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Colodette NM, Franco LS, Maia RC, Fokoue HH, Sant'Anna CMR, Barreiro EJ. Novel phosphatidylinositol 4-kinases III beta (PI4KIIIβ) inhibitors discovered by virtual screening using free energy models. J Comput Aided Mol Des 2020; 34:1091-1103. [PMID: 32601839 PMCID: PMC7324290 DOI: 10.1007/s10822-020-00327-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 06/17/2020] [Indexed: 12/19/2022]
Abstract
Herein, the LASSBio Chemical Library is presented as a valuable source of compounds for screening to identify hits suitable for subsequent hit-to-lead optimization stages. A feature of the LASSBio Chemical Library worth highlighting is the fact that it is a smart library designed by medicinal chemists with pharmacological activity as the main priority. The great majority of the compounds part of this library have shown in vivo activity in animal models, which is an indication that they possess overall favorable bioavailability properties and, hence, adequate pharmacokinetic profiles. This, in turn, is supported by the fact that approximately 85% of the compounds are compliant with Lipinski's rule of five and ca. 95% are compliant with Veber's rules, two important guidelines for oral bioavailability. In this work it is presented a virtual screening methodology combining a pharmacophore-based model and an empirical Gibbs free energy-based model for the ligand-protein interaction to explore the LASSBio Chemical Library as a source of new hits for the inhibition of the phosphatidylinositol 4-kinase IIIβ (PI4KIIIβ) enzyme, which is related to the development of viral infections (including enteroviruses, SARS coronavirus, and hepatitis C virus), cancers and neurological diseases. The approach resulted in the identification of two hits, LASSBio-1799 (7) and LASSBio-1814 (10), which inhibited the target enzyme with IC50 values of 3.66 μM and IC50 and 6.09 μM, respectively. This study also enabled the determination of the structural requirements for interactions with the active site of PI4KIIIβ, demonstrating the importance of both acceptor and donor hydrogen bonding groups for forming interactions with binding site residues Val598 and Lys549.
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Affiliation(s)
- Natalie M Colodette
- LASSBio - Laboratório de Avaliação e Síntese de Substâncias Bioativas, Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, CCS, Cidade Universitária, Avenida Carlos Chagas Filho 373, Rio de Janeiro, RJ, ZIP 21941-910, Brazil.,Programa de Pós-Graduação em Farmacologia e Química Medicinal, Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, CCS, Cidade Universitária, Rio de Janeiro, RJ, Brazil
| | - Lucas S Franco
- LASSBio - Laboratório de Avaliação e Síntese de Substâncias Bioativas, Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, CCS, Cidade Universitária, Avenida Carlos Chagas Filho 373, Rio de Janeiro, RJ, ZIP 21941-910, Brazil.,Programa de Pós-Graduação em Farmacologia e Química Medicinal, Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, CCS, Cidade Universitária, Rio de Janeiro, RJ, Brazil
| | - Rodolfo C Maia
- LASSBio - Laboratório de Avaliação e Síntese de Substâncias Bioativas, Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, CCS, Cidade Universitária, Avenida Carlos Chagas Filho 373, Rio de Janeiro, RJ, ZIP 21941-910, Brazil
| | - Harold H Fokoue
- LASSBio - Laboratório de Avaliação e Síntese de Substâncias Bioativas, Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, CCS, Cidade Universitária, Avenida Carlos Chagas Filho 373, Rio de Janeiro, RJ, ZIP 21941-910, Brazil
| | - Carlos Mauricio R Sant'Anna
- LASSBio - Laboratório de Avaliação e Síntese de Substâncias Bioativas, Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, CCS, Cidade Universitária, Avenida Carlos Chagas Filho 373, Rio de Janeiro, RJ, ZIP 21941-910, Brazil.,Departamento de Química Fundamental, Instituto de Química, Universidade Federal Rural do Rio de Janeiro, Rodovia BR465, km 7, Seropédica, RJ, ZIP 23897-000, Brazil
| | - Eliezer J Barreiro
- LASSBio - Laboratório de Avaliação e Síntese de Substâncias Bioativas, Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, CCS, Cidade Universitária, Avenida Carlos Chagas Filho 373, Rio de Janeiro, RJ, ZIP 21941-910, Brazil. .,Programa de Pós-Graduação em Farmacologia e Química Medicinal, Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, CCS, Cidade Universitária, Rio de Janeiro, RJ, Brazil. .,Programa de Pesquisas em Desenvolvimento de Fármacos, Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, CCS, Cidade Universitária, Rio de Janeiro, RJ, Brazil.
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Kim SK, Lee S, Lee MK, Lee S. A systems pharmacology approach to investigate the mechanism of Oryeong-san formula for the treatment of hypertension. JOURNAL OF ETHNOPHARMACOLOGY 2019; 244:112129. [PMID: 31376514 DOI: 10.1016/j.jep.2019.112129] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 07/10/2019] [Accepted: 07/30/2019] [Indexed: 06/10/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Oryeong-san (ORS) is a traditional formula that has long been used for the treatment of dysfunctions of body fluids and electrolyte homeostasis in Korea, China and Japan. Recent reports have shown that ORS may suppress hypertension by controlling the renin-angiotensin-aldosterone system (RAAS) in the kidney, but its action mechanism has not been well defined. AIM OF THE STUDY The aim of this study was to decipher the ORS mechanisms in the treatment of hypertension using a systems pharmacology approach. MATERIALS AND METHODS The compounds of ORS were obtained from the TM-MC (database of medicinal materials and chemical compounds in Northeast Asian traditional medicine), and the drug-likeness (DL) and oral bioavailability (OB) of the compounds were evaluated. The potential targets of the compounds were identified using various pharmacology databases. To analyze the mechanisms of the ORS for hypertension, a Compound-Target-Disease (C-T-D) network was established with respect to the genes related to hypertension. RESULTS A screening evaluation of the DL and OB of the ORS compounds identified a list of 232 active compounds. The pharmacological activity of the targets was investigated by exploring the interaction network between the compounds and the targets. Analysis of the interactions between the compounds and the hypertension-related targets revealed that 14 ORS compounds regulate the RAAS and vasoconstrictors in the kidney. CONCLUSIONS This study used the systems pharmacology approach to decipher the mechanisms of action of ORS for the treatment of hypertension. When hypertension drugs and ORS are used in combination for treatment, possible side effects should be considered because most hypertension drugs are related to the RAAS. The results of this study may provide clues to not only analyze the pharmacological activity of ORS for the treatment of hypertension but other diseases as well.
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Affiliation(s)
- Sang-Kyun Kim
- Future Medicine Division, Korea Institute of Oriental Medicine, 1672 Yuseong-daero, Yuseong-gu, Daejeon, 34054, Republic of Korea.
| | - Seungho Lee
- Future Medicine Division, Korea Institute of Oriental Medicine, 1672 Yuseong-daero, Yuseong-gu, Daejeon, 34054, Republic of Korea.
| | - Myung-Ku Lee
- Future Medicine Division, Korea Institute of Oriental Medicine, 1672 Yuseong-daero, Yuseong-gu, Daejeon, 34054, Republic of Korea.
| | - Sanghun Lee
- Future Medicine Division, Korea Institute of Oriental Medicine, 1672 Yuseong-daero, Yuseong-gu, Daejeon, 34054, Republic of Korea.
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Shultz MD. Two Decades under the Influence of the Rule of Five and the Changing Properties of Approved Oral Drugs. J Med Chem 2018; 62:1701-1714. [DOI: 10.1021/acs.jmedchem.8b00686] [Citation(s) in RCA: 177] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Michael D. Shultz
- Global Discovery Chemistry, Novartis Institutes for Biomedical Research, Inc., 181 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
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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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O′Hagan S, Swainston N, Handl J, Kell DB. A 'rule of 0.5' for the metabolite-likeness of approved pharmaceutical drugs. Metabolomics 2014; 11:323-339. [PMID: 25750602 PMCID: PMC4342520 DOI: 10.1007/s11306-014-0733-z] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Accepted: 09/08/2014] [Indexed: 12/20/2022]
Abstract
We exploit the recent availability of a community reconstruction of the human metabolic network ('Recon2') to study how close in structural terms are marketed drugs to the nearest known metabolite(s) that Recon2 contains. While other encodings using different kinds of chemical fingerprints give greater differences, we find using the 166 Public MDL Molecular Access (MACCS) keys that 90 % of marketed drugs have a Tanimoto similarity of more than 0.5 to the (structurally) 'nearest' human metabolite. This suggests a 'rule of 0.5' mnemonic for assessing the metabolite-like properties that characterise successful, marketed drugs. Multiobjective clustering leads to a similar conclusion, while artificial (synthetic) structures are seen to be less human-metabolite-like. This 'rule of 0.5' may have considerable predictive value in chemical biology and drug discovery, and may represent a powerful filter for decision making processes.
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Affiliation(s)
- Steve O′Hagan
- School of Chemistry, The University of Manchester, 131 Princess St, Manchester, M1 7DN UK
- The Manchester Institute of Biotechnology, The University of Manchester, 131 Princess St, Manchester, M1 7DN UK
| | - Neil Swainston
- The Manchester Institute of Biotechnology, The University of Manchester, 131 Princess St, Manchester, M1 7DN UK
- School of Computer Science, The University of Manchester, 131 Princess St, Manchester, M1 7DN UK
| | - Julia Handl
- Manchester Business School, The University of Manchester, 131 Princess St, Manchester, M1 7DN UK
| | - Douglas B. Kell
- School of Chemistry, The University of Manchester, 131 Princess St, Manchester, M1 7DN UK
- The Manchester Institute of Biotechnology, The University of Manchester, 131 Princess St, Manchester, M1 7DN UK
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Deng ZL, Du CX, Li X, Hu B, Kuang ZK, Wang R, Feng SY, Zhang HY, Kong DX. Exploring the Biologically Relevant Chemical Space for Drug Discovery. J Chem Inf Model 2013; 53:2820-8. [DOI: 10.1021/ci400432a] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | | | - Xiao Li
- Center
for Bioinformatics, College of Life Science, Shandong University of Technology, Zibo 255049, China
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7
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Molinari G. Impact of Microbial Natural Products on Antibacterial Drug Discovery. Antibiotics (Basel) 2013. [DOI: 10.1002/9783527659685.ch3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Focused enumeration and assessing the structural diversity of scaffold libraries: conformationally restricted bicyclic secondary diamines. Mol Divers 2012; 16:477-87. [DOI: 10.1007/s11030-012-9381-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2012] [Accepted: 06/05/2012] [Indexed: 10/28/2022]
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Singh N, Sun H, Chaudhury S, Abdulhameed MDM, Wallqvist A, Tawa G. A physicochemical descriptor-based scoring scheme for effective and rapid filtering of kinase-like chemical space. J Cheminform 2012; 4:4. [PMID: 22316383 PMCID: PMC3299594 DOI: 10.1186/1758-2946-4-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2011] [Accepted: 02/08/2012] [Indexed: 01/26/2023] Open
Abstract
Background The current chemical space of known small molecules is estimated to exceed 1060 structures. Though the largest physical compound repositories contain only a few tens of millions of unique compounds, virtual screening of databases of this size is still difficult. In recent years, the application of physicochemical descriptor-based profiling, such as Lipinski's rule-of-five for drug-likeness and Oprea's criteria of lead-likeness, as early stage filters in drug discovery has gained widespread acceptance. In the current study, we outline a kinase-likeness scoring function based on known kinase inhibitors. Results The method employs a collection of 22,615 known kinase inhibitors from the ChEMBL database. A kinase-likeness score is computed using statistical analysis of nine key physicochemical descriptors for these inhibitors. Based on this score, the kinase-likeness of four publicly and commercially available databases, i.e., National Cancer Institute database (NCI), the Natural Products database (NPD), the National Institute of Health's Molecular Libraries Small Molecule Repository (MLSMR), and the World Drug Index (WDI) database, is analyzed. Three of these databases, i.e., NCI, NPD, and MLSMR are frequently used in the virtual screening of kinase inhibitors, while the fourth WDI database is for comparison since it covers a wide range of known chemical space. Based on the kinase-likeness score, a kinase-focused library is also developed and tested against three different kinase targets selected from three different branches of the human kinome tree. Conclusions Our proposed methodology is one of the first that explores how the narrow chemical space of kinase inhibitors and its relevant physicochemical information can be utilized to build kinase-focused libraries and prioritize pre-existing compound databases for screening. We have shown that focused libraries generated by filtering compounds using the kinase-likeness score have, on average, better docking scores than an equivalent number of randomly selected compounds. Beyond library design, our findings also impact the broader efforts to identify kinase inhibitors by screening pre-existing compound libraries. Currently, the NCI library is the most commonly used database for screening kinase inhibitors. Our research suggests that other libraries, such as MLSMR, are more kinase-like and should be given priority in kinase screenings.
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Affiliation(s)
- Narender Singh
- DoD Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U,S, Army Medical Research and Materiel Command, Fort Detrick, MD 21702, USA.
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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: 911] [Impact Index Per Article: 75.9] [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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11
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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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Ursu O, Rayan A, Goldblum A, Oprea TI. Understanding drug‐likeness. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2011. [DOI: 10.1002/wcms.52] [Citation(s) in RCA: 100] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Oleg Ursu
- Division of Biocomputing, Department of Biochemistry and Molecular Biology, University of New Mexico School of Medicine Albuquerque, NM, USA
- UNM Center for Molecular Discovery, University of New Mexico School of Medicine Albuquerque, NM, USA
| | - Anwar Rayan
- Molecular Modeling and Drug Design Lab and the Alex Grass Center for Drug Design and Synthesis, Institute of Drug Research, The Hebrew University of Jerusalem, Jerusalem, Israel
- Drug Discovery Informatics Lab, QRC‐Qasemi Research Center, Al‐Qasemi Academic College, Baqa‐El‐Gharbia, Israel
| | - Amiram Goldblum
- Molecular Modeling and Drug Design Lab and the Alex Grass Center for Drug Design and Synthesis, Institute of Drug Research, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Tudor I. Oprea
- Division of Biocomputing, Department of Biochemistry and Molecular Biology, University of New Mexico School of Medicine Albuquerque, NM, USA
- UNM Center for Molecular Discovery, University of New Mexico School of Medicine Albuquerque, NM, USA
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Oashi T, Ringer AL, Raman EP, MacKerell AD. Automated selection of compounds with physicochemical properties to maximize bioavailability and druglikeness. J Chem Inf Model 2011; 51:148-58. [PMID: 21142079 PMCID: PMC3160130 DOI: 10.1021/ci100359a] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Adequate bioavailability is one of the essential properties for an orally administered drug. Lipinski and others have formulated simplified rules in which compounds that satisfy selected physiochemical properties, for example, molecular weight (MW) ≤ 500 or the logarithm of the octanol-water partition coefficient, log P(o/w) < 5, are anticipated to likely have pharmacokinetic properties appropriate for oral administration. However, these schemes do not simultaneously consider the combination of the physiochemical properties, complicating their application in a more automated fashion. To overcome this, we present a novel method to select compounds with a combination of physicochemical properties that maximize bioavailability and druglikeness based on compounds in the World Drug Index database. In the study four properties, MW, log P(o/w), number of hydrogen bond donors, and number of hydrogen acceptors, were combined into a 4-dimensional (4D) histogram, from which a scoring function was defined on the basis of a 4D dependent multivariate Gaussian model. The resulting equation allows for assigning compounds a bioavailability score, termed 4D-BA, such that chemicals with higher 4D-BA scores are more likely to have oral druglike characteristics. The descriptor is validated by applying the function to drugs previously categorized in the Biopharmaceutics Classification System, and examples of application of the descriptor are given in the context of previously published studies targeting heme oxygenase and SHP2 phosphatase. The approach is anticipated to be useful in early lead identification studies in combination with clustering methods to maximize chemical and structural diversity when selecting compounds for biological assays from large database screens. It may also be applied to prioritize synthetically feasible chemical modifications during lead compound optimization.
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Affiliation(s)
- Taiji Oashi
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, 20 Penn Street, Baltimore, MD 21201
| | - Ashley L. Ringer
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, 20 Penn Street, Baltimore, MD 21201
| | - E. Prabhu Raman
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, 20 Penn Street, Baltimore, MD 21201
| | - Alexander D. MacKerell
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, 20 Penn Street, Baltimore, MD 21201
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