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Suriyaamporn P, Pamornpathomkul B, Patrojanasophon P, Ngawhirunpat T, Rojanarata T, Opanasopit P. The Artificial Intelligence-Powered New Era in Pharmaceutical Research and Development: A Review. AAPS PharmSciTech 2024; 25:188. [PMID: 39147952 DOI: 10.1208/s12249-024-02901-y] [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: 04/28/2024] [Accepted: 07/22/2024] [Indexed: 08/17/2024] Open
Abstract
Currently, artificial intelligence (AI), machine learning (ML), and deep learning (DL) are gaining increased interest in many fields, particularly in pharmaceutical research and development, where they assist in decision-making in complex situations. Numerous research studies and advancements have demonstrated how these computational technologies are used in various pharmaceutical research and development aspects, including drug discovery, personalized medicine, drug formulation, optimization, predictions, drug interactions, pharmacokinetics/ pharmacodynamics, quality control/quality assurance, and manufacturing processes. Using advanced modeling techniques, these computational technologies can enhance efficiency and accuracy, handle complex data, and facilitate novel discoveries within minutes. Furthermore, these technologies offer several advantages over conventional statistics. They allow for pattern recognition from complex datasets, and the models, typically developed from data-driven algorithms, can predict a given outcome (model output) from a set of features (model inputs). Additionally, this review discusses emerging trends and provides perspectives on the application of AI with quality by design (QbD) and the future role of AI in this field. Ethical and regulatory considerations associated with integrating AI into pharmaceutical technology were also examined. This review aims to offer insights to researchers, professionals, and others on the current state of AI applications in pharmaceutical research and development and their potential role in the future of research and the era of pharmaceutical Industry 4.0 and 5.0.
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Affiliation(s)
- Phuvamin Suriyaamporn
- Pharmaceutical Development of Green Innovations Group (PDGIG), Department of Industrial Pharmacy, Faculty of Pharmacy, Silpakorn University, Nakhon Pathom, Thailand
| | - Boonnada Pamornpathomkul
- Pharmaceutical Development of Green Innovations Group (PDGIG), Department of Industrial Pharmacy, Faculty of Pharmacy, Silpakorn University, Nakhon Pathom, Thailand
| | - Prasopchai Patrojanasophon
- Pharmaceutical Development of Green Innovations Group (PDGIG), Department of Industrial Pharmacy, Faculty of Pharmacy, Silpakorn University, Nakhon Pathom, Thailand
| | - Tanasait Ngawhirunpat
- Pharmaceutical Development of Green Innovations Group (PDGIG), Department of Industrial Pharmacy, Faculty of Pharmacy, Silpakorn University, Nakhon Pathom, Thailand
| | - Theerasak Rojanarata
- Pharmaceutical Development of Green Innovations Group (PDGIG), Department of Industrial Pharmacy, Faculty of Pharmacy, Silpakorn University, Nakhon Pathom, Thailand
| | - Praneet Opanasopit
- Pharmaceutical Development of Green Innovations Group (PDGIG), Department of Industrial Pharmacy, Faculty of Pharmacy, Silpakorn University, Nakhon Pathom, Thailand.
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2
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Abdelrazek FM, Zaki ME, Al-Hussain SA, Farag B, Hebishy AM, Abdelfattah MS, Hassan SM, El-Farargy AF, Iovkova L, Mross D, Gomha SM. Facile one-pot synthesis and in silico study of new heterocyclic scaffolds with 4-pyridyl moiety: Mechanistic insights and X-ray crystallographic elucidation. Heliyon 2024; 10:e29221. [PMID: 38617929 PMCID: PMC11015136 DOI: 10.1016/j.heliyon.2024.e29221] [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: 10/19/2023] [Revised: 03/08/2024] [Accepted: 04/03/2024] [Indexed: 04/16/2024] Open
Abstract
4-Acetylpyridine 1 and malononitrile 2 were allowed to react in a 3MCRs with dimedone 3a or cyclohexa-1,3-dione 3b under reflux to afford 4-methyl-4-(pyridin-4-yl)-5,6,7,8-tetrahydro-4H-chromene derivatives 4a,b respectively. The mechanism of the reaction has been studied and the structures elucidated by analytical, spectral as well as X-ray crystallographic data. Heterocyclic compounds find widespread application in pharmaceutical and agrochemical products. Docking analyses were performed on the synthesized compounds to assess their binding modes with various amino acids of the target protein tubulin (PDB Code - 1SA0). The results indicated promising binding scores for compounds 4a and 4b, suggesting a strong affinity for the tubulin binding site. Finally, ADMET for the synthesized compounds 4a, 4b, 5, 8a and 8b were carried out. The drug likeness and pharmacokinetic properties of the prepared compounds were also evaluated. Notably, all of the novel compounds adhered to Lipinski's rule (Ro5) without any violations.
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Affiliation(s)
- Fathy M. Abdelrazek
- Chemistry Department, Faculty of Science, Cairo University, Giza, 12613, Egypt
| | - Magdi E.A. Zaki
- Department of Chemistry, Faculty of Science, Imam Mohammed Ibn Saud Islamic University (IMSIU), Riyadh, 11623, Saudi Arabia
| | - Sami A. Al-Hussain
- Department of Chemistry, Faculty of Science, Imam Mohammed Ibn Saud Islamic University (IMSIU), Riyadh, 11623, Saudi Arabia
| | - Basant Farag
- Department of Chemistry, Faculty of Science, Zagazig University, Zagazig, 44519, Egypt
| | - Ali M. Hebishy
- Chemistry Department, Faculty of Science, Helwan University, Helwan, 11795, Cairo, Egypt
| | - Mohamed S. Abdelfattah
- Chemistry Department, Faculty of Science, Helwan University, Helwan, 11795, Cairo, Egypt
| | - Safaa M. Hassan
- Chemistry Department, Faculty of Science, Cairo University, Giza, 12613, Egypt
- Chemistry Department, Faculty of Science, Helwan University, Helwan, 11795, Cairo, Egypt
| | - Ahmed F. El-Farargy
- Department of Chemistry, Faculty of Science, Zagazig University, Zagazig, 44519, Egypt
- Fakultät für Chemie und Chemische Biologie, TU Dortmund, Dortmund, 44227, Germany
| | - Lyuba Iovkova
- Fakultät für Chemie und Chemische Biologie, TU Dortmund, Dortmund, 44227, Germany
| | - David Mross
- Fakultät für Chemie und Chemische Biologie, TU Dortmund, Dortmund, 44227, Germany
| | - Sobhi M. Gomha
- Department of Chemistry, Faculty of Science, Islamic University of Madinah, Madinah, 42351, Saudi Arabia
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3
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Mallidi K, Gundla R, Makam P, Katari NK, Jonnalagadda SB. Dual active pyrimidine-based carbocyclic nucleoside derivatives: synthesis, and in silico and in vitro anti-diabetic and anti-microbial studies. RSC Adv 2024; 14:9559-9569. [PMID: 38516166 PMCID: PMC10955399 DOI: 10.1039/d4ra00304g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 03/02/2024] [Indexed: 03/23/2024] Open
Abstract
Diabetes mellitus (DM) is a chronic metabolic disorder marked by high blood glucose levels, impairing glucose production in the body. Its prevalence has steadily risen over the past decades, leading to compromised immunity and heightened susceptibility to microbial infections. Immune dysfunction associated with diabetes raises vulnerability, while neuropathy dulls sensation in the extremities, reducing injury awareness. Hence, the development of novel chemical compounds for anti-diabetic and anti-infective treatments is imperative to mitigate adverse effects. In this study, we designed and synthesized pyrimidine-based carbocyclic nucleoside derivatives with C-4 substitution to assess their potential in inhibiting α-glucosidase for managing diabetes mellitus (DM) and microbial infections. Compounds 8b and 10a displayed promising IC50 values against α-glucosidase (43.292 nmol and 48.638 nmol, respectively) and noteworthy docking energies (-9.4 kcal mol-1 and -10.3 kcal mol-1, respectively). Additionally, compounds 10a and 10b exhibited better antimicrobial activity against Bacillus cereus, with the zone of inhibition values of 2.2 ± 0.25 mm and 1.4 ± 0.1 mm at a 100 μl concentration, respectively. Compound 10a also exhibited a modest zone of inhibition of 1.2 ± 0.15 mm against Escherichia coli at 100 μl.
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Affiliation(s)
- Kalyani Mallidi
- Department of Chemistry, GITAM School of Science, GITAM Deemed to be University Hyderabad Telangana 502329 India
| | - Rambabu Gundla
- Department of Chemistry, GITAM School of Science, GITAM Deemed to be University Hyderabad Telangana 502329 India
| | - Parameshwar Makam
- Department of Chemistry, School of Applied and Life Sciences, Uttaranchal University Arcadia Grant, P.O. Chandanwari, Premnagar Dehradun Uttarakhand 248007 India
| | - Naresh Kumar Katari
- Department of Chemistry, GITAM School of Science, GITAM Deemed to be University Hyderabad Telangana 502329 India
- School of Chemistry & Physics, College of Agriculture, Engineering & Science, WestvilleCampus, University of KwaZulu-Natal P Bag X 54001 Durban 4000 South Africa
| | - Sreekantha Babu Jonnalagadda
- School of Chemistry & Physics, College of Agriculture, Engineering & Science, WestvilleCampus, University of KwaZulu-Natal P Bag X 54001 Durban 4000 South Africa
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4
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Llompart P, Minoletti C, Baybekov S, Horvath D, Marcou G, Varnek A. Will we ever be able to accurately predict solubility? Sci Data 2024; 11:303. [PMID: 38499581 PMCID: PMC10948805 DOI: 10.1038/s41597-024-03105-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 02/29/2024] [Indexed: 03/20/2024] Open
Abstract
Accurate prediction of thermodynamic solubility by machine learning remains a challenge. Recent models often display good performances, but their reliability may be deceiving when used prospectively. This study investigates the origins of these discrepancies, following three directions: a historical perspective, an analysis of the aqueous solubility dataverse and data quality. We investigated over 20 years of published solubility datasets and models, highlighting overlooked datasets and the overlaps between popular sets. We benchmarked recently published models on a novel curated solubility dataset and report poor performances. We also propose a workflow to cure aqueous solubility data aiming at producing useful models for bench chemist. Our results demonstrate that some state-of-the-art models are not ready for public usage because they lack a well-defined applicability domain and overlook historical data sources. We report the impact of factors influencing the utility of the models: interlaboratory standard deviation, ionic state of the solute and data sources. The herein obtained models, and quality-assessed datasets are publicly available.
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Affiliation(s)
- P Llompart
- Laboratory of Chemoinformatics, UMR7140, University of Strasbourg, Strasbourg, France
- IDD/CADD, Sanofi, Vitry-Sur-Seine, France
| | | | - S Baybekov
- Laboratory of Chemoinformatics, UMR7140, University of Strasbourg, Strasbourg, France
| | - D Horvath
- Laboratory of Chemoinformatics, UMR7140, University of Strasbourg, Strasbourg, France
| | - G Marcou
- Laboratory of Chemoinformatics, UMR7140, University of Strasbourg, Strasbourg, France.
| | - A Varnek
- Laboratory of Chemoinformatics, UMR7140, University of Strasbourg, Strasbourg, France
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5
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Anaikutti P, Adhikari P, Baskaran S, Selvaraj M, Afzal M, Makam P. Indolyl-4H-Chromene Derivatives as Antibacterial Agents: Synthesis, in Vitro and in Silico Studies. Chem Biodivers 2024; 21:e202301392. [PMID: 38050777 DOI: 10.1002/cbdv.202301392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Revised: 12/03/2023] [Accepted: 12/04/2023] [Indexed: 12/06/2023]
Abstract
In this study, indolyl-4H-chromene derivatives are designed and synthesised using an eco-friendly multicomponent one-pot synthesis using benzaldehydes, nitroketene N, S-acetals, and indoles combine with InCl3 , a Lewis acid catalyst, and ethanol, an environmentally acceptable solvent. Due to antibiotic resistance, assessed these Indolyl-4H-chromene derivatives for their in vitro antibacterial activity against Gram-positive and Gram-negative bacteria, including Streptococcus pyogenes, Staphylococcus aureus, Clostridium pyrogenes, Bacillus subtilis, Escherichia coli, and Pseudomonas aeruginosa, using the agar well diffusion method and Minimum Inhibition Concentration (MIC) assay. Three compounds, 4-(1H-indol-3-yl)-6-methoxy-N-methyl-3-nitro-4H-chromen-2-amine, 4-(1H-indol-3-yl)-3-nitro-N-phenyl-4H-chromen-2-amine and 4-(6-Fluoro-1H-Indol-3-yl)-N-methyl-3-nitro-4H-chromen-2-amine showed better zone of inhibition (mm) and Minimum Inhibition Concentration (MIC) values of 10 μg/mL to 25 μg/mL against all bacterial types. The Ki values of 278.60 nM and 2.21 nM for compound 4-(1H-indol-3-yl)-3-nitro-N-phenyl-4H-chromen-2-amine showed improved interactions with DNA gyrase B and topoIV ParE's ATP binding sites in in silico studies.
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Affiliation(s)
- Parthiban Anaikutti
- Centre for GMP Extraction Facility, National Institute of Pharmaceutical Education and Research (NIPER-G), Guwahati, 781101, Assam, India
| | - Priyanka Adhikari
- Centre for GMP Extraction Facility, National Institute of Pharmaceutical Education and Research (NIPER-G), Guwahati, 781101, Assam, India
| | - Sambath Baskaran
- Department of Chemistry, University of Ulsan, Ulsan, 44776, Republic of, Korea
| | - Mangalaraj Selvaraj
- Department of Chemistry, St. Joseph's College (Autonomous), Tiruchirappalli, 620002, India
| | - Mohd Afzal
- Department of Chemistry, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Parameshwar Makam
- Department of Chemistry, School of Applied and Life Sciences, Uttaranchal University, Arcadia Grant, P.O. Chandanwari, Premnagar, Dehradun, Uttarakhand, 248007, India
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6
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Liu J, Lei X, Ji C, Pan Y. Fragment-pair based drug molecule solubility prediction through attention mechanism. Front Pharmacol 2023; 14:1255181. [PMID: 37881183 PMCID: PMC10595153 DOI: 10.3389/fphar.2023.1255181] [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: 07/08/2023] [Accepted: 09/26/2023] [Indexed: 10/27/2023] Open
Abstract
The purpose of drug discovery is to identify new drugs, and the solubility of drug molecules is an important physicochemical property in medicinal chemistry, that plays a crucial role in drug discovery. In solubility prediction, high-precision computational methods can significantly reduce the experimental costs and time associated with drug development. Therefore, artificial intelligence technologies have been widely used for solubility prediction. This study utilized the attention layer in mechanism in the deep learning model to consider the atomic-level features of the molecules, and used gated recurrent neural networks to aggregate vectors between layers. It also utilized molecular fragment technology to divide the complete molecule into pairs of fragments, extracted characteristics from each fragment pair, and finally fused the characteristics to predict the solubility of drug molecules. We compared and evaluated our method with five existing models using two performance evaluation indicators, demonstrating that our method has better performance and greater robustness.
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Affiliation(s)
- Jianping Liu
- School of Computer Science, Shaanxi Normal University, Xi’an, China
| | - Xiujuan Lei
- School of Computer Science, Shaanxi Normal University, Xi’an, China
| | - Chunyan Ji
- Computer Science Department, BNU-HKBU United International College, Zhuhai, China
| | - Yi Pan
- Faculty of Computer Science and Control Engineering, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- Shenzhen Key Laboratory of Intelligent Bioinformatics, Shenzhen Institute of Advanced Technology, Shenzhen, China
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7
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Kawamura M, Kobashi Y, Tanaka H, Bohno-Mikami A, Hamada M, Ito Y, Hirata T, Ohara H, Kojima N, Koretsune H, Gunji E, Fukunaga T, Inatani S, Hasegawa Y, Suzuki A, Takahashi T, Kakinuma H. Discovery of Novel Pyrazolylpyridine Derivatives for 20-Hydroxyeicosatetraenoic Acid Synthase Inhibitors with Selective CYP4A11/4F2 Inhibition. J Med Chem 2022; 65:14599-14613. [DOI: 10.1021/acs.jmedchem.2c01089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Madoka Kawamura
- Discovery Research Laboratories, Taisho Pharmaceutical Co., Ltd., 1-403, Yoshino-Cho, Kita-Ku, Saitama, Saitama331-9530, Japan
| | - Yohei Kobashi
- Discovery Research Laboratories, Taisho Pharmaceutical Co., Ltd., 1-403, Yoshino-Cho, Kita-Ku, Saitama, Saitama331-9530, Japan
| | - Hiroaki Tanaka
- Discovery Research Laboratories, Taisho Pharmaceutical Co., Ltd., 1-403, Yoshino-Cho, Kita-Ku, Saitama, Saitama331-9530, Japan
| | - Ayako Bohno-Mikami
- Discovery Research Laboratories, Taisho Pharmaceutical Co., Ltd., 1-403, Yoshino-Cho, Kita-Ku, Saitama, Saitama331-9530, Japan
| | - Makoto Hamada
- Discovery Research Laboratories, Taisho Pharmaceutical Co., Ltd., 1-403, Yoshino-Cho, Kita-Ku, Saitama, Saitama331-9530, Japan
| | - Yuji Ito
- Discovery Research Laboratories, Taisho Pharmaceutical Co., Ltd., 1-403, Yoshino-Cho, Kita-Ku, Saitama, Saitama331-9530, Japan
| | - Takashi Hirata
- Discovery Research Laboratories, Taisho Pharmaceutical Co., Ltd., 1-403, Yoshino-Cho, Kita-Ku, Saitama, Saitama331-9530, Japan
| | - Hiroki Ohara
- Discovery Research Laboratories, Taisho Pharmaceutical Co., Ltd., 1-403, Yoshino-Cho, Kita-Ku, Saitama, Saitama331-9530, Japan
| | - Naoki Kojima
- Discovery Research Laboratories, Taisho Pharmaceutical Co., Ltd., 1-403, Yoshino-Cho, Kita-Ku, Saitama, Saitama331-9530, Japan
| | - Hiroko Koretsune
- Discovery Research Laboratories, Taisho Pharmaceutical Co., Ltd., 1-403, Yoshino-Cho, Kita-Ku, Saitama, Saitama331-9530, Japan
| | - Emi Gunji
- Discovery Research Laboratories, Taisho Pharmaceutical Co., Ltd., 1-403, Yoshino-Cho, Kita-Ku, Saitama, Saitama331-9530, Japan
| | - Takuya Fukunaga
- Discovery Research Laboratories, Taisho Pharmaceutical Co., Ltd., 1-403, Yoshino-Cho, Kita-Ku, Saitama, Saitama331-9530, Japan
| | - Shoko Inatani
- Drug Safety and Pharmacokinetics Laboratories, Taisho Pharmaceutical Co., Ltd., 1-403, Yoshino-Cho, Kita-Ku, Saitama, Saitama331-9530, Japan
| | - Yoshitaka Hasegawa
- Drug Safety and Pharmacokinetics Laboratories, Taisho Pharmaceutical Co., Ltd., 1-403, Yoshino-Cho, Kita-Ku, Saitama, Saitama331-9530, Japan
| | - Akinori Suzuki
- Pharmaceutical Sciences Laboratories, Taisho Pharmaceutical Co., Ltd., 1-403, Yoshino-Cho, Kita-Ku, Saitama, Saitama331-9530, Japan
| | - Teisuke Takahashi
- Discovery Research Laboratories, Taisho Pharmaceutical Co., Ltd., 1-403, Yoshino-Cho, Kita-Ku, Saitama, Saitama331-9530, Japan
| | - Hiroyuki Kakinuma
- Discovery Research Laboratories, Taisho Pharmaceutical Co., Ltd., 1-403, Yoshino-Cho, Kita-Ku, Saitama, Saitama331-9530, Japan
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8
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Bandaru NR, Makam P, Akshinthala P, Katari NK, Banoth V, Kolli B, Gundla R. Molecular Hybrids of Pyazolo[3,4- b]pyridine and Triazole: Design, Synthesis and In Vitro Antibacterial Studies. Molecules 2022; 27:7647. [PMID: 36364469 PMCID: PMC9655101 DOI: 10.3390/molecules27217647] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 10/31/2022] [Accepted: 11/02/2022] [Indexed: 09/13/2023] Open
Abstract
Antimicrobial resistance is on the rise, and there aren't enough new treatments to combat it. This might send the modern world back to the pre-antibiotic age. The molecular hybrids of pyrazolo[3,4-b]pyridine and triazole have been designed, synthesized, and analyzed for their drug-like molecule nature and in vitro analyses for their inhibition potentials against S. aureus and K. pneumoniae. The compounds 24 and 27 have been identified as the high potential molecules in this series based on in vitro experiments. Compound 24 has zone of inhibition values of 15 ± 0.82 mm and 14 ± 0.7 mm, whilst compound 27 has zone of inhibition values of 18 ± 0.95 mm and 16 ± 0.82 mm against S. aureus and K. pneumoniae, respectively. MIC and MIB values for compounds 24 and 27 against S. aureus and K. pneumoniae are 0.25 and 0.5, respectively.
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Affiliation(s)
- Narasimha Rao Bandaru
- Department of Chemistry, GITAM School of Science, GITAM Deemed to be University Hyderabad, Rudraram 502329, India
| | - Parameshwar Makam
- Department of Chemistry, School of Applied and Life Sciences, Uttaranchal University, Arcadia Grant, Chandanwari, Premnagar, Dehradun 248007, India
| | - Parameswari Akshinthala
- Department of Science and Humanities, MLR Institute of Technology, Dundigal, Medchal, Hyderabad, Rudraram 500043, India
| | - Naresh Kumar Katari
- Department of Chemistry, GITAM School of Science, GITAM Deemed to be University Hyderabad, Rudraram 502329, India
| | - Venkanna Banoth
- Department of Biotechnology, University Post Graduate College of Science and Technology, Jawaharlal Nehru Technological University Hyderabad, Rudraram 500085, India
| | - Balakrishna Kolli
- Department of Chemistry, GITAM School of Science, GITAM Deemed to be University Hyderabad, Rudraram 502329, India
- Department of Chemistry, GITAM School of Science, GITAM Deemed to Be University Visakhapatnam, Visakhapatnam 530045, India
| | - Rambabu Gundla
- Department of Chemistry, GITAM School of Science, GITAM Deemed to be University Hyderabad, Rudraram 502329, India
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9
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Indolyl-4H-chromenes: Multicomponent one-pot green synthesis, in vitro and in silico, anticancer and antioxidant studies. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133464] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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10
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Hublikar M, Kadu V, Raut D, Shirame S, Anbarasu S, Al-Muhanna MK, Makam P, Bhosale R. 3-Substituted-2-oxindole derivatives: Design, synthesis and their anti-tuberculosis and radical scavenging dual-action studies. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.132903] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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11
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Structural modification aimed for improving solubility of lead compounds in early phase drug discovery. Bioorg Med Chem 2022; 56:116614. [DOI: 10.1016/j.bmc.2022.116614] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 12/15/2021] [Accepted: 01/06/2022] [Indexed: 12/19/2022]
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12
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Gnocchi D, Cavalluzzi MM, Mangiatordi GF, Rizzi R, Tortorella C, Spennacchio M, Lentini G, Altomare A, Sabbà C, Mazzocca A. Xanthenylacetic Acid Derivatives Effectively Target Lysophosphatidic Acid Receptor 6 to Inhibit Hepatocellular Carcinoma Cell Growth. ChemMedChem 2021; 16:2121-2129. [PMID: 33831272 DOI: 10.1002/cmdc.202100032] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 04/02/2021] [Indexed: 12/22/2022]
Abstract
Despite the increasing incidence of hepatocellular carcinoma (HCC) worldwide, current pharmacological treatments are still unsatisfactory. We have previously shown that lysophosphatidic acid receptor 6 (LPAR6) supports HCC growth and that 9-xanthenylacetic acid (XAA) acts as an LPAR6 antagonist inhibiting HCC growth without toxicity. Here, we synthesized four novel XAA derivatives, (±)-2-(9H-xanthen-9-yl)propanoic acid (compound 4 - MC9), (±)-2-(9H-xanthen-9-yl)butanoic acid (compound 5 - MC6), (±)-2-(9H-xanthen-9-yl)hexanoic acid (compound 7 - MC11), and (±)-2-(9H-xanthen-9-yl)octanoic acid (compound 8 - MC12, sodium salt) by introducing alkyl groups of increasing length at the acetic α-carbon atom. Two of these compounds were characterized by X-ray powder diffraction and quantum mechanical calculations, while molecular docking simulations suggested their enantioselectivity for LPAR6. Biological data showed anti-HCC activity for all XAA derivatives, with the maximum effect observed for MC11. Our findings support the view that increasing the length of the alkyl group improves the inhibitory action of XAA and that enantioselectivity can be exploited for designing novel and more effective XAA-based LPAR6 antagonists.
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Affiliation(s)
- Davide Gnocchi
- Interdisciplinary Department of Medicine, University of Bari, School of Medicine, Piazza G. Cesare, 11, 70124, Bari, Italy
| | - Maria M Cavalluzzi
- Department of Pharmacy - Drug Sciences, University of Bari Aldo Moro, via Orabona, 4, 70125, Bari, Italy
| | | | - Rosanna Rizzi
- Institute of Crystallography CNR, Via Amendola 122/o, 70126, Bari, Italy
| | - Cosimo Tortorella
- Interdisciplinary Department of Medicine, University of Bari, School of Medicine, Piazza G. Cesare, 11, 70124, Bari, Italy
| | - Mauro Spennacchio
- Department of Pharmacy - Drug Sciences, University of Bari Aldo Moro, via Orabona, 4, 70125, Bari, Italy.,Institute of Crystallography CNR, Via Amendola 122/o, 70126, Bari, Italy
| | - Giovanni Lentini
- Department of Pharmacy - Drug Sciences, University of Bari Aldo Moro, via Orabona, 4, 70125, Bari, Italy
| | - Angela Altomare
- Institute of Crystallography CNR, Via Amendola 122/o, 70126, Bari, Italy
| | - Carlo Sabbà
- Interdisciplinary Department of Medicine, University of Bari, School of Medicine, Piazza G. Cesare, 11, 70124, Bari, Italy
| | - Antonio Mazzocca
- Interdisciplinary Department of Medicine, University of Bari, School of Medicine, Piazza G. Cesare, 11, 70124, Bari, Italy
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13
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Perryman A, Inoyama D, Patel JS, Ekins S, Freundlich JS. Pruned Machine Learning Models to Predict Aqueous Solubility. ACS OMEGA 2020; 5:16562-16567. [PMID: 32685821 PMCID: PMC7364544 DOI: 10.1021/acsomega.0c01251] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 05/13/2020] [Indexed: 05/03/2023]
Abstract
Solubility is a key metric for therapeutic compounds. Conversely, insoluble compounds cloud the accuracy of assays at all stages of chemical biology and drug discovery. Herein, we disclose naïve Bayesian classifier models to predict aqueous solubility. Publicly accessible aqueous solubility data were used to create two full, or nonpruned, training sets. These two sets were also combined to create a full fused set, and a training set comprised of a literature collation of solubility data was also considered as a reference. We tested different extents of data pruning on the training sets and constructed machine learning models that were evaluated with two independent, external test sets that contained compounds that were different from the training sets. The best pruned and fused model was significantly more accurate, in comparison to either the full model or the full fused model, with the prediction of these external test sets. By carefully removing data from the training set, less information can be used to create more accurate machine learning models for aqueous solubility. This knowledge and the curated training sets should prove useful to future machine learning approaches.
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Affiliation(s)
- Alexander
L. Perryman
- Department
of Pharmacology, Physiology, and Neuroscience, Rutgers University—New Jersey Medical School, Newark, New Jersey 07103, United States
| | - Daigo Inoyama
- Department
of Pharmacology, Physiology, and Neuroscience, Rutgers University—New Jersey Medical School, Newark, New Jersey 07103, United States
| | - Jimmy S. Patel
- Department
of Pharmacology, Physiology, and Neuroscience, Rutgers University—New Jersey Medical School, Newark, New Jersey 07103, United States
| | - Sean Ekins
- Collaborations
in Chemistry, Inc., 5616
Hilltop Needmore Road, Fuquay-Varina, North Carolina 27526, United States
| | - Joel S. Freundlich
- Department
of Pharmacology, Physiology, and Neuroscience, Rutgers University—New Jersey Medical School, Newark, New Jersey 07103, United States
- Division
of Infectious Disease, Department of Medicine and the Ruy V. Lourenço
Center for the Study of Emerging and Re-emerging Pathogens, Rutgers University—New Jersey Medical School, Newark, New Jersey 07103, United States
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14
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Tinworth CP, Young RJ. Facts, Patterns, and Principles in Drug Discovery: Appraising the Rule of 5 with Measured Physicochemical Data. J Med Chem 2020; 63:10091-10108. [PMID: 32324397 DOI: 10.1021/acs.jmedchem.9b01596] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The rule of 5 was designed to estimate the likelihood of poor absorption or permeation, noting the impact of poor solubility. This Perspective explores the impact of various physicochemical descriptors and contemporary lipophilicity measurements on permeability and solubility, showing that the distribution coefficient log D7.4 (rather than log P) is the most impactful parameter. Molecular weight, almost invariably the defining characteristic of "beyond the rule of 5" compounds, has little impact on solubility when log D7.4 measurements and aromaticity are considered. Predicting permeation is more complex, given passive and carrier transport mechanisms; however, notable patterns of behavior are apparent, giving insight even "beyond the rule of 5". Recommended best practices should involve using the facts (measurements) and the patterns they reveal to establish informative principles rather than fastidious rules.
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Affiliation(s)
- Christopher P Tinworth
- Medicinal Sciences and Technology, GlaxoSmithKline, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Robert J Young
- Medicinal Sciences and Technology, GlaxoSmithKline, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K.,Blue Burgundy Ltd., Bedford, Bedfordshire MK45 2AD, U.K
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15
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Matsa R, Makam P, Kaushik M, Hoti SL, Kannan T. Thiosemicarbazone derivatives: Design, synthesis and in vitro antimalarial activity studies. Eur J Pharm Sci 2019; 137:104986. [PMID: 31283946 DOI: 10.1016/j.ejps.2019.104986] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 06/11/2019] [Accepted: 07/03/2019] [Indexed: 10/26/2022]
Abstract
Different types of thiosemicarbazone derivatives were designed and tested for their Drug-Like Molecular (DLM) nature by using Lipinski and Veber rules. Subsequently, compounds with DLM properties were synthesized and characterized by spectral methods. In vitro antimalarial activity studies of the synthesized thiosemicarbazone derivatives have been carried out against Plasmodium falciparum, 3D7 strain using fluorescence assay method and found that the compounds, (E)-2-(1-(4-fluorophenyl)ethylidene)hydrazine-1-carbothioamide (6), (E)-2-(1-(3-bromophenyl) ethylidene) hydrazine-1-carbothioamide (15) and (E)-2-(3,4,5-trimethoxybenzylidene) hydrazine-1-carbothioamide (29) showed notable antimalarial activity with EC50 values of 13.54 μM, 15.83 μM and 14.52 μM respectively.
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Affiliation(s)
- Ramkishore Matsa
- Department of Chemistry, Pondicherry University, Kalapet, Puducherry 605 014, India
| | - Parameshwar Makam
- Chemical Science Research Group, Division of Research and Development, Lovely Professional University, Phagwara 144 411, India
| | - Meenakshi Kaushik
- ICMR-National Institute of Traditional Medicine, Nehru Nagar, Belagavi 590 010, India
| | - S L Hoti
- ICMR-National Institute of Traditional Medicine, Nehru Nagar, Belagavi 590 010, India
| | - Tharanikkarasu Kannan
- Department of Chemistry, Pondicherry University, Kalapet, Puducherry 605 014, India.
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16
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Affiliation(s)
- Brian Raymer
- Medicine Design, Pfizer Worldwide Research and Development, 1 Portland Street, Cambridge, Massachusetts 02139, United States
| | - Samit K. Bhattacharya
- Medicine Design, Pfizer Worldwide Research and Development, 1 Portland Street, Cambridge, Massachusetts 02139, United States
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17
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Pianovich NA, Dean M, Lassak A, Reiss K, Jursic BS. Anticancer potential of aminomethylidene-diazinanes I. Synthesis of arylaminomethylidene of diazinetriones and its cytotoxic effects tested in glioblastoma cells. Bioorg Med Chem 2017; 25:5068-5076. [PMID: 28864149 DOI: 10.1016/j.bmc.2017.08.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 08/09/2017] [Accepted: 08/10/2017] [Indexed: 10/19/2022]
Abstract
Diazinane and aryl moieties with vinylamine linkers were synthesized to investigate the importance of their structural variations as potential anti-glioblastoma agents. Structural variations incorporated on to the diazinane moiety included oxa and thio derivatives, each with a variety of nitrogen-bound substituents. The size and shape of the aromatic moiety was varied, with the final variation introducing two carbonyl groups, yielding a substituted anthraquinone. Readily available diazinanes and aryl amines were used asan advantageous foundation. Several parameters were calculated whilst engineering these compounds, including: ClogP, molecular polarizability, polar surface area, minimal molecular projected area, and pKa. In addition, a simple and efficient procedure was developed to synthesize these compounds. It was demonstrated that a vinylamine with 1,3-diazinane-2,4,6-trione and 1-anthraquinone moiety is the most promising drug candidate causing almost 70% of LN229 tumor cell death at 1µg/ml. In addition, its molecular polarizability, polar surface area and minimal molecular projected area indicate a possible potential of this molecule for crossing BBB.
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Affiliation(s)
- Nichole A Pianovich
- Department of Chemistry, University of New Orleans, New Orleans, LA 70148, USA
| | - Mathew Dean
- Neurological Cancer Research, Stanley S. Scott Cancer Center, Department of Medicine, LSU Health Sciences Center, New Orleans, LA 70119 USA
| | - Adam Lassak
- Neurological Cancer Research, Stanley S. Scott Cancer Center, Department of Medicine, LSU Health Sciences Center, New Orleans, LA 70119 USA
| | - Krzysztof Reiss
- Neurological Cancer Research, Stanley S. Scott Cancer Center, Department of Medicine, LSU Health Sciences Center, New Orleans, LA 70119 USA
| | - Branko S Jursic
- Department of Chemistry, University of New Orleans, New Orleans, LA 70148, USA; STEPHARM, LLC., PO Box 24220, New Orleans, LA 70184, USA.
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18
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Descriptors and their selection methods in QSAR analysis: paradigm for drug design. Drug Discov Today 2016; 21:1291-302. [DOI: 10.1016/j.drudis.2016.06.013] [Citation(s) in RCA: 162] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 04/25/2016] [Accepted: 06/13/2016] [Indexed: 12/22/2022]
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19
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Zafar A, Reynisson J. Hydration Free Energy as a Molecular Descriptor in Drug Design: A Feasibility Study. Mol Inform 2016; 35:207-14. [PMID: 27492087 DOI: 10.1002/minf.201501035] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 03/11/2016] [Indexed: 01/29/2023]
Abstract
In this work the idea was investigated whether calculated hydration energy (ΔGhyd ) can be used as a molecular descriptor in defining promising regions of chemical space for drug design. Calculating ΔGhyd using the Density Solvation Model (SMD) in conjunction with the density functional theory (DFT) gave an excellent correlation with experimental values. Furthermore, calculated ΔGhyd correlates reasonably well with experimental water solubility (r(2) =0.545) and also log P (r(2) =0.530). Three compound collections were used: Known drugs (n=150), drug-like compounds (n=100) and simple organic compounds (n=140). As an approximation only molecules, which do not de/protonate at physiological pH were considered. A relatively broad distribution was seen for the known drugs with an average at -15.3 kcal/mol and a standard deviation of 7.5 kcal/mol. Interestingly, much lower averages were found for the drug-like compounds (-7.5 kcal/mol) and the simple organic compounds (-3.1 kcal/mol) with tighter distributions; 4.3 and 3.2 kcal/mol, respectively. This trend was not observed for these collections when calculated log P and log S values were used. The considerable greater exothermic ΔGhyd average for the known drugs clearly indicates in order to develop a successful drug candidate value of ΔGhyd <-5 kcal/mol or less is preferable.
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Affiliation(s)
- Ayesha Zafar
- School of Chemical Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand, Tel. +64-9-373-7599 ext. 83746, Fax. +64-9-373-7422
| | - Jóhannes Reynisson
- School of Chemical Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand, Tel. +64-9-373-7599 ext. 83746, Fax. +64-9-373-7422.
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20
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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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21
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Bergs D, Merz J, Delp A, Joehnck M, Martin G, Schembecker G. A Standard Procedure for the Selection of Solvents for Natural Plant Extraction in the Early Stages of Process Development. Chem Eng Technol 2013. [DOI: 10.1002/ceat.201300276] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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22
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Frølund S, Nøhr M, Holm R, Brodin B, Nielsen C. Potential involvement of the proton-coupled amino acid transporter PAT1 (SLC36A1) in the delivery of pharmaceutical agents. J Drug Deliv Sci Technol 2013. [DOI: 10.1016/s1773-2247(13)50046-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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23
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Erić S, Kalinić M, Popović A, Zloh M, Kuzmanovski I. Prediction of aqueous solubility of drug-like molecules using a novel algorithm for automatic adjustment of relative importance of descriptors implemented in counter-propagation artificial neural networks. Int J Pharm 2012; 437:232-41. [DOI: 10.1016/j.ijpharm.2012.08.022] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2012] [Revised: 08/12/2012] [Accepted: 08/16/2012] [Indexed: 10/28/2022]
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24
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Sabitha K. Nilotinib based pharmacophore models for BCRABL. Bioinformation 2012; 8:658-63. [PMID: 23055606 PMCID: PMC3449370 DOI: 10.6026/97320630008658] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2012] [Accepted: 07/05/2012] [Indexed: 11/23/2022] Open
Abstract
UNLABELLED Tyrosine kinase inhibitors have revolutionized the treatment of several malignancies, converting lethal diseases in a manageable aspect. Imitanib, a small molecule ABL kinase inhibitor is a highly effective therapy for early phase chronic myeloid leukemia (CML), which has constitutively active ABL kinase activity owing to the over expression of the BCR-ABL fusion protein. But some patients develop imatinib resistance, particularly in the advanced phases of CML.The discovery of resistance mechanisms of imitanib; urge forward the development of second generation drugs. Nilotinib, a second generation drug is more potent inhibitor of BCR-ABL than imatinib. But nilotinib also develops dermatologic events and headache in patients. Large information about BCR-ABL structure and its inhibitors are now available. Based on the pharmacophore modeling approaches, it is possible to decipher the molecular determinants to inhibit BCR-ABL. We conducted a structure based and ligand based study to identify potent natural compounds as BCR-ABL inhibitor. First kinase inhibitors were docked with the receptor (BCR-ABL) and nilotinib was selected as a pharmacophore due its high binding efficiency. Eleven compounds were selected out of 1457 substances which have mutual pharmacopohre features with nilotinib. These eleven compounds were validated and used for docking study to find the drug like molecules. The best molecules from the final set of screening candidates can be evaluated in cell lines and may represent a novel class of BCR-ABL inhibitors. ABBREVIATIONS CML - Chronic myeloid leukemia, PDGFR - Platelet derived growth factor receptor, TKI - Tyrosine kinase inhibitors.
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Affiliation(s)
- Kesavan Sabitha
- Department of Bioinformatics, Guru Nanak College, Velacherry, Chennai-600 036
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25
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QSPR with extended topochemical atom (ETA) indices. 4. Modeling aqueous solubility of drug like molecules and agrochemicals following OECD guidelines. Struct Chem 2012. [DOI: 10.1007/s11224-012-0080-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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26
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Schnieders MJ, Baltrusaitis J, Shi Y, Chattree G, Zheng L, Yang W, Ren P. The Structure, Thermodynamics and Solubility of Organic Crystals from Simulation with a Polarizable Force Field. J Chem Theory Comput 2012; 8:1721-1736. [PMID: 22582032 PMCID: PMC3348590 DOI: 10.1021/ct300035u] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
An important unsolved problem in materials science is prediction of the thermodynamic stability of organic crystals and their solubility from first principles. Solubility can be defined as the saturating concentration of a molecule within a liquid solvent, where the physical picture is of solvated molecules in equilibrium with their solid phase. Despite the importance of solubility in determining the oral bioavailability of pharmaceuticals, prediction tools are currently limited to quantitative structure-property relationships that are fit to experimental solubility measurements. For the first time, we describe a consistent procedure for the prediction of the structure, thermodynamic stability and solubility of organic crystals from molecular dynamics simulations using the polarizable multipole AMOEBA force field. Our approach is based on a thermodynamic cycle that decomposes standard state solubility into the sum of solid-vapor sublimation and vapor-liquid solvation free energies [Formula: see text], which are computed via the orthogonal space random walk (OSRW) sampling strategy. Application to the n-alkylamides series from aeetamide through octanamide was selected due to the dependence of their solubility on both amide hydrogen bonding and the hydrophobic effect, which are each fundamental to protein structure and solubility. On average, the calculated absolute standard state solubility free energies are accurate to within 1.1 kcal/mol. The experimental trend of decreasing solubility as a function of n-alkylamide chain length is recapitulated by the increasing stability of the crystalline state and to a lesser degree by decreasing favorability of solvation (i.e. the hydrophobic effect). Our results suggest that coupling the polarizable AMOEBA force field with an orthogonal space based free energy algorithm, as implemented in the program Force Field X, is a consistent procedure for predicting the structure, thermodynamic stability and solubility of organic crystals.
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Affiliation(s)
- Michael J. Schnieders
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX 78712
| | - Jonas Baltrusaitis
- Departments of Chemistry and Chemical/Biochemical Engineering, University of Iowa, Iowa City, IA, 52242
| | - Yue Shi
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX 78712
| | - Gaurav Chattree
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX 78712
| | - Lianqing Zheng
- The Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306
| | - Wei Yang
- The Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306
| | - Pengyu Ren
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX 78712
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27
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Abstract
Physicochemical properties are key factors in controlling the interactions of xenobiotics with living organisms. Computational approaches to toxicity prediction therefore generally rely to a very large extent on the physicochemical properties of the query compounds. Consequently it is important that reliable in silico methods are available for the rapid calculation of physicochemical properties. The key properties are partition coefficient, aqueous solubility, and pKa and, to a lesser extent, melting point, boiling point, vapor pressure, and Henry's law constant (air-water partition coefficient). The calculation of each of these properties from quantitative structure-property relationships (QSPRs) and from available software is discussed in detail, and recommendations made. Finally, detailed consideration is given of guidelines for the development of QSPRs and QSARs.
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Affiliation(s)
- John C Dearden
- School of Pharmacy & Biomolecular Sciences, Liverpool John Moores University, Liverpool, UK.
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28
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29
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Katritzky AR, Kuanar M, Slavov S, Hall CD, Karelson M, Kahn I, Dobchev DA. Quantitative Correlation of Physical and Chemical Properties with Chemical Structure: Utility for Prediction. Chem Rev 2010; 110:5714-89. [DOI: 10.1021/cr900238d] [Citation(s) in RCA: 386] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Alan R. Katritzky
- Center for Heterocyclic Compounds, Department of Chemistry, University of Florida, Gainesville, Florida 32611
| | - Minati Kuanar
- Center for Heterocyclic Compounds, Department of Chemistry, University of Florida, Gainesville, Florida 32611
| | - Svetoslav Slavov
- Center for Heterocyclic Compounds, Department of Chemistry, University of Florida, Gainesville, Florida 32611
| | - C. Dennis Hall
- Center for Heterocyclic Compounds, Department of Chemistry, University of Florida, Gainesville, Florida 32611
| | - Mati Karelson
- Institute of Chemistry, Tallinn University of Technology, Akadeemia tee 15, Tallinn 19086, Estonia, and MolCode, Ltd., Soola 8, Tartu 51013, Estonia
| | - Iiris Kahn
- Institute of Chemistry, Tallinn University of Technology, Akadeemia tee 15, Tallinn 19086, Estonia, and MolCode, Ltd., Soola 8, Tartu 51013, Estonia
| | - Dimitar A. Dobchev
- Institute of Chemistry, Tallinn University of Technology, Akadeemia tee 15, Tallinn 19086, Estonia, and MolCode, Ltd., Soola 8, Tartu 51013, Estonia
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30
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Chebil L, Chipot C, Archambault F, Humeau C, Engasser JM, Ghoul M, Dehez F. Solubilities Inferred from the Combination of Experiment and Simulation. Case Study of Quercetin in a Variety of Solvents. J Phys Chem B 2010; 114:12308-13. [DOI: 10.1021/jp104569k] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Latifa Chebil
- Laboratoire d’ingénierie des biomolécules (LIBio), Nancy Université, 2 avenue de la forêt de Haye, 54500 Vandœuvre-lès-Nancy, France, Equipe de Dynamique des Assemblages Membranaires, UMR CNRS-UHP No. 7565, Nancy Université, BP 70239, 54506 Vandœuvre-lès-Nancy, France, and Theoretical and Computational Biophysics Group, Beckman Institute for Advanced Science and Engineering, University of Illinois at Urbana-Champaign, 405 North Mathews, Urbana, Illinois 61801
| | - Christophe Chipot
- Laboratoire d’ingénierie des biomolécules (LIBio), Nancy Université, 2 avenue de la forêt de Haye, 54500 Vandœuvre-lès-Nancy, France, Equipe de Dynamique des Assemblages Membranaires, UMR CNRS-UHP No. 7565, Nancy Université, BP 70239, 54506 Vandœuvre-lès-Nancy, France, and Theoretical and Computational Biophysics Group, Beckman Institute for Advanced Science and Engineering, University of Illinois at Urbana-Champaign, 405 North Mathews, Urbana, Illinois 61801
| | - Fabien Archambault
- Laboratoire d’ingénierie des biomolécules (LIBio), Nancy Université, 2 avenue de la forêt de Haye, 54500 Vandœuvre-lès-Nancy, France, Equipe de Dynamique des Assemblages Membranaires, UMR CNRS-UHP No. 7565, Nancy Université, BP 70239, 54506 Vandœuvre-lès-Nancy, France, and Theoretical and Computational Biophysics Group, Beckman Institute for Advanced Science and Engineering, University of Illinois at Urbana-Champaign, 405 North Mathews, Urbana, Illinois 61801
| | - Catherine Humeau
- Laboratoire d’ingénierie des biomolécules (LIBio), Nancy Université, 2 avenue de la forêt de Haye, 54500 Vandœuvre-lès-Nancy, France, Equipe de Dynamique des Assemblages Membranaires, UMR CNRS-UHP No. 7565, Nancy Université, BP 70239, 54506 Vandœuvre-lès-Nancy, France, and Theoretical and Computational Biophysics Group, Beckman Institute for Advanced Science and Engineering, University of Illinois at Urbana-Champaign, 405 North Mathews, Urbana, Illinois 61801
| | - Jean Marc Engasser
- Laboratoire d’ingénierie des biomolécules (LIBio), Nancy Université, 2 avenue de la forêt de Haye, 54500 Vandœuvre-lès-Nancy, France, Equipe de Dynamique des Assemblages Membranaires, UMR CNRS-UHP No. 7565, Nancy Université, BP 70239, 54506 Vandœuvre-lès-Nancy, France, and Theoretical and Computational Biophysics Group, Beckman Institute for Advanced Science and Engineering, University of Illinois at Urbana-Champaign, 405 North Mathews, Urbana, Illinois 61801
| | - Mohamed Ghoul
- Laboratoire d’ingénierie des biomolécules (LIBio), Nancy Université, 2 avenue de la forêt de Haye, 54500 Vandœuvre-lès-Nancy, France, Equipe de Dynamique des Assemblages Membranaires, UMR CNRS-UHP No. 7565, Nancy Université, BP 70239, 54506 Vandœuvre-lès-Nancy, France, and Theoretical and Computational Biophysics Group, Beckman Institute for Advanced Science and Engineering, University of Illinois at Urbana-Champaign, 405 North Mathews, Urbana, Illinois 61801
| | - François Dehez
- Laboratoire d’ingénierie des biomolécules (LIBio), Nancy Université, 2 avenue de la forêt de Haye, 54500 Vandœuvre-lès-Nancy, France, Equipe de Dynamique des Assemblages Membranaires, UMR CNRS-UHP No. 7565, Nancy Université, BP 70239, 54506 Vandœuvre-lès-Nancy, France, and Theoretical and Computational Biophysics Group, Beckman Institute for Advanced Science and Engineering, University of Illinois at Urbana-Champaign, 405 North Mathews, Urbana, Illinois 61801
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31
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Ghafourian T, Bozorgi AHA. Estimation of drug solubility in water, PEG 400 and their binary mixtures using the molecular structures of solutes. Eur J Pharm Sci 2010; 40:430-40. [DOI: 10.1016/j.ejps.2010.04.016] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2010] [Revised: 03/30/2010] [Accepted: 04/29/2010] [Indexed: 10/19/2022]
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32
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Kramer C, Beck B, Clark T. Insolubility classification with accurate prediction probabilities using a MetaClassifier. J Chem Inf Model 2010; 50:404-14. [PMID: 20088498 DOI: 10.1021/ci900377e] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Insolubility is a crucial issue in drug design because insoluble compounds are often measured to be inactive although they might be active if they were soluble. We provide and analyze various insolubility classification models based on a recently published data set and compounds measured in-house at Boehringer-Ingelheim. The 2D descriptor sets from pharmacophore fingerprints and MOE and the 3D descriptor sets from ParaSurf and VolSurf were examined in conjunction with support vector machines, Bayesian regularized neural networks, and random forests. We introduce a classifier-fusion strategy, called metaclassifier, which improves upon the best single prediction and at the same time avoids descriptor selection, a potential source of overfitting. The metaclassifier strategy is compared to the simpler fusion strategies of maximum vote and highest probability picking. A prediction accuracy of 72.6% on a three class model is achieved with the metaclassifier, with nearly perfect separation of soluble and insoluble compounds and prediction as good as our calculated maximum possible agreement with experiment.
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Affiliation(s)
- Christian Kramer
- Department of Lead Discovery, Boehringer-Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
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33
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Nantasenamat C, Isarankura-Na-Ayudhya C, Prachayasittikul V. Advances in computational methods to predict the biological activity of compounds. Expert Opin Drug Discov 2010; 5:633-54. [DOI: 10.1517/17460441.2010.492827] [Citation(s) in RCA: 127] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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34
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Ruether F, Sadowski G. Modeling the Solubility of Pharmaceuticals in Pure Solvents and Solvent Mixtures for Drug Process Design. J Pharm Sci 2009; 98:4205-15. [DOI: 10.1002/jps.21725] [Citation(s) in RCA: 156] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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