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Kibet S, Kimani NM, Mwanza SS, Mudalungu CM, Santos CBR, Tanga CM. Unveiling the Potential of Ent-Kaurane Diterpenoids: Multifaceted Natural Products for Drug Discovery. Pharmaceuticals (Basel) 2024; 17:510. [PMID: 38675469 PMCID: PMC11054903 DOI: 10.3390/ph17040510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 03/29/2024] [Accepted: 04/02/2024] [Indexed: 04/28/2024] Open
Abstract
Natural products hold immense potential for drug discovery, yet many remain unexplored in vast libraries and databases. In an attempt to fill this gap and meet the growing demand for effective drugs, this study delves into the promising world of ent-kaurane diterpenoids, a class of natural products with huge therapeutic potential. With a dataset of 570 ent-kaurane diterpenoids obtained from the literature, we conducted an in silico analysis, evaluating their physicochemical, pharmacokinetic, and toxicological properties with a focus on their therapeutic implications. Notably, these natural compounds exhibit drug-like properties, aligning closely with those of FDA-approved drugs, indicating a high potential for drug development. The ranges of the physicochemical parameters were as follows: molecular weights-288.47 to 626.82 g/mol; number of heavy atoms-21 to 44; the number of hydrogen bond donors and acceptors-0 to 8 and 1 to 11, respectively; the number of rotatable bonds-0 to 11; fraction Csp3-0.65 to 1; and TPSA-20.23 to 189.53 Ų. Additionally, the majority of these molecules display favorable safety profiles, with only 0.70%, 1.40%, 0.70%, and 46.49% exhibiting mutagenic, tumorigenic, reproduction-enhancing, and irritant properties, respectively. Importantly, ent-kaurane diterpenoids exhibit promising biopharmaceutical properties. Their average lipophilicity is optimal for drug absorption, while over 99% are water-soluble, facilitating delivery. Further, 96.5% and 28.20% of these molecules exhibited intestinal and brain bioavailability, expanding their therapeutic reach. The predicted pharmacological activities of these compounds encompass a diverse range, including anticancer, immunosuppressant, chemoprotective, anti-hepatic, hepatoprotectant, anti-inflammation, antihyperthyroidism, and anti-hepatitis activities. This multi-targeted profile highlights ent-kaurane diterpenoids as highly promising candidates for further drug discovery endeavors.
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Affiliation(s)
- Shadrack Kibet
- Department of Physical Sciences, University of Embu, Embu P.O. Box 6-60100, Kenya; (S.K.); (S.S.M.)
- International Centre of Insects Physiology and Ecology, Nairobi P.O. Box 30772-00100, Kenya;
| | - Njogu M. Kimani
- Department of Physical Sciences, University of Embu, Embu P.O. Box 6-60100, Kenya; (S.K.); (S.S.M.)
- Natural Product Chemistry and Computational Drug Discovery Laboratory, Embu P.O. Box 6-60100, Kenya
| | - Syombua S. Mwanza
- Department of Physical Sciences, University of Embu, Embu P.O. Box 6-60100, Kenya; (S.K.); (S.S.M.)
- International Centre of Insects Physiology and Ecology, Nairobi P.O. Box 30772-00100, Kenya;
| | - Cynthia M. Mudalungu
- International Centre of Insects Physiology and Ecology, Nairobi P.O. Box 30772-00100, Kenya;
- School of Chemistry and Material Science, The Technical University of Kenya, Nairobi P.O. Box 52428-00200, Kenya
| | - Cleydson B. R. Santos
- Graduate Program in Medicinal Chemistry and Molecular Modelling, Health Science Institute, Federal University of Pará, Belém 66075-110, Brazil;
- Laboratory of Modelling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapá 68902-280, Brazil
| | - Chrysantus M. Tanga
- International Centre of Insects Physiology and Ecology, Nairobi P.O. Box 30772-00100, Kenya;
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Atmaca H, Ilhan S, Dundar BA, Zora M. Bioevaluation of Spiro N-Propargylic β-Enaminones as Anti-Breast Cancer Agents: In Vitro and Molecular Docking Studies. Chem Biodivers 2023; 20:e202301228. [PMID: 37837366 DOI: 10.1002/cbdv.202301228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 10/10/2023] [Accepted: 10/12/2023] [Indexed: 10/16/2023]
Abstract
The study aimed to investigate the in vitro inhibitory activities of spiro N-propargylic β-enaminones, SPEs 1-31, against BCa cells, to perform in silico molecular docking studies to understand the nature of the interaction between the compounds and the ERα, PR, EGFR, and Her2, and to determine the ADMET and drug-likeness properties. Cytotoxic activity was investigated via MTT assay. DNA fragmentation was evaluated via ELISA assay. Cell cycle distributions were investigated by flow cytometry. Expression levels of Bcl-2, Bax, p21 and Cyclin D1 were measured by qRT-PCR and western blot analysis. Molecular docking was done using Autodock/vina software. ADMET analysis was calculated using the ADMETlab 2.0 tool. SPEs 1, 22, and 28 showed selective cytotoxic activity against all BCa cells with SI values >2. SPEs induced apoptosis and caused significant changes in Bcl-2 and Bax levels. The cell cycle was arrested at the S phase and levels of p21 and Cyclin D1 were induced in all BCa cells. Molecular docking analysis revealed that SPE1, SPE22, and SPE28 showed high binding affinities with ERα, PR, EGFR, and Her2. ADMET analysis revealed that SPEs are drug-like compounds as they obey the five rules of Lipinsky and are not toxic. Therefore, these potential anticancer compounds should be further validated by in vivo studies for their appropriate function in human health with a safety profile, and a comprehensive drug interaction study should be performed.
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Affiliation(s)
- Harika Atmaca
- Department of Biology, Faculty of Science and Letters, Manisa Celal Bayar University, 45140, Manisa, Turkey
| | - Suleyman Ilhan
- Department of Biology, Faculty of Science and Letters, Manisa Celal Bayar University, 45140, Manisa, Turkey
| | - Buse Aysen Dundar
- Department of Chemistry, Middle East Technical University, 06800, Ankara, Turkey
| | - Metin Zora
- Department of Chemistry, Middle East Technical University, 06800, Ankara, Turkey
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Xue Y, Mu S, Sun P, Sun Y, Liu N, Sun Y, Wang L, Zhao D, Cheng M. Design, synthesis, and biological evaluation of novel pyrimidin-2-amine derivatives as potent PLK4 inhibitors. RSC Med Chem 2023; 14:1787-1802. [PMID: 37731702 PMCID: PMC10507801 DOI: 10.1039/d3md00267e] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 07/12/2023] [Indexed: 09/22/2023] Open
Abstract
Serine/threonine protein kinase PLK4 is a master regulator of centriole duplication, which is significant for maintaining genome integrity. Accordingly, due to the detection of PLK4 overexpression in a variety of cancers, PLK4 has been identified as a candidate anticancer target. Thus, it is a very meaningful to find effective and safe PLK4 inhibitors for the treatment of cancer. However, the reported PLK4 inhibitors are scarce and have potential safety issues. In this study, a series of novel and potent PLK4 inhibitors with an aminopyrimidine core was obtained utilizing the scaffold hopping strategy. The in vitro enzyme activity results showed that compound 8h (PLK4 IC50 = 0.0067 μM) displayed high PLK4 inhibitory activity. In addition, compound 8h exhibited a good plasma stability (t1/2 > 289.1 min), liver microsomal stability (t1/2 > 145 min), and low risk of DDIs. At the cellular level, it presented excellent antiproliferative activity against breast cancer cells. Taken together, these results suggest that compound 8h has potential value in the further research of PLK4-targeted anticancer drugs.
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Affiliation(s)
- Yanli Xue
- Key Laboratory of Structure-Based Drug Design and Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University 103 Wenhua Road, Shenhe District 110016 Shenyang China
| | - Shuyi Mu
- Key Laboratory of Structure-Based Drug Design and Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University 103 Wenhua Road, Shenhe District 110016 Shenyang China
| | - Pengkun Sun
- Key Laboratory of Structure-Based Drug Design and Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University 103 Wenhua Road, Shenhe District 110016 Shenyang China
| | - Yin Sun
- Key Laboratory of Structure-Based Drug Design and Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University 103 Wenhua Road, Shenhe District 110016 Shenyang China
| | - Nian Liu
- Key Laboratory of Structure-Based Drug Design and Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University 103 Wenhua Road, Shenhe District 110016 Shenyang China
| | - Yu Sun
- Key Laboratory of Structure-Based Drug Design and Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University 103 Wenhua Road, Shenhe District 110016 Shenyang China
| | - Lin Wang
- Key Laboratory of Structure-Based Drug Design and Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University 103 Wenhua Road, Shenhe District 110016 Shenyang China
| | - Dongmei Zhao
- Key Laboratory of Structure-Based Drug Design and Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University 103 Wenhua Road, Shenhe District 110016 Shenyang China
| | - Maosheng Cheng
- Key Laboratory of Structure-Based Drug Design and Discovery of Ministry of Education, School of Pharmaceutical Engineering, Shenyang Pharmaceutical University 103 Wenhua Road, Shenhe District 110016 Shenyang China
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Park SB, Jung WH, Choi KJ, Koh B, Kim KY. A Comparative Systematic Analysis of The Influence of Microplastics on Colon Cells, Mouse and Colon Organoids. Tissue Eng Regen Med 2023; 20:49-58. [PMID: 36374371 PMCID: PMC9852409 DOI: 10.1007/s13770-022-00496-8] [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: 07/19/2022] [Revised: 09/16/2022] [Accepted: 09/23/2022] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Microplastics (MPs) are small fragments from any type of plastic formed from various sources, including plastic waste and microfibers from clothing. MPs degrades slowly, resulting in a high probability of human inhalation, ingestion and accumulation in bodies and tissues. As its impact on humans is a prolonged event, the evaluation of its toxicity and influence on human health are critical. In particular, MPs can enter the human digestive system through food and beverage consumption, and its effect on the human colon needs to be carefully examined. METHODS We monitored the influence of small MPs (50 and 100 nm) on human colon cells, human colon organoids and also examined their toxicity and changes in gene expression in vivo in a mouse model. RESULTS The data suggested that 5 mg/mL concentrations of 50 and 100 nm MPs induced a > 20% decrease in colon organoid viability and an increase in the expression of inflammatory-, apoptosis- and immunity-related genes. In addition, in vivo data suggested that 50 nm MPs accumulate in various mouse organs, including the colon, liver, pancreas and testicles after 7 d of exposure. CONCLUSION Taken together, our data suggest that smaller MPs can induce more toxic effects in the human colon and that human colon organoids have the potential to be used as a predictive tool for colon toxicity.
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Affiliation(s)
- Sung Bum Park
- Therapeutics and Biotechnology Division, Korea Research Institute of Chemical Technology, 141 Gajeong-ro, Yuseong-gu, Daejeon, 34114, Republic of Korea
| | - Won Hoon Jung
- Therapeutics and Biotechnology Division, Korea Research Institute of Chemical Technology, 141 Gajeong-ro, Yuseong-gu, Daejeon, 34114, Republic of Korea
| | - Kyoung Jin Choi
- Therapeutics and Biotechnology Division, Korea Research Institute of Chemical Technology, 141 Gajeong-ro, Yuseong-gu, Daejeon, 34114, Republic of Korea
| | - Byumseok Koh
- Therapeutics and Biotechnology Division, Korea Research Institute of Chemical Technology, 141 Gajeong-ro, Yuseong-gu, Daejeon, 34114, Republic of Korea.
| | - Ki Young Kim
- Therapeutics and Biotechnology Division, Korea Research Institute of Chemical Technology, 141 Gajeong-ro, Yuseong-gu, Daejeon, 34114, Republic of Korea.
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Luo J, Wen W, Chen J, Zeng X, Wang P, Xu S. Differences in tissue distribution ability of evodiamine and dehydroevodiamine are due to the dihedral angle of the molecule stereo-structure. Front Pharmacol 2023; 14:1109279. [PMID: 37089948 PMCID: PMC10117637 DOI: 10.3389/fphar.2023.1109279] [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: 11/27/2022] [Accepted: 03/27/2023] [Indexed: 04/25/2023] Open
Abstract
Introduction: This researcher focused at the evodiamine and dehydroevodiamine tissue distribution and structure-pharmacokinetics (PK) relationship after intravenous injection in mice. Methods: Using a transmembrane transport experiment, the permeability of evodiamine and dehydroevodiamine on Caco-2 cells was evaluated. The tissue distribution and pharmacokinetics (PK) of evodiamine and dehydroevodiamine in mice were studied. To comprehend the connection between structure and tissue distribution, physicochemical property evaluations and molecular electrostatic potential (MEP) calculations were performed. Results: Dehydroevodiamine's Papp values in vitro were 10-5 cm/s, whereas evodiamine's were 10-6 cm/s. At a dose of 5 mg/kg, the brain concentration of dehydroevodiamine was 6.44 times more than that of evodiamine. By MEP or physicochemical measures, the permeability difference between evodiamine and dehydroevodiamine is unaffected. The dihedral angle of the stereo-structure appears to be the main cause of the difference in tissue distribution ability between evodiamine and dehydroevodiamine. Discussion: Dehydroevodiamine has a dihedral angle of 3.71° compared to 82.34° for evodiamine. Dehydroevodiamine can more easily pass through the phospholipid bilayer than evodiamine because it has a more planar stereo-structure. Dehydroevodiamine is therefore more likely to pass cross the blood-brain barrier and enter the brain in a tissue-specific manner.
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Affiliation(s)
- Jie Luo
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- Institute of Meterial Medica Integration and Transformation for Brain Disorders, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Wen Wen
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- Institute of Meterial Medica Integration and Transformation for Brain Disorders, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Jie Chen
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- Institute of Meterial Medica Integration and Transformation for Brain Disorders, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Xiaobo Zeng
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- Institute of Meterial Medica Integration and Transformation for Brain Disorders, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Ping Wang
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- Institute of Meterial Medica Integration and Transformation for Brain Disorders, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
- *Correspondence: Ping Wang, ; Shijun Xu,
| | - Shijun Xu
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- Institute of Meterial Medica Integration and Transformation for Brain Disorders, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
- *Correspondence: Ping Wang, ; Shijun Xu,
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6
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Artem’eva EV, Duffin RN, Munuganti S, Efremov AN, Andrews PC, Sharutina OK, Sharutin VV. Modulating aryl substitution: Does it play a role in the anti-leishmanial activity of a series of tetra-aryl Sb(V) fluorinated carboxylates? J Inorg Biochem 2022; 234:111864. [DOI: 10.1016/j.jinorgbio.2022.111864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 05/04/2022] [Accepted: 05/15/2022] [Indexed: 10/18/2022]
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Kang SG, Morrone JA, Weber JK, Cornell WD. Analysis of Training and Seed Bias in Small Molecules Generated with a Conditional Graph-Based Variational Autoencoder─Insights for Practical AI-Driven Molecule Generation. J Chem Inf Model 2022; 62:801-816. [PMID: 35130440 DOI: 10.1021/acs.jcim.1c01545] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The application of deep learning to generative molecule design has shown early promise for accelerating lead series development. However, questions remain concerning how factors like training, data set, and seed bias impact the technology's utility to medicinal and computational chemists. In this work, we analyze the impact of seed and training bias on the output of an activity-conditioned graph-based variational autoencoder (VAE). Leveraging a massive, labeled data set corresponding to the dopamine D2 receptor, our graph-based generative model is shown to excel in producing desired conditioned activities and favorable unconditioned physical properties in generated molecules. We implement an activity-swapping method that allows for the activation, deactivation, or retention of activity of molecular seeds, and we apply independent deep learning classifiers to verify the generative results. Overall, we uncover relationships between noise, molecular seeds, and training set selection across a range of latent-space sampling procedures, providing important insights for practical AI-driven molecule generation.
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Affiliation(s)
- Seung-Gu Kang
- Computational Biology Center, IBM Thomas J. Watson Research Center, 1101 Kitchawan Road, Yorktown Heights, New York 10594, United States
| | - Joseph A Morrone
- Computational Biology Center, IBM Thomas J. Watson Research Center, 1101 Kitchawan Road, Yorktown Heights, New York 10594, United States
| | - Jeffrey K Weber
- Computational Biology Center, IBM Thomas J. Watson Research Center, 1101 Kitchawan Road, Yorktown Heights, New York 10594, United States
| | - Wendy D Cornell
- Computational Biology Center, IBM Thomas J. Watson Research Center, 1101 Kitchawan Road, Yorktown Heights, New York 10594, United States
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RNA-Targeting Splicing Modifiers: Drug Development and Screening Assays. Molecules 2021; 26:molecules26082263. [PMID: 33919699 PMCID: PMC8070285 DOI: 10.3390/molecules26082263] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 04/05/2021] [Accepted: 04/09/2021] [Indexed: 02/06/2023] Open
Abstract
RNA splicing is an essential step in producing mature messenger RNA (mRNA) and other RNA species. Harnessing RNA splicing modifiers as a new pharmacological modality is promising for the treatment of diseases caused by aberrant splicing. This drug modality can be used for infectious diseases by disrupting the splicing of essential pathogenic genes. Several antisense oligonucleotide splicing modifiers were approved by the U.S. Food and Drug Administration (FDA) for the treatment of spinal muscular atrophy (SMA) and Duchenne muscular dystrophy (DMD). Recently, a small-molecule splicing modifier, risdiplam, was also approved for the treatment of SMA, highlighting small molecules as important warheads in the arsenal for regulating RNA splicing. The cellular targets of these approved drugs are all mRNA precursors (pre-mRNAs) in human cells. The development of novel RNA-targeting splicing modifiers can not only expand the scope of drug targets to include many previously considered “undruggable” genes but also enrich the chemical-genetic toolbox for basic biomedical research. In this review, we summarized known splicing modifiers, screening methods for novel splicing modifiers, and the chemical space occupied by the small-molecule splicing modifiers.
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Barlow SR, Callaghan LJ, Franckevičius V. Investigation of the palladium-catalysed cyclisation of α-amido malonates with propargylic compounds. Tetrahedron 2021. [DOI: 10.1016/j.tet.2020.131866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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10
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Design and synthesis of nature-inspired chromenopyrroles as potential modulators of mitochondrial metabolism. Med Chem Res 2020. [DOI: 10.1007/s00044-020-02669-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Talele TT. Opportunities for Tapping into Three-Dimensional Chemical Space through a Quaternary Carbon. J Med Chem 2020; 63:13291-13315. [PMID: 32805118 DOI: 10.1021/acs.jmedchem.0c00829] [Citation(s) in RCA: 140] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
A quaternary carbon bears four other carbon substituents or combination of four non-hydrogen substituents at four vertices of a tetrahedron. The spirocyclic quaternary carbon positioned at the center of a bioactive molecule offers conformational rigidity, which in turn reduces the penalty for conformational entropy. The quaternary carbon is a predominant feature of natural product structures and has been associated with more effective and selective binding to target proteins compared to planar compounds with a high sp2 count. The presence of a quaternary carbon stereocenter allows the exploration of novel chemical space to obtain new molecules with enhanced three-dimensionality. These characteristics, coupled to an increasing awareness to develop sp3-rich molecules, boosted utility of quaternary carbon stereocenters in bioactive compounds. It is hoped that this Perspective will inspire the chemist to utilize quaternary carbon stereocenters to enhance potency, selectivity, and other drug-like properties.
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Affiliation(s)
- Tanaji T Talele
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John's University, Queens, New York 11439, United States
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Yukawa T, Naven R. Utility of Physicochemical Properties for the Prediction of Toxicological Outcomes: Takeda Perspective. ACS Med Chem Lett 2020; 11:203-209. [PMID: 32071689 DOI: 10.1021/acsmedchemlett.9b00536] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 01/29/2020] [Indexed: 01/17/2023] Open
Abstract
The role that physicochemical properties play toward increasing the likelihood of toxicity findings in in vivo studies has been well reported, albeit sometimes with different conclusions. We decided to understand the role that physicochemical properties play toward the prediction of in vivo toxicological outcomes for Takeda chemistry using 284 internal compounds. In support of the previously reported "3/75 rule", reducing lipophilicity of molecules decreases toxicity odds noticeably; however, we also found that the trend of toxicity odds is different between compounds classified by their ionization state. For basic molecules, the odds of in vivo toxicity outcomes were significantly impacted by both lipophilicity and polar surface area, whereas neutral molecules were impacted less so. Through an analysis of several project-related compounds, we herein demonstrate that the utilization of the 3/75 rule coupled with consideration of ionization state is a rational strategy for medicinal chemistry design of safer drugs.
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Affiliation(s)
- Tomoya Yukawa
- Drug Safety Research and Evaluation, Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, 35 Landsdowne Street, Cambridge, Massachusetts 02139, United States
- Drug Safety Research and Evaluation, Pharmaceutical Research Division, Takeda Pharmaceuticals International Company Limited, 9625 Towne Centre Drive, San Diego, California 92121, United States
| | - Russell Naven
- Drug Safety Research and Evaluation, Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, 35 Landsdowne Street, Cambridge, Massachusetts 02139, United States
- Drug Safety Research and Evaluation, Pharmaceutical Research Division, Takeda Pharmaceuticals International Company Limited, 9625 Towne Centre Drive, San Diego, California 92121, United States
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Zhu Y, Yao X, Long J, Li R, Liu Y, Yang Z, Zheng X. Fluorine-Containing Chrysin Derivatives. Nat Prod Commun 2019. [DOI: 10.1177/1934578x19878921] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Chrysin, a flavonoid, has played a great role in the fields of anticancer, antibacterial, and antiviral drug discovery. A large number of chrysin derivatives have been synthesized recently. The fluorine atom represents an important substituent group for a great number of natural products and pharmaceuticals. Taking into account the importance of both chrysin and the fluorine atom in medicinal chemistry, the synthesis of fluorine-containing chrysin derivatives has gained great interest. Chemically, the synthetic methods for these new chrysin derivatives have also been developed rapidly. In recent years, research on their synthesis has been focused on speeding up the reaction process by changing the catalyst. Biologically, the purpose of introducing fluorine into chrysin was to improve its lipophilicity, but today it is mainly focused on the enhancement and improvement of either its anticancer or antimicrobial activities by incorporating the special properties of fluorine atoms. In this review, synthetic methods for the introduction of fluorine atoms into chrysin are summarized, and their anticancer, antibacterial, antiviral, and hypoglycemic effects are discussed.
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Affiliation(s)
- Yue Zhu
- Group of Lead Compound, Institute of Pharmacy & Pharmacology, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, University of South China, Hengyang, China
| | - Xu Yao
- Group of Lead Compound, Institute of Pharmacy & Pharmacology, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, University of South China, Hengyang, China
| | - Jin Long
- Group of Lead Compound, Institute of Pharmacy & Pharmacology, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, University of South China, Hengyang, China
| | - Rong Li
- Group of Lead Compound, Institute of Pharmacy & Pharmacology, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, University of South China, Hengyang, China
| | - Yi Liu
- Group of Lead Compound, Institute of Pharmacy & Pharmacology, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, University of South China, Hengyang, China
| | - ZeHua Yang
- Group of Lead Compound, Institute of Pharmacy & Pharmacology, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, University of South China, Hengyang, China
| | - Xing Zheng
- Group of Lead Compound, Institute of Pharmacy & Pharmacology, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, University of South China, Hengyang, China
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Rao MS, Gupta R, Liguori MJ, Hu M, Huang X, Mantena SR, Mittelstadt SW, Blomme EAG, Van Vleet TR. Novel Computational Approach to Predict Off-Target Interactions for Small Molecules. Front Big Data 2019; 2:25. [PMID: 33693348 PMCID: PMC7931946 DOI: 10.3389/fdata.2019.00025] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 06/26/2019] [Indexed: 12/01/2022] Open
Abstract
Most small molecule drugs interact with unintended, often unknown, biological targets and these off-target interactions may lead to both preclinical and clinical toxic events. Undesired off-target interactions are often not detected using current drug discovery assays, such as experimental polypharmacological screens. Thus, improvement in the early identification of off-target interactions represents an opportunity to reduce safety-related attrition rates during preclinical and clinical development. In order to better identify potential off-target interactions that could be linked to predictable safety issues, a novel computational approach to predict safety-relevant interactions currently not covered was designed and evaluated. These analyses, termed Off-Target Safety Assessment (OTSA), cover more than 7,000 targets (~35% of the proteome) and > 2,46,704 preclinical and clinical alerts (as of January 20, 2019). The approach described herein exploits a highly curated training set of >1 million compounds (tracking >20 million compound-structure activity relationship/SAR data points) with known in vitro activities derived from patents, journals, and publicly available databases. This computational process was used to predict both the primary and secondary pharmacological activities for a selection of 857 diverse small molecule drugs for which extensive secondary pharmacology data are readily available (456 discontinued and 401 FDA approved). The OTSA process predicted a total of 7,990 interactions for these 857 molecules. Of these, 3,923 and 4,067 possible high-scoring interactions were predicted for the discontinued and approved drugs, respectively, translating to an average of 9.3 interactions per drug. The OTSA process correctly identified the known pharmacological targets for >70% of these drugs, but also predicted a significant number of off-targets that may provide additional insight into observed in vivo effects. About 51.5% (2,025) and 22% (900) of these predicted high-scoring interactions have not previously been reported for the discontinued and approved drugs, respectively, and these may have a potential for repurposing efforts. Moreover, for both drug categories, higher promiscuity was observed for compounds with a MW range of 300 to 500, TPSA of ~200, and clogP ≥7. This computation also revealed significantly lower promiscuity (i.e., number of confirmed off-targets) for compounds with MW > 700 and MW<200 for both categories. In addition, 15 internal small molecules with known off-target interactions were evaluated. For these compounds, the OTSA framework not only captured about 56.8% of in vitro confirmed off-target interactions, but also identified the right pharmacological targets for 14 compounds as one of the top scoring targets. In conclusion, the OTSA process demonstrates good predictive performance characteristics and represents an additional tool with utility during the lead optimization stage of the drug discovery process. Additionally, the computed physiochemical properties such as clogP (i.e., lipophilicity), molecular weight, pKa and logS (i.e., solubility) were found to be statistically different between the approved and discontinued drugs, but the internal compounds were close to the approved drugs space in most part.
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Affiliation(s)
- Mohan S Rao
- Global Preclinical Safety, Abbvie, North Chicago, IL, United States
| | - Rishi Gupta
- Information Research, Abbvie, North Chicago, IL, United States
| | | | - Mufeng Hu
- Discovery and Early Pipeline Statistics, Abbvie, North Chicago, IL, United States
| | - Xin Huang
- Discovery and Early Pipeline Statistics, Abbvie, North Chicago, IL, United States
| | | | | | - Eric A G Blomme
- Global Preclinical Safety, Abbvie, North Chicago, IL, United States
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15
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Huffman BJ, Shenvi RA. Natural Products in the "Marketplace": Interfacing Synthesis and Biology. J Am Chem Soc 2019; 141:3332-3346. [PMID: 30682249 PMCID: PMC6446556 DOI: 10.1021/jacs.8b11297] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Drugs are discovered through the biological screening of collections of compounds, followed by optimization toward functional end points. The properties of screening collections are often balanced between diversity, physicochemical favorability, intrinsic complexity, and synthetic tractability (Huggins, D. J.; et al. ACS Chem. Biol. 2011, 6, 208; DOI: 10.1021/cb100420r ). Whereas natural product (NP) collections excel in the first three attributes, NPs suffer a disadvantage on the last point. Academic total synthesis research has worked to solve this problem by devising syntheses of NP leads, diversifying late-stage intermediates, or derivatizing the NP target. This work has led to the discovery of reaction mechanisms, the invention of new methods, and the development of FDA-approved drugs. Few drugs, however, are themselves NPs; instead, NP analogues predominate. Here we highlight past examples of NP analogue development and successful NP-derived drugs. More recently, chemists have explored how NP analogues alter the retrosynthetic analysis of complex scaffolds, merging structural design and synthetic design. This strategy maintains the intrinsic complexity of the NP but can alter the physicochemical properties of the scaffold, like core instability that renders the NP a poor chemotype. Focused libraries based on these syntheses may exclude the NP but maintain the molecular properties that distinguish NP space from synthetic space (Stratton, C. F.; et al. Bioorg. Med. Chem. Lett. 2015, 25, 4802; DOI: 10.1016/j.bmcl.2015.07.014 ), properties that have statistical advantages in clinical progression (Luker, T.; et al. Bioorg. Med. Chem. Lett. 2011, 21, 5673, DOI: 10.1016/j.bmcl.2011.07.074 ; Ritchie, T. J.; Macdonald, S. J. F. Drug Discovery Today 2009, 14, 1011, DOI: 10.1016/j.drudis.2009.07.014 ). Research that expedites synthetic access to NP motifs can prevent homogeneity of chemical matter available for lead discovery. Easily accessed, focused libraries of NP scaffolds can fill empty but active gaps in screening sets and expand the molecular diversity of synthetic collections.
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Affiliation(s)
- Benjamin J. Huffman
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Ryan A. Shenvi
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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16
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Broccatelli F, E.C.A Hop C, Wright M. Strategies to optimize drug half-life in lead candidate identification. Expert Opin Drug Discov 2019; 14:221-230. [DOI: 10.1080/17460441.2019.1569625] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Fabio Broccatelli
- Department of Drug Metabolism and Pharmacokinetics, Genentech, South San Francisco, CA, USA
| | - Cornelis E.C.A Hop
- Department of Drug Metabolism and Pharmacokinetics, Genentech, South San Francisco, CA, USA
| | - Matthew Wright
- Department of Drug Metabolism and Pharmacokinetics, Genentech, South San Francisco, CA, USA
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17
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Fujii H, Hirayama S, Obayashi K, Wada N, Ohyama K, Fuku S, Koyano K, Karaki F, Itoh K, Nagase H. The Practical Synthesis of Dissymmetrical 1,3,5-Trioxazatriquinane Derivatives Comprised of Three Distinct Carbonyl Compounds. HETEROCYCLES 2019. [DOI: 10.3987/com-18-s(f)65] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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18
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N-Thiazolylamide-based free fatty-acid 2 receptor agonists: Discovery, lead optimization and demonstration of off-target effect in a diabetes model. Bioorg Med Chem 2018; 26:5169-5180. [PMID: 30253886 DOI: 10.1016/j.bmc.2018.09.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 09/13/2018] [Accepted: 09/16/2018] [Indexed: 01/14/2023]
Abstract
Free fatty acid-2 (FFA2) receptor is a G-protein coupled receptor of interest in the development of therapeutics in metabolic and inflammatory disease areas. The discovery and optimization of an N-thiazolylamide carboxylic acid FFA2 agonist scaffold is described. Dual key objectives were to i) evaluate the potential of this scaffold for lead optimization in particular with respect to safety de-risking physicochemical properties, i.e. lipophilicity and aromatic content, and ii) to demonstrate the utility of selected lead analogues from this scaffold in a pertinent in vivo model such as oral glucose tolerance test (OGTT). As such, a concomitant improvement in bioactivity together with lipophilic ligand efficiency (LLE) and fraction sp3 content (Fsp3) parameters guided these efforts. Compound 10 was advanced into studies in mice on the basis of its optimized profile vs initial lead 1 (ΔLLE = 0.3, ΔFsp3 = 0.24). Although active in OGTT, 10 also displayed similar activity in the FFA2-knockout mice. Given this off-target OGTT effect, we discontinued development of this FFA2 agonist scaffold.
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19
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Guney T, Wenderski TA, Boudreau MW, Tan DS. Synthesis of Benzannulated Medium-ring Lactams via a Tandem Oxidative Dearomatization-Ring Expansion Reaction. Chemistry 2018; 24:13150-13157. [PMID: 29936701 PMCID: PMC6242278 DOI: 10.1002/chem.201802880] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Indexed: 12/19/2022]
Abstract
Medium-ring natural products exhibit diverse biological activities but such scaffolds are underrepresented in probe and drug discovery efforts due to the limitations of classical macrocyclization reactions. We report herein a tandem oxidative dearomatization-ring-expanding rearomatization (ODRE) reaction that generates benzannulated medium-ring lactams directly from simple bicyclic substrates. The reaction accommodates diverse aryl substrates (haloarenes, aryl ethers, aryl amides, heterocycles) and strategic incorporation of a bridgehead alcohol generates a versatile ketone moiety in the products amenable to downstream modifications. Cheminformatic analysis indicates that these medium rings access regions of chemical space that overlap with related natural products and are distinct from synthetic drugs, setting the stage for their use in discovery screening against novel biological targets.
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Affiliation(s)
- Tezcan Guney
- Dr. T. Guney, Dr. T. A. W enderski, Prof. Dr. D. S. Tan,
Chemical Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer
Center, 1275 York Avenue, Box 422, New York, New York, 10065, USA
| | - Todd A. Wenderski
- Dr. T. Guney, Dr. T. A. W enderski, Prof. Dr. D. S. Tan,
Chemical Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer
Center, 1275 York Avenue, Box 422, New York, New York, 10065, USA
| | - Matthew W. Boudreau
- M. W. Boudreau, Gerstner Sloan Kettering Summer
Undergraduate Research Program, Memorial Sloan Kettering Cancer Center, 1275 York
Avenue, Box 422, New York, New York, 10065, USA
| | - Derek S. Tan
- Dr. T. Guney, Dr. T. A. W enderski, Prof. Dr. D. S. Tan,
Chemical Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer
Center, 1275 York Avenue, Box 422, New York, New York, 10065, USA
- Prof. Dr. D. S. Tan, Tri-Institutional Research Program,
Memorial Sloan Kettering Cancer Center, 1275 York Avenue, Box 422, New York, New
York, 10065, USA
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20
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Ford KA. Refinement, Reduction, and Replacement of Animal Toxicity Tests by Computational Methods. ILAR J 2017; 57:226-233. [DOI: 10.1093/ilar/ilw031] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Revised: 10/12/2016] [Indexed: 12/16/2022] Open
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21
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Quality guidelines for oral drug candidates: dose, solubility and lipophilicity. Drug Discov Today 2016; 21:1719-1727. [DOI: 10.1016/j.drudis.2016.07.007] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 06/01/2016] [Accepted: 07/07/2016] [Indexed: 12/30/2022]
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22
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Leeson PD. Molecular inflation, attrition and the rule of five. Adv Drug Deliv Rev 2016; 101:22-33. [PMID: 26836397 DOI: 10.1016/j.addr.2016.01.018] [Citation(s) in RCA: 121] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Revised: 01/12/2016] [Accepted: 01/18/2016] [Indexed: 12/18/2022]
Abstract
Physicochemical properties underlie all aspects of drug action and are critical for solubility, permeability and successful formulation. Specific physicochemical properties shown to be relevant to oral drugs are size, lipophilicity, ionisation, hydrogen bonding, polarity, aromaticity and shape. The rule of 5 (Ro5) and subsequent studies have raised awareness of the importance of compound quality amongst bioactive molecules. Lipophilicity, probably the most important physical property of oral drugs, has on average changed little over time in oral drugs, until increases in drugs published after 1990. In contrast other molecular properties such as average size have increased significantly. Factors influencing property inflation include the targets pursued, where antivirals frequently violate the Ro5, risk/benefit considerations, and variable drug discovery practices. The compounds published in patents from the pharmaceutical industry are on average larger, more lipophilic and less complex than marketed oral drugs. The variation between individual companies' patented compounds is due to different practices and not to the targets pursued. Overall, there is demonstrable physical property attrition in moving from patents to candidate drugs to marketed drugs. The pharmaceutical industry's recent poor productivity has been due, in part, to progression of molecules that are unable to unambiguously test clinical efficacy, and attrition can therefore be improved by ensuring candidate drug quality is 'fit for purpose.' The combined ligand efficiency (LE) and lipophilic ligand efficiency (LLE) values of many marketed drugs are optimised relative to other molecules acting at the same target. Application of LLE in optimisation can help identify improved leads, even with challenging targets that seem to require lipophilic ligands. Because of their targets, some projects may need to pursue 'beyond Ro5' physicochemical space; such projects will require non-standard lead generation and optimisation and should not dominate in a well-balanced portfolio. Compound quality is controllable by lead selection and optimisation and should not be a cause of clinical failure.
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Affiliation(s)
- Paul D Leeson
- Paul Leeson Consulting Ltd, The Malt House, Main Street, Congerstone, Nuneaton, Warks CV13 6LZ, UK.
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23
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Structure Based Docking and Molecular Dynamic Studies of Plasmodial Cysteine Proteases against a South African Natural Compound and its Analogs. Sci Rep 2016; 6:23690. [PMID: 27030511 PMCID: PMC4814779 DOI: 10.1038/srep23690] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 03/09/2016] [Indexed: 11/09/2022] Open
Abstract
Identification of potential drug targets as well as development of novel antimalarial chemotherapies with unique mode of actions due to drug resistance by Plasmodium parasites are inevitable. Falcipains (falcipain-2 and falcipain-3) of Plasmodium falciparum, which catalyse the haemoglobin degradation process, are validated drug targets. Previous attempts to develop peptide based drugs against these enzymes have been futile due to the poor pharmacological profiles and susceptibility to degradation by host enzymes. This study aimed to identify potential non-peptide inhibitors against falcipains and their homologs from other Plasmodium species. Structure based virtual docking approach was used to screen a small non-peptidic library of natural compounds from South Africa against 11 proteins. A potential hit, 5α-Pregna-1,20-dien-3-one (5PGA), with inhibitory activity against plasmodial proteases and selectivity on human cathepsins was identified. A 3D similarity search on the ZINC database using 5PGA identified five potential hits based on their docking energies. The key interacting residues of proteins with compounds were identified via molecular dynamics and free binding energy calculations. Overall, this study provides a basis for further chemical design for more effective derivatives of these compounds. Interestingly, as these compounds have cholesterol-like nuclei, they and their derivatives might be well tolerated in humans.
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24
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Szymańska-Michalak A, Wawrzyniak D, Framski G, Kujda M, Zgoła P, Stawinski J, Barciszewski J, Boryski J, Kraszewski A. New 3'-O-aromatic acyl-5-fluoro-2'-deoxyuridine derivatives as potential anticancer agents. Eur J Med Chem 2016; 115:41-52. [PMID: 26994842 DOI: 10.1016/j.ejmech.2016.03.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Revised: 03/02/2016] [Accepted: 03/03/2016] [Indexed: 12/29/2022]
Abstract
New aromatic and aliphatic 3'-O-acyl-5-fluoro-2'-deoxyuridine derivatives were synthesized and evaluated as candidates for prodrugs against various cancer cell lines. As the most promising candidate for antimalignant therapeutics was found a dual-acting acyl derivative 7h, which apparently released not only the known anticancer nucleoside, 5-fluoro-2'-deoxyuridine (FdU), but also an additional active metabolite, acetylsalicylic acid, reinforcing thus therapeutic effect of FdU. Promising therapeutic indices showed also some aromatic dicarboxylic acids derivatives decorated with FdU esters (11 and 12).
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Affiliation(s)
| | - Dariusz Wawrzyniak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznań, Poland
| | - Grzegorz Framski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznań, Poland
| | - Marta Kujda
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239, Cracow, Poland
| | - Paulina Zgoła
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznań, Poland
| | - Jacek Stawinski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznań, Poland
| | - Jan Barciszewski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznań, Poland
| | - Jerzy Boryski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznań, Poland
| | - Adam Kraszewski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznań, Poland.
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25
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Wenlock MC. Profiling the estimated plasma concentrations of 215 marketed oral drugs. MEDCHEMCOMM 2016. [DOI: 10.1039/c5md00583c] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The human pharmacokinetic parameters of 215 marketed oral drugs have been collated and their estimated plasma concentrations (following repeat dosing) profiled against time using a one-compartment model.
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26
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Stratton CF, Newman DJ, Tan DS. Cheminformatic comparison of approved drugs from natural product versus synthetic origins. Bioorg Med Chem Lett 2015; 25:4802-4807. [PMID: 26254944 PMCID: PMC4607632 DOI: 10.1016/j.bmcl.2015.07.014] [Citation(s) in RCA: 112] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 07/08/2015] [Indexed: 11/27/2022]
Abstract
Despite the recent decline of natural product discovery programs in the pharmaceutical industry, approximately half of all new drug approvals still trace their structural origins to a natural product. Herein, we use principal component analysis to compare the structural and physicochemical features of drugs from natural product-based versus completely synthetic origins that were approved between 1981 and 2010. Drugs based on natural product structures display greater chemical diversity and occupy larger regions of chemical space than drugs from completely synthetic origins. Notably, synthetic drugs based on natural product pharmacophores also exhibit lower hydrophobicity and greater stereochemical content than drugs from completely synthetic origins. These results illustrate that structural features found in natural products can be successfully incorporated into synthetic drugs, thereby increasing the chemical diversity available for small-molecule drug discovery.
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Affiliation(s)
- Christopher F Stratton
- Tri-Institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, 1275 York Ave, Box 422, New York, NY 10065, USA
| | - David J Newman
- Natural Products Branch, Developmental Therapeutics Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Frederick, PO Box B, Frederick, MD 21702, USA
| | - Derek S Tan
- Tri-Institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, 1275 York Ave, Box 422, New York, NY 10065, USA; Chemical Biology Program and Tri-Institutional Research Program, Memorial Sloan Kettering Cancer Center, 1275 York Ave, Box 422, New York, NY 10065, USA
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27
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Abstract
The development of resistance to existing antimicrobials has created a threat to human health that is not being addressed through our current drug pipeline. Limitations with the use of commercial vendor libraries and natural products have created a need for new types of small molecules to be screened in antimicrobial assays. Diversity oriented synthesis (DOS) is a strategy for the efficient generation of compound collections with a high degree of structural diversity. Diversity-oriented synthesis molecules occupy the middle ground of both complexity and efficiency of synthesis between natural products and commercial libraries. In this review we focus upon the use of diversity-oriented synthesis compound collections for the discovery of new antimicrobial agents.
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28
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Waring MJ, Arrowsmith J, Leach AR, Leeson PD, Mandrell S, Owen RM, Pairaudeau G, Pennie WD, Pickett SD, Wang J, Wallace O, Weir A. An analysis of the attrition of drug candidates from four major pharmaceutical companies. Nat Rev Drug Discov 2015; 14:475-86. [PMID: 26091267 DOI: 10.1038/nrd4609] [Citation(s) in RCA: 786] [Impact Index Per Article: 87.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The pharmaceutical industry remains under huge pressure to address the high attrition rates in drug development. Attempts to reduce the number of efficacy- and safety-related failures by analysing possible links to the physicochemical properties of small-molecule drug candidates have been inconclusive because of the limited size of data sets from individual companies. Here, we describe the compilation and analysis of combined data on the attrition of drug candidates from AstraZeneca, Eli Lilly and Company, GlaxoSmithKline and Pfizer. The analysis reaffirms that control of physicochemical properties during compound optimization is beneficial in identifying compounds of candidate drug quality and indicates for the first time a link between the physicochemical properties of compounds and clinical failure due to safety issues. The results also suggest that further control of physicochemical properties is unlikely to have a significant effect on attrition rates and that additional work is required to address safety-related failures. Further cross-company collaborations will be crucial to future progress in this area.
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Affiliation(s)
| | | | | | - Paul D Leeson
- 1] GlaxoSmithKline, Stevenage, Hertfordshire SG1 2NY, UK. [2] Paul Leeson Consulting, The Malt House, Main Street, Congerstone, Nuneaton, Warwickshire CV13 6LZ, UK
| | - Sam Mandrell
- Thomson Reuters, 77 Hatton Garden, London EC1N 8JS, UK
| | | | | | - William D Pennie
- 1] Pfizer, Groton, Connecticut 06340, USA. [2] Takeda Pharmaceuticals, Cambridge, Massachusetts 02139, USA
| | | | - Jibo Wang
- Eli Lilly, Indianapolis, Indiana 46285, USA
| | - Owen Wallace
- 1] Eli Lilly, Indianapolis, Indiana 46285, USA. [2] Novartis Institutes for Biomedical Research, Cambridge, Massachusetts 02139, USA
| | - Alex Weir
- Thomson Reuters, 77 Hatton Garden, London EC1N 8JS, UK
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29
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Hoveyda HR, Fraser GL, Roy MO, Dutheuil G, Batt F, El Bousmaqui M, Korac J, Lenoir F, Lapin A, Noël S, Blanc S. Discovery and optimization of novel antagonists to the human neurokinin-3 receptor for the treatment of sex-hormone disorders (Part I). J Med Chem 2015; 58:3060-82. [PMID: 25738882 DOI: 10.1021/jm5017413] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Neurokinin-3 receptor (NK3R) has recently emerged as important in modulating the tonic pulsatile gonadotropin-releasing hormone (GnRH) release. We therefore decided to explore NK3R antagonists as therapeutics for sex-hormone disorders that can potentially benefit from lowering GnRH pulsatility with consequent diminished levels of plasma luteinizing hormone (LH) and correspondingly attenuated levels of circulating androgens and estrogens. The discovery and lead optimization of a novel N-acyl-triazolopiperazine NK3R antagonist chemotype achieved through bioisosteric lead change from the high-throughput screening (HTS) hit is described. A concomitant improvement in the antagonist bioactivity and ligand lipophilic efficiency (LLE) parameter were the principal guidelines in the lead optimization efforts. Examples of advanced lead analogues to demonstrate the amenability of this chemotype to achieving a suitable pharmacokinetic (PK) profile are provided as well as pharmacokinetic-pharmacodynamic (PKPD) correlations to analyze the trends observed for LH inhibition in castrated rats and monkeys that served as preliminary in vivo efficacy models.
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Affiliation(s)
- Hamid R Hoveyda
- Euroscreen SA, 47 Rue Adrienne Bolland, 6041 Gosselies, Belgium
| | - Graeme L Fraser
- Euroscreen SA, 47 Rue Adrienne Bolland, 6041 Gosselies, Belgium
| | - Marie-Odile Roy
- Euroscreen SA, 47 Rue Adrienne Bolland, 6041 Gosselies, Belgium
| | | | - Frédéric Batt
- Euroscreen SA, 47 Rue Adrienne Bolland, 6041 Gosselies, Belgium
| | | | - Julien Korac
- Euroscreen SA, 47 Rue Adrienne Bolland, 6041 Gosselies, Belgium
| | - François Lenoir
- Euroscreen SA, 47 Rue Adrienne Bolland, 6041 Gosselies, Belgium
| | - Alexey Lapin
- Euroscreen SA, 47 Rue Adrienne Bolland, 6041 Gosselies, Belgium
| | - Sophie Noël
- Euroscreen SA, 47 Rue Adrienne Bolland, 6041 Gosselies, Belgium
| | - Sébastien Blanc
- Euroscreen SA, 47 Rue Adrienne Bolland, 6041 Gosselies, Belgium
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30
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Abstract
Since its first use in the steroid field in the late 1950s, the use of fluorine in medicinal chemistry has become commonplace, with the small electronegative fluorine atom being a key part of the medicinal chemist's repertoire of substitutions used to modulate all aspects of molecular properties including potency, physical chemistry and pharmacokinetics. This review will highlight the special nature of fluorine, drawing from a survey of marketed fluorinated pharmaceuticals and the medicinal chemistry literature, to illustrate key concepts exploited by medicinal chemists in their attempts to optimize drug molecules. Some of the potential pitfalls in the use of fluorine will also be highlighted.
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31
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Alza E, Laraia L, Ibbeson BM, Collins S, Galloway WRJD, Stokes JE, Venkitaraman AR, Spring DR. Synthesis of a novel polycyclic ring scaffold with antimitotic properties via a selective domino Heck-Suzuki reaction. Chem Sci 2015; 6:390-396. [PMID: 28966765 PMCID: PMC5586250 DOI: 10.1039/c4sc02547d] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Accepted: 09/03/2014] [Indexed: 01/20/2023] Open
Abstract
The synthesis of a previously undescribed sp3-rich 6-5-5-6 tetracyclic ring scaffold using a palladium catalysed domino Heck-Suzuki reaction is reported. This reaction is high-yielding, selective for the domino process over the direct Suzuki reaction and tolerant towards a variety of boronic acids. The novel scaffold can also be accessed via domino Heck-Stille and radical cyclisations. Compounds based around this scaffold were found to be effective antimitotic agents in a human cancer cell line. Detailed phenotypic profiling showed that the compounds affected the congression of chromosomes to give mitotic arrest and apoptotic cell death. Thus, a novel structural class of antimitotic agents that does not disrupt the tubulin network has been identified.
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Affiliation(s)
- Esther Alza
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge , CB2 1EW , UK . ; ; Tel: +44 (0)1223 336498
| | - Luca Laraia
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge , CB2 1EW , UK . ; ; Tel: +44 (0)1223 336498
- MRC Cancer Unit , University of Cambridge , Hutchison/MRC Research Centre , Biomedical Campus , Hills Road , Cambridge , CB2 0XZ , UK
| | - Brett M Ibbeson
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge , CB2 1EW , UK . ; ; Tel: +44 (0)1223 336498
| | - Súil Collins
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge , CB2 1EW , UK . ; ; Tel: +44 (0)1223 336498
| | - Warren R J D Galloway
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge , CB2 1EW , UK . ; ; Tel: +44 (0)1223 336498
| | - Jamie E Stokes
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge , CB2 1EW , UK . ; ; Tel: +44 (0)1223 336498
- MRC Cancer Unit , University of Cambridge , Hutchison/MRC Research Centre , Biomedical Campus , Hills Road , Cambridge , CB2 0XZ , UK
| | - Ashok R Venkitaraman
- MRC Cancer Unit , University of Cambridge , Hutchison/MRC Research Centre , Biomedical Campus , Hills Road , Cambridge , CB2 0XZ , UK
| | - David R Spring
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge , CB2 1EW , UK . ; ; Tel: +44 (0)1223 336498
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Grossmann A, Bartlett S, Janecek M, Hodgkinson JT, Spring DR. Diversity-Oriented Synthesis of Drug-Like Macrocyclic Scaffolds Using an Orthogonal Organo- and Metal Catalysis Strategy. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201406865] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Grossmann A, Bartlett S, Janecek M, Hodgkinson JT, Spring DR. Diversity-Oriented Synthesis of Drug-Like Macrocyclic Scaffolds Using an Orthogonal Organo- and Metal Catalysis Strategy. Angew Chem Int Ed Engl 2014; 53:13093-7. [DOI: 10.1002/anie.201406865] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Indexed: 01/05/2023]
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Ritchie TJ, Macdonald SJF. Physicochemical Descriptors of Aromatic Character and Their Use in Drug Discovery. J Med Chem 2014; 57:7206-15. [DOI: 10.1021/jm500515d] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
| | - Simon J. F. Macdonald
- Respiratory
CEDD, GlaxoSmithKline Medicines Research Centre, Gunnels Wood
Road, Stevenage SG1 2NY, United Kingdom
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Shah F, Louise-May S, Greene N. Chemotypes sensitivity and predictivity of in vivo outcomes for cytotoxic assays in THLE and HepG2 cell lines. Bioorg Med Chem Lett 2014; 24:2753-7. [PMID: 24794102 DOI: 10.1016/j.bmcl.2014.04.039] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Revised: 04/08/2014] [Accepted: 04/09/2014] [Indexed: 11/30/2022]
Abstract
In the present study, we demonstrate the utility of in vitro ATP depletion assays in both THLE and HepG2 cells for predicting the toxicological outcome in Exploratory Toxicology Studies across 446 Pfizer proprietary compounds. Our results suggest a higher likelihood of selecting suitable compounds for in vivo safety studies by using cytotoxicity assays in multiple cell-lines over a single cell line. In addition, we demonstrate that different cell-lines have different sensitivities to compounds depending on their ionization state, that is, acid, base or neutral. HepG2 cells are more sensitive for basic compounds, whereas THLE cells have a relatively higher sensitivity for the acidic and neutral compounds. These in vitro cytotoxicity assays when combined with physicochemical properties (cLogP >3 and topological polar surface area (TPSA) <75Å(2)), are the most effective means to prioritize compounds having a lower probability of causing adverse events in vivo.
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Affiliation(s)
- Falgun Shah
- Compound Safety Prediction, Pfizer Global Research & Development, Groton, CT, United States.
| | - Shirley Louise-May
- Compound Safety Prediction, Pfizer Global Research & Development, Groton, CT, United States
| | - Nigel Greene
- Compound Safety Prediction, Pfizer Global Research & Development, Groton, CT, United States
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36
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Hopkins AL, Keserü GM, Leeson PD, Rees DC, Reynolds CH. The role of ligand efficiency metrics in drug discovery. Nat Rev Drug Discov 2014; 13:105-21. [DOI: 10.1038/nrd4163] [Citation(s) in RCA: 706] [Impact Index Per Article: 70.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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37
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Diversity-oriented synthesis as a tool for identifying new modulators of mitosis. Nat Commun 2014; 5:3155. [PMID: 24434687 DOI: 10.1038/ncomms4155] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Accepted: 12/18/2013] [Indexed: 02/02/2023] Open
Abstract
The synthesis of diverse three-dimensional libraries has become of paramount importance for obtaining better leads for drug discovery. Such libraries are predicted to fare better than traditional compound collections in phenotypic screens and against difficult targets. Herein we report the diversity-oriented synthesis of a compound library using rhodium carbenoid chemistry to access structurally diverse three-dimensional molecules and show that they access biologically relevant areas of chemical space using cheminformatic analysis. High-content screening of this library for antimitotic activity followed by chemical modification identified 'Dosabulin', which causes mitotic arrest and cancer cell death by apoptosis. Its mechanism of action is determined to be microtubule depolymerization, and the compound is shown to not significantly affect vinblastine binding to tubulin; however, experiments suggest binding to a site vicinal or allosteric to Colchicine. This work validates the combination of diversity-oriented synthesis and phenotypic screening as a strategy for the discovery of biologically relevant chemical entities.
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Abstract
Drug discovery is a complex process with the aim of discovering efficacious molecules where their potency and selectivity are balanced against ADMET properties to set the appropriate dose and dosing interval. The link between physicochemical properties and molecular structure are well established. The subsequent connections between physicochemical properties and a drug's biological behavior provide an indirect link back to structure, facilitating the prediction of a biological property as a consequence of a particular molecular manipulation. Due to this understanding, during early drug discovery in vitro physicochemical property assays are commonly performed to eliminate compounds with properties commensurate with high attrition risks. However, the goal is to accurately predict physicochemical properties to prevent the synthesis of high risk compounds and hence minimize wasted drug discovery efforts. This paper will review the relevance to ADMET behaviors of key physicochemical properties, such as ionization, aqueous solubility, hydrogen bonding strength and hydrophobicity, and the in silico methodology for predicting them.
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Affiliation(s)
- Mark C Wenlock
- AstraZeneca R&D Alderley Park, DMPK, Mereside, Macclesfield, Cheshire, SK10 4TF, United Kingdom.
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40
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Ritchie TJ, Macdonald SJF, Peace S, Pickett SD, Luscombe CN. Increasing small molecule drug developability in sub-optimal chemical space. MEDCHEMCOMM 2013. [DOI: 10.1039/c3md00003f] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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41
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Muthas D, Boyer S, Hasselgren C. A critical assessment of modeling safety-related drug attrition. MEDCHEMCOMM 2013. [DOI: 10.1039/c3md00072a] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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42
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Hits, leads and drugs against malaria through diversity-oriented synthesis. Future Med Chem 2012; 4:2279-94. [PMID: 23234551 DOI: 10.4155/fmc.12.178] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Malaria is a devastating infectious disease and approximately half the world’s population is at risk. Since vaccination is not yet available, small-molecule-based medicines are currently the best option for the treatment of patients suffering from malaria and combating the spread of infection. Development of resistance against existing drugs has created a need for new types of small molecules to be screened against Plasmodium falciparum, the etiological agent of malaria. The advent of diversity-oriented synthesis has enabled access to novel chemical structures. Evaluation of diversity-oriented synthesis compounds in phenotypic assays for growth inhibition of P. falciparum has resulted in novel hits, leads and even investigational drugs against malaria.
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43
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What is the most important approach in current drug discovery: doing the right things or doing things right? Drug Discov Today 2012; 17:1166-9. [DOI: 10.1016/j.drudis.2012.04.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2012] [Revised: 04/20/2012] [Accepted: 04/23/2012] [Indexed: 11/23/2022]
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Bickerton GR, Paolini GV, Besnard J, Muresan S, Hopkins AL. Quantifying the chemical beauty of drugs. Nat Chem 2012; 4:90-8. [PMID: 22270643 PMCID: PMC3524573 DOI: 10.1038/nchem.1243] [Citation(s) in RCA: 909] [Impact Index Per Article: 75.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2011] [Accepted: 12/02/2011] [Indexed: 01/15/2023]
Abstract
Drug-likeness is a key consideration when selecting compounds during the early stages of drug discovery. However, evaluation of drug-likeness in absolute terms does not reflect adequately the whole spectrum of compound quality. More worryingly, widely used rules may inadvertently foster undesirable molecular property inflation as they permit the encroachment of rule-compliant compounds towards their boundaries. We propose a measure of drug-likeness based on the concept of desirability called the quantitative estimate of drug-likeness (QED). The empirical rationale of QED reflects the underlying distribution of molecular properties. QED is intuitive, transparent, straightforward to implement in many practical settings and allows compounds to be ranked by their relative merit. We extended the utility of QED by applying it to the problem of molecular target druggability assessment by prioritizing a large set of published bioactive compounds. The measure may also capture the abstract notion of aesthetics in medicinal chemistry.
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Affiliation(s)
- G Richard Bickerton
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
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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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