicrobial target) through hydrogen bonding interactions. Hemolytic activity have been also investigated to ascertain the effect of compounds over RBC lysis and results indicate good prospects for biocompatibility. The expedient synthesis of steroidal heterocycles, effective antibacterial and antifungal behavior against various clinically relevant human pathogens, promising biocompatibility offer opportunities for further modification and potential applications as therapeutic agents.
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Affiliation(s)
- Anam Ansari
- Steroid Research Laboratory, Department of Chemistry, Aligarh Muslim University, Aligarh 202 002, India
| | - Abad Ali
- Steroid Research Laboratory, Department of Chemistry, Aligarh Muslim University, Aligarh 202 002, India; Organometallic Synthesis and Catalysis Group, Chemical Engineering Division, CSIR-National Chemical Laboratory (CSIR-NCL), Dr. Homi Bhabha Road, Pune 411 008, Maharashtra, India
| | - Mohd Asif
- Steroid Research Laboratory, Department of Chemistry, Aligarh Muslim University, Aligarh 202 002, India
| | - Mohd Ahmar Rauf
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India
| | - Mohammad Owais
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India
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Rampogu S, Baek A, Zeb A, Lee KW. Exploration for novel inhibitors showing back-to-front approach against VEGFR-2 kinase domain (4AG8) employing molecular docking mechanism and molecular dynamics simulations. BMC Cancer 2018. [PMID: 29514608 PMCID: PMC5842552 DOI: 10.1186/s12885-018-4050-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Background Angiogenesis is a process of formation of new blood vessels and is an important criteria demonstrated by cancer cells. Over a period of time, these cancer cells infect the other parts of the healthy body by a process called progression. The objective of the present article is to identify a drug molecule that inhibits angiogenesis and progression. Methods In this pursuit, ligand based pharmacophore virtual screening was employed, generating a pharmacophore model, Hypo1 consisting of four features. Furthermore, this Hypo1 was validated recruiting, Fischer’s randomization, test set method and decoy set method. Later, Hypo1 was allowed to screen databases such as Maybridge, Chembridge, Asinex and NCI and were further filtered by ADMET filters and Lipinski’s Rule of Five. A total of 699 molecules that passed the above criteria, were challenged against 4AG8, an angiogenic drug target employing GOLD v5.2.2. Results The results rendered by molecular docking, DFT and the MD simulations showed only one molecule (Hit) obeyed the back-to-front approach. This molecule displayed a dock score of 89.77, involving the amino acids, Glu885 and Cys919, Asp1046, respectively and additionally formed several important hydrophobic interactions. Furthermore, the identified lead molecule showed interactions with key residues when challenged with CDK2 protein, 1URW. Conclusion The lead candidate showed several interactions with the crucial residues of both the targets. Furthermore, we speculate that the residues Cys919 and Leu83 are important in the development of dual inhibitor. Therefore, the identified lead molecule can act as a potential inhibitor for angiogenesis and progression. Electronic supplementary material The online version of this article (10.1186/s12885-018-4050-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shailima Rampogu
- Division of Applied Life Science (BK21 Plus Program), Systems and Synthetic Agrobiotech Center (SSAC), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju, 52828, Republic of Korea
| | - Ayoung Baek
- Division of Applied Life Science (BK21 Plus Program), Systems and Synthetic Agrobiotech Center (SSAC), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju, 52828, Republic of Korea
| | - Amir Zeb
- Division of Applied Life Science (BK21 Plus Program), Systems and Synthetic Agrobiotech Center (SSAC), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju, 52828, Republic of Korea
| | - Keun Woo Lee
- Division of Applied Life Science (BK21 Plus Program), Systems and Synthetic Agrobiotech Center (SSAC), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Jinju, 52828, Republic of Korea.
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Cavalluzzi MM, Mangiatordi GF, Nicolotti O, Lentini G. Ligand efficiency metrics in drug discovery: the pros and cons from a practical perspective. Expert Opin Drug Discov 2017; 12:1087-1104. [PMID: 28814111 DOI: 10.1080/17460441.2017.1365056] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
INTRODUCTION Ligand efficiency metrics are almost universally accepted as a valuable indicator of compound quality and an aid to reduce attrition. Areas covered: In this review, the authors describe ligand efficiency metrics giving a balanced overview on their merits and points of weakness in order to enable the readers to gain an informed opinion. Relevant theoretical breakthroughs and drug-like properties are also illustrated. Several recent exemplary case studies are discussed in order to illustrate the main fields of application of ligand efficiency metrics. Expert opinion: As a medicinal chemist guide, ligand efficiency metrics perform in a context- and chemotype-dependent manner; thus, they should not be used as a magic box. Since the 'big bang' of efficiency metrics occurred more or less ten years ago and the average time to develop a new drug is over the same period, the next few years will give a clearer outlook on the increased rate of success, if any, gained by means of these new intriguing tools.
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Affiliation(s)
| | | | - Orazio Nicolotti
- a Department of Pharmacy - Drug Sciences , University of Bari Aldo Moro , Bari , Italy
| | - Giovanni Lentini
- a Department of Pharmacy - Drug Sciences , University of Bari Aldo Moro , Bari , Italy
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Razzaghi-Asl N, Seydi E, Alikhani R, Rezvani S, Miri R, Salimi A. Synthesis and toxicity assessment of 3-oxobutanamides against human lymphocytes and isolated mitochondria. ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY 2017; 51:71-84. [PMID: 28292652 DOI: 10.1016/j.etap.2017.03.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Revised: 03/03/2017] [Accepted: 03/05/2017] [Indexed: 06/06/2023]
Abstract
To reduce costly late-phase compound scrubbing, there has been an increased focus on assessing compounds within in vitro assays that predict properties of human safety liabilities, before preclinical in vivo studies. The aim of our study was to answer the questions that whether the toxicity risk of a series of 3-oxobutanamide derivatives could be predicted by using of human lymphocytes and their isolated mitochondria. Using biochemical and flow cytometry assessments, we demonstrated that exposure of lymphocytes and isolated mitochondria to five 3-oxobutanamide derivatives (1-5) did not exhibit remarkable toxicity at low concentrations (50-500μM) but toxicity could be observed at high concentrations (1000 and 2000μM), particularly for N-(5-(4-bromophenyl)-3-isoxazolyl)-3-oxobutanamide (4) and N-(2-benzothiazolyl)-3-oxo butanamide (5). Compounds 4, 5 and partly N-(5-methyl-3-isoxazol yl)-3-oxo butanamide (1) also showed a marked cellular and mitochondrial toxicity while compound 5 displayed superior toxicity. Compound 5 induced cytotoxicity on human blood lymphocytes which was associated with the generation of intracellular reactive oxygen species (ROS), mitochondrial membrane potential (MMP) collapse, lysosomal membrane injury, lipid peroxidation and depletion of glutathione. Our results suggested that among assessed compounds, increased toxicity of compound 5 compared to other compounds could be likely attributed to the presence of bromine substituent in 5. Finally our findings proposed that using of antioxidants and mitochondrial/lysosomal protective agents could be beneficial in decreasing the toxicity of 5.
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Affiliation(s)
- Nima Razzaghi-Asl
- Department of Medicinal Chemistry, School of Pharmacy, Ardabil University of Medical Science, Ardabil, Iran
| | - Enaytollah Seydi
- Research Center for Health, Safety and Environment (RCHSE), Department of Occupational Health Engineering, Alborz University of Medical Sciences, Karaj, Iran
| | - Radin Alikhani
- Department of Medicinal Chemistry, School of Pharmacy, Ardabil University of Medical Science, Ardabil, Iran
| | - Saba Rezvani
- Department of Medicinal Chemistry, School of Pharmacy, Ardabil University of Medical Science, Ardabil, Iran
| | - Ramin Miri
- Medicinal and Natural Products Chemistry Research Center, Shiraz University of Medical Science, Shiraz, Iran
| | - Ahmad Salimi
- Department of Pharmacology and Toxicology, School of Pharmacy, Ardabil University of Medical Science, Ardabil, Iran.
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Setlur AS, Naik SY, Skariyachan S. Herbal Lead as Ideal Bioactive Compounds Against Probable Drug Targets of Ebola Virus in Comparison with Known Chemical Analogue: A Computational Drug Discovery Perspective. Interdiscip Sci 2016; 9:254-277. [DOI: 10.1007/s12539-016-0149-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Revised: 01/05/2016] [Accepted: 01/25/2016] [Indexed: 12/17/2022]
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13
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Kwong E. Advancing drug discovery: a pharmaceutics perspective. J Pharm Sci 2014; 104:865-71. [PMID: 25482223 DOI: 10.1002/jps.24294] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Revised: 09/25/2014] [Accepted: 11/04/2014] [Indexed: 01/10/2023]
Abstract
Current industry perspective of how discovery is conducted seems to be fragmented and does not have a unified overall outlook of how discovery challenges are being addressed. Consequently, well-defined processes and drug-likeness criteria are being viewed as "broken" and will not maintain future R&D productivity. In this commentary, an analysis of existing practices for defining successful development candidates resulted in a 5 "must do" list to help advance Drug Discovery as presented from a Pharmaceutics perspective. The 5 "must do" list includes: what an ideal discovery team model should look like, what criteria should be considered for the desired development candidate profile, what the building blocks of the development candidate should look like, and how to assess the development risks of the candidate.
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Villalobos-Rocha JC, Sánchez-Torres L, Nogueda-Torres B, Segura-Cabrera A, García-Pérez CA, Bocanegra-García V, Palos I, Monge A, Rivera G. Anti-Trypanosoma cruzi and anti-leishmanial activity by quinoxaline-7-carboxylate 1,4-di-N-oxide derivatives. Parasitol Res 2014; 113:2027-35. [PMID: 24691716 DOI: 10.1007/s00436-014-3850-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Accepted: 03/04/2014] [Indexed: 10/25/2022]
Abstract
In this work, a novel series of ethyl and methyl quinoxaline-7-carboxylate 1,4-di-N-oxide derivatives were evaluated in vitro on Trypanosoma cruzi trypomastigotes and Leishmania mexicana promastigotes, and cytotoxicity activity in murine macrophages was tested. In silico molecular docking simulations of trypanothione reductase were also done. Three compounds of 33 quinoxaline-7-carboxylate 1,4-di-N-oxide derivatives showed better anti-T. cruzi activity than nifurtimox and beznidazole; two compounds had better anti-leishmanial activity that amphotericin-B, and two compounds showed better activity against both parasites than reference drugs. Compounds M2, M7, M8 and E5, showed low cytotoxic activity on the host cell. The in silico studies suggest that compound M2 is a potential trypanothione reductase inhibitor.
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Affiliation(s)
- Juan Carlos Villalobos-Rocha
- Departamento de Parasitología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Carpio y Plan de Ayala, s/n, 11340, D.F., Mexico
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15
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Camp D, Campitelli M, Carroll AR, Davis RA, Quinn RJ. Front-Loading Natural-Product-Screening Libraries for logP:Background, Development, and Implementation. Chem Biodivers 2013; 10:524-37. [DOI: 10.1002/cbdv.201200302] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2012] [Indexed: 01/22/2023]
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16
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Kutchukian PS, Vasilyeva NY, Xu J, Lindvall MK, Dillon MP, Glick M, Coley JD, Brooijmans N. Inside the mind of a medicinal chemist: the role of human bias in compound prioritization during drug discovery. PLoS One 2012. [PMID: 23185259 PMCID: PMC3504051 DOI: 10.1371/journal.pone.0048476] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Medicinal chemists' "intuition" is critical for success in modern drug discovery. Early in the discovery process, chemists select a subset of compounds for further research, often from many viable candidates. These decisions determine the success of a discovery campaign, and ultimately what kind of drugs are developed and marketed to the public. Surprisingly little is known about the cognitive aspects of chemists' decision-making when they prioritize compounds. We investigate 1) how and to what extent chemists simplify the problem of identifying promising compounds, 2) whether chemists agree with each other about the criteria used for such decisions, and 3) how accurately chemists report the criteria they use for these decisions. Chemists were surveyed and asked to select chemical fragments that they would be willing to develop into a lead compound from a set of ~4,000 available fragments. Based on each chemist's selections, computational classifiers were built to model each chemist's selection strategy. Results suggest that chemists greatly simplified the problem, typically using only 1-2 of many possible parameters when making their selections. Although chemists tended to use the same parameters to select compounds, differing value preferences for these parameters led to an overall lack of consensus in compound selections. Moreover, what little agreement there was among the chemists was largely in what fragments were undesirable. Furthermore, chemists were often unaware of the parameters (such as compound size) which were statistically significant in their selections, and overestimated the number of parameters they employed. A critical evaluation of the problem space faced by medicinal chemists and cognitive models of categorization were especially useful in understanding the low consensus between chemists.
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Affiliation(s)
- Peter S. Kutchukian
- Center for Proteomic Chemistry, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts, United States of America
| | - Nadya Y. Vasilyeva
- Department of Psychology, Northeastern University, Boston, Massachusetts, United States of America
| | - Jordan Xu
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Emeryville, California, United States of America
| | - Mika K. Lindvall
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Emeryville, California, United States of America
| | - Michael P. Dillon
- Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Emeryville, California, United States of America
| | - Meir Glick
- Center for Proteomic Chemistry, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts, United States of America
| | - John D. Coley
- Department of Psychology, Northeastern University, Boston, Massachusetts, United States of America
- * E-mail: (JDC); (NB)
| | - Natasja Brooijmans
- Blueprint Medicines, Cambridge, Massachusetts, United States of America
- * E-mail: (JDC); (NB)
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Namasivayam V, Bajorath J. Multiobjective Particle Swarm Optimization: Automated Identification of Structure–Activity Relationship-Informative Compounds with Favorable Physicochemical Property Distributions. J Chem Inf Model 2012; 52:2848-55. [DOI: 10.1021/ci300402g] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Vigneshwaran Namasivayam
- 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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18
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Abstract
Natural products (NPs) have historically been a fertile source of new drugs for the pharmaceutical industry. However, this once-popular approach has waned considerably over the past two decades as the high-throughput screening of megalibraries comprised mainly of molecules with non-natural (synthetic) motifs has unfolded. Contemporary high-throughput screening libraries contain molecules compliant with physicochemical profiles considered essential for downstream development. Until recently, there was no strategy that aligned NP screening with the same physicochemical profiles. An approach based on Log P has addressed these concerns and, together with advances in isolation, afforded NP leads in timelines compatible with pure compound screening. Concomitant progress related to access of biological resources has provided long-awaited legal certainty to further facilitate NP drug discovery.
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Camp D, Davis RA, Campitelli M, Ebdon J, Quinn RJ. Drug-like properties: guiding principles for the design of natural product libraries. JOURNAL OF NATURAL PRODUCTS 2012; 75:72-81. [PMID: 22204643 DOI: 10.1021/np200687v] [Citation(s) in RCA: 132] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
While natural products or their derivatives and mimics have contributed around 50% of current drugs, there has been no approach allowing front-loading of chemical space compliant with lead- and drug-like properties. The importance of physicochemical properties of molecules in the development of orally bioavailable drugs has been recognized. Classical natural product drug discovery has only been able to undertake this analysis retrospectively after compounds are isolated and structures elucidated. The present approach addresses front-loading of both extracts and subsequent fractions with desired physicochemical properties prior to screening for drug discovery. The physicochemical profiles of natural products active against two neglected disease targets, malaria and African trypanosomiasis, are presented based on this strategy. This approach can ensure timely development of natural product leads at a hitherto unachievable rate.
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Affiliation(s)
- David Camp
- Eskitis Institute, Griffith University, Brisbane, QLD 4111, Australia
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20
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The influence of the 'organizational factor' on compound quality in drug discovery. Nat Rev Drug Discov 2011; 10:749-65. [DOI: 10.1038/nrd3552] [Citation(s) in RCA: 134] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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21
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Cheshire DR. How well do medicinal chemists learn from experience? Drug Discov Today 2011; 16:817-21. [DOI: 10.1016/j.drudis.2011.06.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2011] [Revised: 04/26/2011] [Accepted: 06/06/2011] [Indexed: 11/29/2022]
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22
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Lusher SJ, McGuire R, Azevedo R, Boiten JW, van Schaik RC, de Vlieg J. A molecular informatics view on best practice in multi-parameter compound optimization. Drug Discov Today 2011; 16:555-68. [DOI: 10.1016/j.drudis.2011.05.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2010] [Revised: 02/25/2011] [Accepted: 05/06/2011] [Indexed: 01/30/2023]
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23
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Gleeson MP, Hersey A, Montanari D, Overington J. Probing the links between in vitro potency, ADMET and physicochemical parameters. Nat Rev Drug Discov 2011; 10:197-208. [PMID: 21358739 DOI: 10.1038/nrd3367] [Citation(s) in RCA: 332] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
A common underlying assumption in current drug discovery strategies is that compounds with higher in vitro potency at their target(s) have greater potential to translate into successful, low-dose therapeutics. This has led to the development of screening cascades with in vitro potency embedded as an early filter. However, this approach is beginning to be questioned, given the bias in physicochemical properties that it can introduce early in lead generation and optimization, which is due to the often diametrically opposed relationship between physicochemical parameters associated with high in vitro potency and those associated with desirable absorption, distribution, metabolism, excretion and toxicity (ADMET) characteristics. Here, we describe analyses that probe these issues further using the ChEMBL database, which includes more than 500,000 drug discovery and marketed oral drug compounds. Key findings include: first, that oral drugs seldom possess nanomolar potency (50 nM on average); second, that many oral drugs have considerable off-target activity; and third, that in vitro potency does not correlate strongly with the therapeutic dose. These findings suggest that the perceived benefit of high in vitro potency may be negated by poorer ADMET properties.
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Affiliation(s)
- M Paul Gleeson
- The Department of Chemistry, Faculty of Science, Kasetsart University, 50 Phaholyothin Road, Chatuchak, Bangkok 10900, Thailand.
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24
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Hegde V, Campitelli M, Quinn RJ, Camp D. Synthesis of novel molecular probes inspired by harringtonolide. Org Biomol Chem 2011; 9:4570-9. [DOI: 10.1039/c1ob05299c] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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25
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26
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Wager TT, Chandrasekaran RY, Hou X, Troutman MD, Verhoest PR, Villalobos A, Will Y. Defining desirable central nervous system drug space through the alignment of molecular properties, in vitro ADME, and safety attributes. ACS Chem Neurosci 2010; 1:420-34. [PMID: 22778836 PMCID: PMC3368653 DOI: 10.1021/cn100007x] [Citation(s) in RCA: 329] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2010] [Accepted: 03/02/2010] [Indexed: 01/20/2023] Open
Abstract
As part of our effort to increase survival of drug candidates and to move our medicinal chemistry design to higher probability space for success in the Neuroscience therapeutic area, we embarked on a detailed study of the property space for a collection of central nervous system (CNS) molecules. We carried out a thorough analysis of properties for 119 marketed CNS drugs and a set of 108 Pfizer CNS candidates. In particular, we focused on understanding the relationships between physicochemical properties, in vitro ADME (absorption, distribution, metabolism, and elimination) attributes, primary pharmacology binding efficiencies, and in vitro safety data for these two sets of compounds. This scholarship provides guidance for the design of CNS molecules in a property space with increased probability of success and may lead to the identification of druglike candidates with favorable safety profiles that can successfully test hypotheses in the clinic.
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Braggio S, Montanari D, Rossi T, Ratti E. Drug efficiency: a new concept to guide lead optimization programs towards the selection of better clinical candidates. Expert Opin Drug Discov 2010; 5:609-18. [DOI: 10.1517/17460441.2010.490553] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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28
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Hammill JT, Contreras-García J, Virshup AM, Beratan D, Yang W, Wipf P. Synthesis and chemical diversity analysis of bicyclo[3.3.1]non-3-en-2-ones. Tetrahedron 2010; 66:5852-5862. [PMID: 20798897 PMCID: PMC2925319 DOI: 10.1016/j.tet.2010.04.112] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Functionalized bicyclo[3.3.1]non-3-en-2-ones are obtained from commercially available phenols by a hypervalent iodine oxidation, enone epoxidation, epoxide thiolysis, and intramolecular aldol reaction sequence. Reaction optimization studies identified room temperature as well as microwave-mediated procedures, providing moderate to good yields (57%-88%) in the thiophenol-mediated epoxide opening and intramolecular aldol reaction. In addition, the isolation of a key intermediate and in situ NMR studies supported the mechanistic hypothesis. The bicyclic ring products occupy novel chemical space according to ChemGPS and Chemaxon chemical diversity and cheminformatics analyses.
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Affiliation(s)
- Jared T Hammill
- Center for Chemical Methodologies and Library Development, University of Pittsburgh, Pittsburgh, PA 15260, USA
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29
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Penesyan A, Kjelleberg S, Egan S. Development of novel drugs from marine surface associated microorganisms. Mar Drugs 2010; 8:438-59. [PMID: 20411108 PMCID: PMC2857370 DOI: 10.3390/md8030438] [Citation(s) in RCA: 166] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2010] [Revised: 02/03/2010] [Accepted: 02/22/2010] [Indexed: 11/16/2022] Open
Abstract
While the oceans cover more than 70% of the Earth's surface, marine derived microbial natural products have been largely unexplored. The marine environment is a habitat for many unique microorganisms, which produce biologically active compounds ("bioactives") to adapt to particular environmental conditions. For example, marine surface associated microorganisms have proven to be a rich source for novel bioactives because of the necessity to evolve allelochemicals capable of protecting the producer from the fierce competition that exists between microorganisms on the surfaces of marine eukaryotes. Chemically driven interactions are also important for the establishment of cross-relationships between microbes and their eukaryotic hosts, in which organisms producing antimicrobial compounds ("antimicrobials"), may protect the host surface against over colonisation in return for a nutrient rich environment. As is the case for bioactive discovery in general, progress in the detection and characterization of marine microbial bioactives has been limited by a number of obstacles, such as unsuitable culture conditions, laborious purification processes, and a lack of de-replication. However many of these limitations are now being overcome due to improved microbial cultivation techniques, microbial (meta-) genomic analysis and novel sensitive analytical tools for structural elucidation. Here we discuss how these technical advances, together with a better understanding of microbial and chemical ecology, will inevitably translate into an increase in the discovery and development of novel drugs from marine microbial sources in the future.
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Affiliation(s)
- Anahit Penesyan
- School of Biotechnology and Biomolecular Sciences and Centre for Marine Bio-Innovation, University of New South Wales, Sydney 2052, Australia; E-Mails:
(A.P.);
(S.K.)
| | - Staffan Kjelleberg
- School of Biotechnology and Biomolecular Sciences and Centre for Marine Bio-Innovation, University of New South Wales, Sydney 2052, Australia; E-Mails:
(A.P.);
(S.K.)
| | - Suhelen Egan
- School of Biotechnology and Biomolecular Sciences and Centre for Marine Bio-Innovation, University of New South Wales, Sydney 2052, Australia; E-Mails:
(A.P.);
(S.K.)
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30
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Leeson PD, Empfield JR. Reducing the Risk of Drug Attrition Associated with Physicochemical Properties. ANNUAL REPORTS IN MEDICINAL CHEMISTRY 2010. [DOI: 10.1016/s0065-7743(10)45024-1] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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31
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32
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vanâ
deâ
Waterbeemd H. Improving Compound Quality throughin vitroandin silicoPhysicochemical Profiling. Chem Biodivers 2009; 6:1760-6. [DOI: 10.1002/cbdv.200900056] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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33
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Gleeson P, Bravi G, Modi S, Lowe D. ADMET rules of thumb II: A comparison of the effects of common substituents on a range of ADMET parameters. Bioorg Med Chem 2009; 17:5906-19. [PMID: 19632124 DOI: 10.1016/j.bmc.2009.07.002] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2009] [Revised: 07/01/2009] [Accepted: 07/02/2009] [Indexed: 11/16/2022]
Affiliation(s)
- Paul Gleeson
- GlaxoSmithKline Medicines Research Centre, Stevenage, Hertfordshire, UK.
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34
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Jenkins ID, Lacrampe F, Ripper J, Alcaraz L, Le PV, Nikolakopoulos G, de Almeida Leone P, White RH, Quinn RJ. Synthesis of four novel natural product inspired scaffolds for drug discovery. J Org Chem 2009; 74:1304-13. [PMID: 19105637 DOI: 10.1021/jo802456w] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Inspired by the novel spiro structures of a number of bioactive natural products such as the histrionicotoxins, a series of novel spiro scaffolds have been designed and robust syntheses developed. The scaffolds are ready-to-use building blocks and can be easily prepared on a 5-20 g scale. They contain two amino groups (one Boc-protected) and have been designed for ease of conversion to a lead generation library, using either amide formation or reductive amination procedures. The synthesis of the 1,9-diazaspiro[5.5]undecane and 3,7-diazaspiro[5.6]dodecane ring systems was achieved using RCM as the key step. A simple workup procedure is reported for the removal of highly colored ruthenium residues. The synthesis of the 1,8-diazaspiro[4.5]decane scaffold has been achieved using a bromine-mediated 5-endo cyclization of the corresponding 4-aminobutene intermediate under acidic conditions. This is the first example of this type of cyclization to be reported. A novel mechanism involving a bromine transfer reaction from an initially formed bromonium ion to a neighboring nitrogen atom is suggested as the reason for the failure of this type of reaction under "normal" bromination conditions. An unusual rearrangement of a 1-acyl-1,9-diazaspiro[5.5]undecane to the corresponding 9-acyl-1,9-diazaspiro[5.5]undecane is reported.
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Affiliation(s)
- Ian D Jenkins
- Eskitis Institute, Griffith University, Brisbane, QLD, 4111, Australia.
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35
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Cavalli A, Lizzi F, Bongarzone S, Brun R, Luise Krauth-Siegel R, Bolognesi ML. Privileged structure-guided synthesis of quinazoline derivatives as inhibitors of trypanothione reductase. Bioorg Med Chem Lett 2009; 19:3031-5. [DOI: 10.1016/j.bmcl.2009.04.060] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2009] [Revised: 04/06/2009] [Accepted: 04/06/2009] [Indexed: 12/13/2022]
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36
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Stocks M, Wilden G, Pairaudeau G, Perry M, Steele J, Stonehouse J. A Practical Method for Targeted Library Design Balancing Lead-like Properties with Diversity. ChemMedChem 2009; 4:800-8. [DOI: 10.1002/cmdc.200900050] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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37
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Ritchie TJ, Luscombe CN, Macdonald SJF. Analysis of the Calculated Physicochemical Properties of Respiratory Drugs: Can We Design for Inhaled Drugs Yet? J Chem Inf Model 2009; 49:1025-32. [DOI: 10.1021/ci800429e] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Timothy J. Ritchie
- Respiratory CEDD, GlaxoSmithKline Research Medicines Centre, Gunnels Wood Road, Stevenage SG1 2NY, U.K
| | - Christopher N. Luscombe
- Respiratory CEDD, GlaxoSmithKline Research Medicines Centre, Gunnels Wood Road, Stevenage SG1 2NY, U.K
| | - Simon J. F. Macdonald
- Respiratory CEDD, GlaxoSmithKline Research Medicines Centre, Gunnels Wood Road, Stevenage SG1 2NY, U.K
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38
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Fotouhi N, Gillespie P, Goodnow, Jr. R. Lead generation: reality check on commonly held views. Expert Opin Drug Discov 2008; 3:733-44. [DOI: 10.1517/17460441.3.7.733] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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39
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Dorbec M, Florent JC, Monneret C, Rager MN, Fosse C, Bertounesque E. Synthesis of Novel Angular Heterocyclic Lignans by an InCl3-Catalyzed Friedel–Crafts-Type Cyclization. European J Org Chem 2008. [DOI: 10.1002/ejoc.200701027] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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41
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Camp D, Avery V, Street I, Quinn RJ. Progress toward establishing an open access molecular screening capability in the Australasian region. ACS Chem Biol 2007; 2:764-7. [PMID: 18154260 DOI: 10.1021/cb7002384] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- David Camp
- Eskitis Institute, Griffith
University, Brisbane, Queensland 4111, Australia,
| | - Vicky Avery
- Eskitis Institute, Griffith
University, Brisbane, Queensland 4111, Australia,
| | - Ian Street
- Walter and Eliza Hall Institute, La Trobe R&D Park, Melbourne, Victoria 3086, Australia
| | - Ronald J. Quinn
- Eskitis Institute, Griffith
University, Brisbane, Queensland 4111, Australia,
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42
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Walsh TA. The emerging field of chemical genetics: potential applications for pesticide discovery. PEST MANAGEMENT SCIENCE 2007; 63:1165-71. [PMID: 17912687 DOI: 10.1002/ps.1452] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The use of small molecules to probe biological systems, generally described as 'chemical genetics', has grown considerably in the past 7 years, especially in areas related to human biology and therapeutics. This review describes some aspects of chemical genetics technologies that can be usefully applied to pesticide target discovery and lead generation. The chemical genetics approach (consisting of a phenotype screen, a chemical library and a robust target identification methodology) is compared with conventional and target-based screening. The outcomes of a chemical genetics approach are novel protein targets coupled with in vivo-active chemical ligands. The 'chemistry-first' paradigm of the chemical genetics approach can circumvent some of the obstacles that have emerged for the exploitation of novel but chemically unvalidated targets identified from genetic or genomic screens. Some of the advantages and challenges in using chemical genetics approaches are reviewed.
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Affiliation(s)
- Terence A Walsh
- Dow AgroSciences, 9330 Zionsville Road, Indianapolis, IN 46268, USA.
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43
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Leeson PD, Springthorpe B. The influence of drug-like concepts on decision-making in medicinal chemistry. Nat Rev Drug Discov 2007; 6:881-90. [PMID: 17971784 DOI: 10.1038/nrd2445] [Citation(s) in RCA: 1671] [Impact Index Per Article: 98.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The application of guidelines linked to the concept of drug-likeness, such as the 'rule of five', has gained wide acceptance as an approach to reduce attrition in drug discovery and development. However, despite this acceptance, analysis of recent trends reveals that the physical properties of molecules that are currently being synthesized in leading drug discovery companies differ significantly from those of recently discovered oral drugs and compounds in clinical development. The consequences of the marked increase in lipophilicity--the most important drug-like physical property--include a greater likelihood of lack of selectivity and attrition in drug development. Tackling the threat of compound-related toxicological attrition needs to move to the mainstream of medicinal chemistry decision-making.
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Affiliation(s)
- Paul D Leeson
- AstraZeneca R&D Charnwood, Bakewell Road, Loughborough LE15 5RH, UK.
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Heeneman S, Donners MMPC, Bai L, Daemen MJAP. Drug-induced immunomodulation to affect the development and progression of atherosclerosis: a new opportunity? Expert Rev Cardiovasc Ther 2007; 5:345-64. [PMID: 17338677 DOI: 10.1586/14779072.5.2.345] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Inflammation and cytokine pathways are crucial for the development and progression of atherosclerotic lesions. In this review, the hypothesis that immunomodulatory drugs provide a possible therapeutic modality for cardiovascular disease is evaluated. Therefore, after a short overview of the specific inflammatory pathways involved in atherosclerosis, literature on the effect of several immunomodulatory drugs, such as nonsteroidal anti-inflammatory drugs, specific cyclooxygenase inhibitors and immunosuppressive drugs, used currently in the prevention of rejection after organ transplant, on the development and progression of atherosclerosis is reviewed. In addition, the pleiotropic immunomodulatory effect of two established cardiovascular drugs (angiotensin-converting enzyme inhibitors and statins) is discussed.
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Affiliation(s)
- Sylvia Heeneman
- University of Maastricht, Department of Pathology, Cardiovascular Research Institute Maastricht, PO Box 5800, 6202 AZ Maastricht, The Netherlands.
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Abstract
We present a new molecular design program, FlexNovo, for structure-based searching within large fragment spaces following a sequential growth strategy. The fragment spaces consist of several thousands of chemical fragments and a corresponding set of rules that specify how the fragments can be connected. FlexNovo is based on the FlexX molecular docking software and makes use of its incremental construction algorithm and the underlying chemical models. Interaction energies are calculated by using standard scoring functions. Several placement geometry, physicochemical property (drug-likeness), and diversity filter criteria are directly integrated into the "build-up" process. FlexNovo has been used to design potential inhibitors for four targets of pharmaceutical interest (dihydrofolate reductase, cyclin-dependant kinase 2, cyclooxygenase-2, and the estrogen receptor). We have carried out calculations using different diversity parameters for each of these targets and generated solution sets containing up to 50 molecules. The compounds obtained show that FlexNovo is able to generate a diverse set of reasonable molecules with drug-like properties. The results, including an automated similarity analysis with the Feature Tree program, indicate that FlexNovo often reproduces structural motifs as well as the corresponding binding modes seen in known active structures.
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Affiliation(s)
- Jörg Degen
- Center for Bioinformatics, ZBH, University of Hamburg, Bundesstrasse 43, 20146 Hamburg, Germany
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Harper G, Pickett SD. Methods for mining HTS data. Drug Discov Today 2006; 11:694-9. [PMID: 16846796 DOI: 10.1016/j.drudis.2006.06.006] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2006] [Revised: 05/08/2006] [Accepted: 06/09/2006] [Indexed: 01/23/2023]
Abstract
Data mining is a fast-growing field that is finding application across a wide range of industries. HTS is a crucial part of the drug discovery process at most large pharmaceutical companies. Accurate analysis of HTS data is, therefore, vital to drug discovery. Given the large quantity of data generated during an HTS, and the importance of analyzing those data effectively, it is unsurprising that data-mining techniques are now increasingly applied to HTS data analysis. Taking a broad view of both the HTS process and the data-mining process, we review recent literature that describes the application of data-mining techniques to HTS data.
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Affiliation(s)
- Gavin Harper
- GSK, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, United Kingdom.
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