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重点文献推荐

【溶解度预测的比较】:化合物水中溶解度的计算预测  

In silico prediction of aqueous solubility.
Dearden JC. (2006) Expert Opin. Drug Discov. 1:31-52 

【摘要】:本文对化合物的水溶解度及其影响因素进行了简要概述,并简短介绍了定量结构-性质关系。汇总了1990年以前关于水溶性预测的工作,并对1990年以后的大多数水溶性计算预测方法进行了详细介绍和深入讨论。1990年以后的水溶性计算预测方法开始使用具有多样性的训练集。本文用21个药物和杀虫剂组成的测试集对这些研究中提及的水溶解度预测模型的准确性进行了验证。最后,我们用122个水溶解度已知的药物分子,对15款商业化软件的水溶解度预测准确性进行了评测。

LogP预测的比较】:分子亲脂性的计算:主流Log P预测方法并用超过96,000个化合物对这些方法进行比较研究

Calculation of molecular lipophilicity: State-of-the-art and comparison of log P methods on more than 96,000 compounds.
Mannhold R, Poda GI, Ostermann C, Tetko IV. (2008) J. Pharm. Sci. 98(3):861-93

【摘要】:Log P的预测方法可以分为两大类:一是基于结构,一是基于性质。我们首先回顾这两大类方法的最新研究进展。然后,我们用一个公开数据集(N=226)和两个分别来自NycomedN=882)和PfizerN=95809)的内部数据集对这两大类预测方法中的代表性方法的预测能力进行了比较。用公开数据集比较了30种预测方法,用工业数据集比较了18中预测方法。所有模型的预测准确性随着非氢原子数目的增加而降低。算术平均模型(AAM)被用来作为比较的基准模型。如果模型的均方根误差(RSME)大于AAM的均方根误差,那么此方法是不可接受的。对于公开数据集,大多数方法都能给出比较合理的结果;但是,对于内部数据集,只有七个方法能够同时对NycomedPfizer的化合物进行成功预测。我们提出了一种基于碳原子(NC)和杂原子数目(NHET)的简单log P计算公式:log P = 1.46±0.02+ 0.11±0.001NC- 0.11±0.001NHET。该计算方法的表现优于大多数本研究中所涉及的方法。最后,本文对影响的log P预测准确性的因素进行了阐述和讨论。

【成药性筛选】:利用生物电子等排原理设计新的monastrol衍生物,并利用计算得到的性质参数进行ADMET性质预测

Bioisosteric approach in designing new monastrol derivatives: An investigation on their ADMET prediction using in silico derived parameters.  

Hassan SF, Rashid U, Ansari FL, Ul-Haq Z. (2013) J Mol Graph Model. 45C:202-210

【摘要】:为了提供更安全、更有效的药物,药物化学家面临的挑战正变得越来越大。如何在各类药性质如溶解度、渗透性、代谢稳定性、药效和毒性之间取得恰当平衡,是在潜在候选药物的优化过程最具挑战性的问题之一。难溶和渗透性差的化合物会导致酶实验和细胞实验产生错误的生物学数据和不可靠的SAR结果。Monastrol是第一个报道的有丝分裂驱动蛋白Eg5 小分子抑制剂;但由于其抑制活性弱、类药性差,从而阻碍了其进一步的发展。本研究,首先,利用生物电子等排方法,得到monastrol C-5羰基被硫代羰基替换后的衍生物。接着,用计算软件ADMET Predictor软件对其进行更进一步的类药性优化。虽然只是微小的结构改造,但是新化合物的人空肠有效渗透率(PEFF)和Madin-Darby犬肾细胞(MDCK)渗透性都有很大改善 。此外,monastrol C-5硫代类似物(命名Special-2)在口服给药的情况下也是安全的。Special-2无磷脂沉积毒性,血清谷氨酸草酰乙酸转氨酶( SGOT )水平没有提高,并且无潜在心脏毒性。最后,分子对接方法被用来研究这些化合物的结合模式。对接研究表明,设计的化合物对于KSP具有高亲和力。因此,ADMET性质预测和分子对接方法的组合应用,可以用来提高预测的成功率并能成为设计KSP抑制剂的有效手段之一。

ADME预测案例】:通过理化参数来对药物的主要清除途径进行分类

In Silico Classification of Major Clearance Pathways of Drugs with Their Physiochemical Parameters
Kusama M, Toshimoto K, Maeda K, Hirai Y, Imai S, Chiba K, Akiyama Y, Sugiyama Y. (2010) Drug Metab Dispos. 38, 1362-1370

【摘要】:药物主要清除途径的预测,对于了解其临床使用上的药代动力学特性非常重要,如药物-药物相互作用及遗传多态性等,并影响其药理/毒理作用。本研究建立了一个计算分类方法来预测药物的主要清除途径。此方法仅需要四个理化参数:电荷、分子量(MW)、亲脂性(log D 和血浆蛋白非结合率(fup)。无需做任何实验,只需药物的分子结构,就可计算得到这四个参数。训练集包含141已上市药物,其主要清除途径包括CYP3A4CYP2C9CYP2D6OATPs肝摄取,或以原型经肾脏排泄。根据电荷进行分组后,每个药物都被绘制在由分子量、log Dfup构成的三维空间中。然后,代表各清除途径的矩形框根据数学标准:最小体积,最大F值(正确率和召回率的调好平均数),进行绘制。通过两种方法进行验证:离一法和新数据集,发现其具有88%的预测精度。如果能够在此模型的基础上进一步修改,朝多个清除路径和/或其它途径方向发展的话。这不仅可以有助于工业科学家在药物开发的早期阶段进行决断,从而选择具有最佳药代动力学性质的候选化合物。而且对于监管机构在评估新的药物并给予合理的药代动力学监管要求的时候也是非常有用的。

【自建模型应用】:药物诱导磷脂质病预测模型的构建

In silico modeling to predict drug-induced phospholipidosis
Choi SS, Kim JS, Valerio Jr. LG, Sadrieh N. (2013) Toxicol. Appl. Pharmacol. 269(2):195-204

【摘要】:药物诱导的磷脂质病(DIPL)通常表现在药物开发的临床前阶段,对药物开发和安全监管审查过程具有重要影响。能够诱导产生DIPL药物的一个主要特性是具有两亲性阳离子结构。这为基于结构的解释提供了证据,并为分析具有DIPL药物的性质和结构提供了机会。虽然,美国FDA的工作表明机器学习方法构建的DIPL定量构效关系(QSAR)预测模型可以成功应用于大多数药物;但是对一些药物仍不能给出准确预测。在本研究中,结合FDA最新的磷脂质病数据库,我们开发了一种新的算法和预测技术。经过验证,发现它是对FDAQSAR预测模型的一个很好补充。特别是,对于具有高可信度的数据能够表现出非常好的性能。我们建立的DIPL预测模型在严格的外部验证测试中表现出8081%的一致性。并且,该预测模型具有高灵敏度和高特异性;在大多数情况下,这两者都高于≥80%。也就是,此模型同时具有很高的阴性和阳性预测能力。因此,此模型可用于预测新的药物是否具有诱导DIPL的性质,以进行筛选。

 

中国客户采用ADMET Predictor软件发表的部分文献列表

英文文献:
001 Design, Synthesis, and Biological Evaluation of Novel PARP-1 Inhibitors Based on a 1H-Thieno[3,4-d] Imidazole-4-Carboxamide Scaffold.  IF= 2.465
Wang L, Liu F, Jiang N, Zhou W, Zhou X, Zheng Z. (2016) Molecules , 21(6), 772. 
002Discovery of new acetylcholinesterase inhibitors with small core structures through shape-based virtual screening.   IF=2.42
Chen Y, Liu Z, Fu T, Li W, Xu X, Sun H. Bioorg. & Med. Chem. Lett., 2015, 25, 3442-3446.
003 Discovery of new scaffolds from approved drugs asacetylcholinesterase inhibitors. IF=5.583
Chen Y, Xu X,Fu T, Li W, Liu Z, Sun H. (2015) RSC Advances, 10(39):90288-90294
004 A Computational Drug-Target Network for Yuanhu Zhitong Prescription. IF= 1.722
Xu H, Tao Y, Lu P, Wang P, Zhang F, Yuan Y, Wang S, Xiao X, Yang H, Huang L. (2013)Evidence-Based Complementary and Alternative Medicine, Article ID 658531

中文文献:
001 李雅秋,王旗.构建用于预测中药化学成分心脏毒性的定量构效关系模型[J]

002 淡墨,闻镍,刘丽等. 雷公藤甲素诱导正常人肝细胞L02的毒性及甘草酸二铵的保护作用[J].药物分析杂志2015, 35( 9)1568-1573
003
淡墨,闻镍,刘丽等. 甘草酸二铵通过上调CYP3A4 拮抗雷公藤甲素诱导肝细胞毒性[J]. 中国新药杂志2015, 24(12): 1349-1357
004
王 晨,李进,冯艳春等. 头孢地尼有关物质定量结构色谱保留模型的建立[J]. 药学学报2015, 50(9): 1161-1166
005 郑永勇,解鹏,张瑾等. 芳基哌嗪苯并噁嗪类化合物的设计、合成及生物活性研究[J]. 药学学报2012, 47 (6): 755−763

006 史少泽,王旗. 两毒性预测软件应用于中药成分毒性预测的验证J]. 中国新药杂质2016, 25(23): 2647−2652

采用ADMET Predictor 发表的部分文献

Predicting ADME Properties of Chemicals.
Shin, HK, Kang, Y, No, KT. (2016) In "Handbook of Computational Chemistry" ed. Jerzy Leszcznski, published by Springer Netherlands.

High throughput virtual screening and in silico ADMET analysis for rapid and efficient identification of potential PAP248-286 aggregation inhibitors as anti-HIV agents.
Malik R, Bunkar D, Choudhary BS, Srivastava S, Mehta P, Sharma M. (2016) J. Mol. Struct., 1122, 239-246. 

Pore blocking: An innovative formulation strategy for the design of alcohol resistant multi-particulate dosage forms.
Schrank S, Jedinger N, Wu S, Piller M, Roblegg E. (2016) Int. J. Pharm. 509, 219-228. 

Design, Synthesis, and Biological Evaluation of Novel PARP-1 Inhibitors Based on a 1H-Thieno[3,4-d] Imidazole-4-Carboxamide Scaffold.
Wang L, Liu F, Jiang N, Zhou W, Zhou X, Zheng Z. (2016) Molecules , 21(6), 772. 

Modeling ADMET.
Ghosh J, Lawless MS, Waldman M, Gombar V, Fraczkiewicz R. (2016) In "In Silico Methods for Predicting Drug Toxicity, for the series Methods in Molecular Biology", ed. Emilio Benfenati, published by Springer New York. 

In Silico Models for Acute Systemic Toxicity.
Burton J, Worth AP, Tsakovska I, Diukendjieva, A. (2016) In "In Silico Methods for Predicting Drug Toxicity, for the series Methods in Molecular Biology", ed. Emilio Benfenati, published by Springer New York. 

In Silico Prediction of Chemically Induced Mutagenicity: How to Use QSAR Models and Interpret Their Results.
Mombelli E, Raitano G, Benfenati E. (2016) In "In Silico Methods for Predicting Drug Toxicity, for the series Methods in Molecular Biology", ed. Emilio Benfenati, published by Springer New York. 

Descriptors and their selection methods in QSAR analysis: paradigm for drug design.
Danishuddin, Khan AU. (2016) Drug Discovery Today, July. 

High-throughput virtual screening and quantum mechanics approach to develop imipramine analogues as leads against trypanothione reductase of leishmania.
Pandey RK, Verma P, Sharma D, Bhatt TK, Sundar S, Prajapati VK. (2016) Biomedicine & Pharmacotherapy, 83, 141-152. 

Evaluating the Impact of Uncertainties in Clearance and Exposure When Prioritizing Chemicals Screened in High-Throughput Assays.
Leonard JA , Leonard AS, Chang D, Edwards S, Lu J, Scholle S, Key P, Winter M, Isaacs KK, Tan YC. (2016) Environ. Sci. Technol., online April 28.

Comparative human in-vivo study of an immediate release tablet over-encapsulated by gelatin and hydroxypropyl methyl cellulose capsules – impact of dissolution rate on bioequivalence.
Stegemann S, Vishwanath S, Kumar R, Cade D, Lowery M, Hutchison K, Michael Morgen M, Goodwin A, Lee C.(2016) Capsugel white paper.

Structure-based virtual screening, molecular docking, ADMET and molecular simulations to develop benzoxaborole analogs as potential inhibitor against Leishmania donovani trypanothione reductase.
Pandey RK, Kumbhar BV, Sundar S, Kunwar A, Prajapati VK. (2016) J. Receptors and Signal Transduction. 

Integration of Life-Stage Physiologically-Based Pharmacokinetic (PBPK) Models with Adverse Outcome Pathways (AOPs) and Environmental Exposure Models to Screen for Environmental Hazards.
El-Masri H, Kleinstreuer N, Hines RN, Adams L, Tal T, Isaacs K, Wetmore BA, Tan Y. (2016), Tox. Sci., online May 4. 

In silico screening of novel inhibitors of M17 Leucine Amino Peptidase (LAP) of Plasmodium vivax as therapeutic candidate.
Rout S, RK Mahapatra RK. (2016) Biomedicine & Pharmacotherapy, 82, 192-201. 

BDDCS, the Rule of 5 and drugability.
Benet LZ, Hosey CM, Ursu O, Oprea TI. (2016) Adv. Drug Delivery Reviews, 101, 89-98. 

Impact of curcumin on the pharmacokinetics of rosuvastatin in rats and dogs based on the conjugated metabolites.
Zhou X, Zhang F, Chen C, Guo Z, Liu J, Yu J, Xu Y, Zhong D, Jiang H. (2016) Xenobiotica, online May 13. 

Synthesis and Preclinical Evaluation of Sulfonamido based [11C-Carbonyl]-Carbamates and Ureas for Imaging Monoacylglycerol Lipase.
Wang L, Mori W, Cheng R, Yui J, Hatori A, Ma L, Zhang Y, Rotstein BH, Fujinaga M, Shimoda Y, Yamasaki T, Xie L, Nagai Y, Minamimoto T, Higuchi M, Vasdev N, Zhang M, Liang SH. (2016) Theranositcs, 6(8), 1145-1159. 

Development of In Vitro In Vivo Correlation Models For Clopidogrel Tablets To Describe Administration Under Fasting And Fed Conditions.
Savu SN, Silvestro L, Mirioiu C, Anuta V. (2016) Farmacia, 64, 2. 

Introduction to Cheminformatics.
Wishart DS. (2016) Current Protocols in Bioinformatics, published online: March 24.

Quantitative structure-retention relationship of selected imidazoline derivatives on alpha1-acid glycoprotein column.
Filipic S, Ruzic D, Vucicevic J, Nikolic K, Agbaba D. (2016) J. Pharm. Biomed. Analysis, online March 3.

Computational prediction of formulation strategies for beyond-rule-of-5 compounds. 
Bergstrom CAS, Charman WN, Porter CJH. (2016) Adv. Drug Delivery Reviews, online Feb. 27.

Novel nonquaternary reactivators showing reactivation efficiency for soman-inhibited human acetylcholinesterase.
Wei Z, Liu Y, Wang Y, Li W, Zhou X, Zhao X, Zhao J, Huang C, Li X, Liu J, Zheng Z, Li S. (2016) Toxicology Letters, 246, 1-6.

Synthesis and Evaluation of Novel Radioligands Based on 3-[5-(Pyridin-2-yl)-2H-tetrazol-2-yl]benzonitrile for Positron Emission Tomography Imaging of Metabotropic Glutamate Receptor Subtype 5.
Shimoda Y, Yamasaki T, Fujinaga M, Ogawa M, Kurihara Y, Nengai N, Kumata K, Yui J, Hatori A, Xie L, Zhang Y, Kawamu K, Zhang M. (2016) J. Med. Chem., 59 (8), 3980–3990.

Exploring dual inhibitory role of febrifugine analogues against Plasmodium utilizing structure-based virtual screening and molecular dynamic simulation.
Pandey RK, Narula A, Naskar M, Srivastava S, Verma P, Malik R, Shah P, Prajapatia VK. (2016) J. Biomolecular Structure and Dynamics, published online: April 18.

In vitro and in vivo evaluations of the P-glycoprotein-mediated efflux of dibenzoylhydrazines.
Miyataa K, Nakagawa Y, Kimura Y, Ueda K, Akamatsua M. (2016) Toxiclogy and Applied Pharmacology, 298, 40-47.

Novel S1P1 receptor agonists – Part 5: From amino-to alkoxy-pyridines.
Bolli MH, Lescop C, Birker M, de Kanter R, Hess P, Kohl C, Nayler O, Rey M, Sieber P, Velker J, Weller T, Steiner B. (2016) Eur. J. Med. Chem., 115, 326-341.

Provenance of Computers in Pharmacy.
Bandameedi R. (2016) Clin Pharmacol Biopharm, 5:153.

Pharmacokinetic evaluation of cefdinir-loaded floating alginate beads in rabbits using LC–MS/MS.
Praveen R, Singh SK, Ranjan P, Verma P. (2016) J. Pharm. Invest. Online March 5.

Development of a Physiologically Based Pharmacokinetic/Pharmacodynamic Model to Predict the Impact of Genetic Polymorphisms on the Pharmacokinetics and Pharmacodynamics Represented by Receptor/Transporter Occupancy of Central Nervous System Drugs.
Alqahtani S, Kaddoumi A. (2016) Clinical Pharmacokinetics, online February 25.

New design of nucleotide excision repair (NER) inihibitors for combination cancer therapy.
Gentile F, Tuszynskia JA, Barakat KH. (2016) J. Mol. Graphics and Modeling, 65, 71-82.

Use of Modeling and Simulation Tools for Understanding the Impact of Formulation on the Absorption of a Low Solubility Compound: Ciprofloxacin.
Marilyn Martinez M, Mistry B, Lukacova V, Polli J, Hoag S, Dowling T, Kona R, Fahmy R.(2016) AAPS J. Online April 26.

In vivo in silico pharmacokinetic simulation studies of carvedilol-loaded nanocapsules using GastroPlus™.
George JK, Singh SK, Verma PRP.(2016) Therapeutic Delivery, 7(5), 305-318.

Characterizing the Dissolution Profiles of Supersaturable Salts, Cocrystals, and Solvates to Enhance In Vivo Oral Absorption.
Hisada N, Takano R, Takata N, Shiraki K, Ueto T, Tanida S, Kataoka M, Yamashita S.(2016) Eur J Pharm Biopharm. Online April 7.

Software and Web Resources for Computer-Aided Molecular Modeling and Drug Discovery.
Yadav DK, Rai R, Pratap R, Singh H.(2016) Chemometrics Applications and Research: QSAR in Medicinal Chemistry, ed. By Andrew G. Mercader, Pablo R. Duchowicz, and PM Sivakumar.

Advantage of the Dissolution/Permeation System for Estimating Oral Absorption of Drug Candidates in the Drug Discovery Stage.
Miyaji Y, Fujii Y, Takeyama S, Kawai Y, Kataoka, M‡, Takahashi M, Yamashita S.(2016) Mol. Pharmaceutics, 13 (5), pp 1564–1574.

Identification of Novel Potential Inhibitors of Aldose Reductase: A Multistage Computational Filtering Approach.
Joseph JM, Kesherwani M, Velmurugan D. (2016) Recent Advance in Diabetes Treatment, Avid Science, ebook.

Physiologically Based Absorption Modeling to Impact Biopharmaceutics and Formulation Strategies in Drug Development—Industry Case Studies.
Kesisoglou F, Chung J, van Asperen J, Heimbach T. (2016) J. Pharmaceutical Sciences, online 23 Jan.

LC-ESI-MS/MS estimation of loratadine-loaded self-nanoemulsifying drug delivery systems in rat plasma: Pharmacokinetic evaluation and computer simulations by GastroPlus™.
Verma S, Singh SK. (2016) Journal of Pharmaceutical and Biomedical Analysis, 124, 10-21.

Estimating Margin of Exposure to Thyroid Peroxidase Inhibitors Using High-throughput In Vitro Data, High-throughput Exposure Modeling, and Physiologically-Based Pharmacokinetic/Pharmacodynamic Modeling.
Leonard JA, Tan Y, Gilbert M, Isaacs K, El-Masri, H. (2016) Toxicological Sciences, 151, 57-70.

Design and synthesis of some new 1-phenyl-3/4-[4-(aryl/heteroaryl/alkyl-piperazine1-yl)-phenyl-ureas as potent anticonvulsant and antidepressant agents.
Mishra CB, Kumari S, Tiwar M. (2016) Archives of Pharmacal Research, online February 18.

Acute Toxicity Tests: Tools for Assessment of Toxicological Effects of Plants.
Balogun ST, Sandabe UK, Jibrin J, Ibrahim E, Fehintola FA. (2016) International Journal of Indigenous Medicinal Plants, ISSN: 2051-4263, Vol.48, Issue 1.

Predicting biopharmaceutical performance of oral drug candidates–Extending the Volume to Dissolve Applied Dose concept
Muenster U, Mueck W, van der Mey D, Schlemmer K, Greschat-Schade S, Haerter M, Pelzetter C, Pruemper C, Verlage J, Goeller AH, Ohm A. (2016) Euro. J. Pharm. And Biopharm., available online March 5.

Development of 3,5-Dinitrobenzylsulfanyl-1,3,4-Oxadiazoles and Thiadiazoles as Selective Antitubercular Agents Active Against Replicating and Nonreplicating Mycobacterium tuberculosis.
Karabanovich G, Zemanová J, Smutný T, Székely R, Šarkan M, Centárová I, Vocat A, Pávková I, Conka P, Nemecek J, Stolaríková J, Vejsová M, Vavrova K, Klimešová V, Hrabalek A, Pavek P, Cole ST, Mikušová K, and Roh J. (2016) J. Med. Chem. web pub. Date March 5.

Radiosynthesis and evaluation of N-(3,4-dimethylisoxazol-5-yl)piperazine-4-[4-(4-fluorophenyl)thiazol-2-yl]-1-[11C]carboxamide for in vivo positron emission tomography imaging of fatty acid amide hydrolase in brain.
Shimoda Y, Yui Y, Zhang Y, Hatori A, Ogawa M, Fujinaga M, Yamasaki T, Xie L, Kumata K, Zhang MR. (2015) RSC Adv., 5, 106122-106127.

Chromatographic lipophilicity as a predictor of antiproliferative activity of 17-picolyl and 17-picolinylidene androstane derivatives toward prostate cancer.
Kovacevic SZ, Podunavac-Kuzmanovic SO, Jevric LR, Djurendic EA, Ajdukovic JJ, Jovanov PT. (2015) APTEFF, 46, 1-269. 

Evaluations of imidazolium ionic liquids as novel skin permeation enhancers for drug transdermal delivery.
Zhang D, Wang H, Cui X, Wang C. (2016) Pharmaceutical Development and Technology, published online Jan 13. 

Discovery of novel S1P 2 antagonists, part 3: Improving the oral bioavailability of a series of 1, 3-bis (aryloxy) benzene derivatives.
Kusumia K, Shinozakib K, Yamauraa Y, Hashimotoa A, Kurataa H, Naganawaa A, Otsukia K, Matsushitaa T, Sekiguchia T, Kakuuchia A, Yamamoto H, Seko T. (2016) Bioorg. & Med. Chem. Lett., 26(4), 1209-1213. 

Ferulic acid-carbazole hybrid compounds: combination of cholinesterase inhibition, antioxidant and neuroprotection as multifunctional anti-Alzheimer agents.
Fang L, Chen M, Liu Z, Fang X, Gou S, Chen L. (2016) Bioorg. & Med. Chem. Lett., 24(4), 886-893. 

Febrifugine analogues as Leishmania donovani trypanothione reductase inhibitors: binding energy analysis assisted by molecular docking, ADMET and molecular dynamics simulation.
Pandey RK, Kumbhar BV, Srivastava S, Malik R, Sundar S, Kunwar A, Prajapati VK. (2016) Journal of Biomolecular Structure and Dynamics, online 3 Jan. 

A Study on in-silico Analysis of Phytochemicals targeting the proteins of Hepatitis B and C Virus.
Vani GS and Rajarajan S. (2015) Int.J.Curr.Microbiol.App.Sci 4(12): 683-691. 

Development of a unified dissolution and precipitation model and its use for the prediction of oral drug absorption.
Jakubiak P, Wagner B, Grimm HP, Petrig-Schaffland J, Schuler F, and Alvarez-Sanchez R. (2016) Mol. Pharm., 13(2), 586-598. 

N-(3, 4-Dimethylisoxazol-5-yl) piperazine-4-[4-(2-fluoro-4-[11C] methylphenyl) thiazol-2-yl]-1-carboxamide: a promising positron emission tomography ligand for fatty acid amide hydrolase.
Shimoda Y, Fujinaga M, Hatori A, Yui J, Zhang Y, Nengaki N, Kurihara Y, Yamasaki T,Xie L, Kumata K, Ishiia H, Zhang M. (2016) Bioorg. & Med. Chem., 24(4), 627-634. 

Tales from the war on error: the art and science of curating QSAR data.
Waldman M, Fraczkiewicz R, and Clark RD. (2015) J Comput Aided Mol Des. 29(9), 897-910.

Discovery of new acetylcholinesterase inhibitors with small core structures through shape-based virtual screening
Chen Y, Liu Z, Fu T, Li W, Xu X, Sun H. Bioorg. & Med. Chem. Lett., 2015, 25, 3442-3446.

Assessment of in silico models for acute aquatic toxicity towards fish under REACH regulation.
Cappelli CI, Cassano A, Golbamaki A, Lombardo A,Colafranceschi M, Benfenati E. SAR and QSAR in Environmental Research, online Nov. 2015.

Benzazaborinines as novel bioisosteric replacements of naphthalene: propranolol as an example.
Rombouts FJR, Tovar F, Austin N, Tresadern G, Trabanco AA. J. Med. Chem., Just Accepted Manuscript, Nov. 13, 2015.

Pharmacologic Activities of 3'-Hydroxypterostilbene: Cytotoxic, Anti-Oxidant, Anti-Adipogenic, Anti-Inflammatory, Histone Deacetylase and Sirtuin 1 Inhibitory Activity.
Takemoto JK, Remsberg CM, Davies NM. J. Pharm. Pharm. Sci 18(4) 713-727, 2015.

Analysis of Intra- and Intersubject Variability in Oral Drug Absorption in Human Bioequivalence Studies of 113 Generic Products.
Sugihara M, Takeuchi S, Sugita M, Higaki K, Kataoka M,Yamashita S. Mol. Pharmaceutics, Article ASAP Nov. 15, 2015. 

Tools for early prediction of drug loading in lipid-based formulations.
Alskar LC, Porter CJH, Bergstrom CAS. Mol. Pharmaceuticals, web., Nov. 15, 2015.

A review of the current state of the art of physiologically-based tests for measuring human dermal in vitro bioavailability of polycyclic aromatic hydrocarbons (PAH) in soil.
Beriro DJ, Cave MR, Wragg J, Thomas R,Wills G, Evansc F. J. Hazardous Materials, Available online 18 November 2015. 

The use of computational chemistry to predict toxicity of antioxidants food additives and its metabolites as a reference for food safety regulation.
Damayanti S, Permana J, Tjahjono DH. Der Pharma Chemica, 2015, 7(9):174-181. 

Novel derivatives of nitro-substituted salicylic acids: Synthesis, antimicrobial activity and cytotoxicity.
Paraskevopoulos G,Krátký M,Mandíková J, Trejtnar F, Stolaríková J, Pávek P,Besra G, Vinšová J. Bioorg. and Med. Chem., Available online 24 October 2015. 

In vitro anticancer properties and biological evaluation of novel natural alkaloid jerantinine B.
Qazzaz ME, Raja VJ, Lim K, Kam T, Lee JB, Gershkovich P, Bradshaw TD. Cancer Letters, online Oct. 26, 2015.

The evolution and future of environmental partition coefficients.
Mackay D, Celsie AKD, Parnis JM. Environmental Reviews, published on the web 04 November 2015.

Discovery of New Scaffolds from Approved Drugs as Acetylcholinesterase Inhibitors
Chen, Y, Xu X, Fu T, Li W, Liu Z, Sun H. RSC Adv., 2015,5, 90288-90294.

Development of Physiologically Based Pharmacokinetic/Pharmacodynamic Model for Indomethacin Disposition in Pregnancy.
S Alqahtani, A Kaddoumi , PLOS One, October 2015.

Role of computer-aided drug design in modern drug discovery.
Macalino, SJY, Gosu V, Hong S, and Choi S. (2015) Archives of Pharmacal Research 38(9), 1686-1701.

Lipidic dispersion to reduce food dependent oral bioavailability of fenofibrate: in vitro, in vivo and in silico assessments
O’Shea JP, Faisal W, Ruane-O’Hora T, Devine, KJ, Kostewicz ES, O’Driscolla CM, and, Griffin BT (2015) European J Pharmaceutics and Biopharmaceutics, 96, 207-216. 

Development of a Physiologically Based Pharmacokinetic/Pharmacodynamic Model to Identify Mechanisms Contributing to Entacapone Low Bioavailability.
Alqahtani S and Kaddoumi A. (2015) Biopharmaceutics & Drug Disposition, accepted online.

Homology Modeling, Molecular Dynamic Simulation and In Silico Screening of Activator for the Intensification of Human Sirtuin Type 1 (SIRT1) By Novel 1, 3, 4-Thiadiazole Derivatives-A Potential Antiaging Approach.
Saha S, Rai A, and Raj V. (2015) J Bioanal Biomed, Volume 7(4), 97-103.

Intestinal solubility and absorption of poorly water soluble compounds: predictions, challenges and solutions.
Fagerberg JH and Bergström CAS. (2015) Therapeutic Delivery online August.

Using Cheminformatics in Drug Discovery.
Lawless MS, Waldman M, Fraczkiewicz R, and Clark RD. (2015) Handbook of Experimental Pharmacology, Springer. 

Identification of a major radiometabolite of [11C]PBB3.
Hashimotoa H, Kawamuraa K, Takeia M, Igarashia N, Fujishiroa T, Shiomia S, Watanabea R, Mutoa M, Furutsukaa K, Itoa T, Yamasakia T, Yuia J, Nemotoa K, Kimuraa Y, Higuchia M, and Zhanga M-R. (2015) Nuclear Medicine and Biology, accepted online.

Physical Stability of Drugs after Storage Above and Below the Glass Transition Temperature: Relationship to Glass-Forming Ability.
Alhalaweha A, Alzghoulb A, Mahlina D, and Bergström, CAS. (2015) International Journal of Pharmaceuticals, 405(1), 312-317. 

Marine Drug Discovery Database (MDDD) – A Database of In silico Predicted Physico-Chemical, Drug Likeness and Toxicological Properties of Marine Compounds.
Sripathy R, Vidya A, Balasubramanian V, Arokiaraj A, Ramchand CN, and Sundararaman M. (2015) Journal of Advanced Bioinformatics Applications and Research, 6(2), 33-44. 

Discovery of novel S1P2 antagonists. Part 2: Improving the profile of a series of 1,3-bis(aryloxy)benzene derivatives. 
Kusumia K, Shinozakib K, Yamauraa Y, Hashimotoa A, Kurataa H, Naganawaa A, Uedac H, Otsukia K, Matsushitaa T, Sekiguchia T, Kakuuchia A, and Sekoc T. (2015) Bioorg. Med. Chem. Letters online 8 Sept. 

1,4-Oxazine beta-secretase (BACE1) inhibitors: from hit generation to orally bioavailable brain penetrant leads.
Rombouts FJR, Tresadern G, Delgado O, Lamenca CM, Van Gool M, García-Molina A, De Diego SAA, Oehlrich D, Prokopcova H, Alonso JM, Austin N, Borghys H, Van Brandt S, Surkyn M, De Cleyn M, Vos A, Alexander R, Macdonald GJ, Moechars D, Gijsen HJM, and Trabanco AA. (2015) J. Med. Chem. just accepted.

Experimental and Computational Prediction of Glass Transition Temperature of Drugs
Alzghoul A,Alhalaweh A,Mahlin D, Bergstrom CAS. J. Chem. Info. Model (2014), 54 (12), 3396-3403

Acute toxicity prediction in multiple species by leveraging mechanistic ToxCast mitochondrial inhibition data and simulation of oral bioavailability.
Bhhatarai B, Wilson DM, Bartels MJ, Chaudhuri S, Price PS, Carney EW. (2015) Toxicol Sci. Jul 2.

QSAR studies and design of new analogs of vitamin E with enhanced antiproliferative activity on MCF-7 breast cancer cells
Gagic Z, Nikolic K, Ivkovic B, Filipic S, and Agbaba, D. (2015) J Taiwan Inst Chem Eng August 20 online.

Effect of SI-591, a new class of cathepsin K inhibitor with peptidomimetic structure, on bone metabolism in vitro and in vivo

Fujii T, Ishikawa M, Kubo A, and Tanaka Y. (2015) Bone August 20 online. - See more at: http://www.simulations-plus.com/publication.aspx?pID=13#sthash.GyXXaI1V.dpuf

A Workflow to Investigate Exposure and Pharmacokinetic Influences on High-Throughput in Vitro Chemical Screening Based on Adverse Outcome Pathways.

Phillips MB, Leonard JA, Grulke CM, Chang DT, Edwards SW, Brooks R, Goldsmith MR, El-Masri H, Tan YM. (2015) Environ Health Perspect. May 15.

An in silico expert system for the identification of eye irritants.
Verma RP, Matthews EJ. (2015) SAR QSAR Environ Res. May;26(5):383-95.

In silico prediction of hERG inhibition.
Jing Y, Easter A, Peters D, Kim N, Enyedy IJ. (2015) Future Med Chem. Apr;7(5):571-86.

In silico optimization of pharmacokinetic properties and receptor binding affinity simultaneously: a 'parallel progression approach to drug design' applied to ß-blockers.
Advani P, Joseph B, Ambre P, Pissurlenkar R, Khedkar V, Iyer K, Gabhe S, Iyer RP, Coutinho E. (2015) J Biomol Struct Dyn. May 20:1-15.

Predicting the extent of metabolism using in vitro permeability rate measurements and in silico permeability rate predictions.
Hosey CM, Benet LZ. (2015) Mol Pharm. May 4;12(5):1456-66.

5-Aryl-1H-pyrazole-3-carboxylic acids as selective inhibitors of human carbonic anhydrases IX and XII.

Cvijetic IN, Tançb M, Juranicc IO, Verbicd TZ, Supuranb CT, Drakulicc BJ. (2015) Bioorganic & Med. Chem. June 4

Discovery of a Potent, Orally Available Dual CysLT1 and CysLT2 Antagonist with Dicarboxylic Acid.

Itadani S, Takahashi S, Ima M, Sekiguchi T, Aratani Y, Egashira H, Matsumura N, Inoue A, Yonetomi Y, Fujita M, Nakayama Y, Takeuchi J. (2015) Bioorganic & Med. Chem. Mar 7

The importance of critical micellar concentration for the prediction of solubility enhancement in biorelevant media.
Ottaviani G, Wendelspiess S, Alvarez-Sanchez R. (2015) Mol Pharm. Feb 9.

The influence of salt chaotropicity, column hydrophobicity and analytes’ molecular properties on the retention of pramipexole and its impurities.
Vemic A, Kalinic M, Eric S, Malenovica A, Medenicac M. (2015) J. of Chromatography Feb. 1


Evaluation and comparison of benchmark QSAR models to predict a relevant REACH endpoint: The bioconcentration factor (BCF).
Gissi A, Lombardo A, Roncaglioni A, Gadaleta D, Mangiatordi GF, Nicolotti O, Benfenati E. (2015) Environ Res. Jan 20;137C:398-409

Prediction of blood-brain barrier permeation of a-adrenergic and imidazoline receptor ligands using PAMPA technique and quantitative-structure permeability relationship analysis.
Vucicevic J, Nikolic K, Dobricic V, Agbaba D. (2015) Eur J Pharm Sci. 68C:94-105

Comparison of in silico tools for evaluating rat oral acute toxicity.
Diaza RG, Manganelli S, Esposito A, Roncaglioni A, Manganaro A, Benfenati E. (2015) SAR QSAR Environ Res. Jan 8:1-27

Design, Synthesis and Pharmacological evaluation of N-[4-(4-(alkyl/aryl/heteroaryl/)-piperazin-1-yl)-phenyl]-carbamic acid ethyl ester derivatives as novel anticonvulsant agents.
Kumari S, Mishra CB, Tiwari M. (2015) Bioorganic & Medicinal Chemistry Letters Jan. 9

Computational classification models for predicting the interaction of drugs with P-glycoprotein and breast cancer resistance protein.
Eric S, Kalinic M, Ilic K, Zloh M. (2014) SAR QSAR Environ Res. 25(12):955-82

Targeting pharmacoresistant epilepsy and epileptogenesis with a dual-purpose antiepileptic drug.
Doeser A, Dickhof G, Reitze M, Uebachs M, Schaub C, Pires NM, Bonifácio MJ, Soares-da-Silva P, Beck H. (2014) Brain. Dec 2.

Estimation of the chemical-induced eye injury using a weight-of-evidence (WoE) battery of 21 artificial neural network (ANN) c-QSAR models (QSAR-21): Part I: Irritation potential.
Verma RP, Matthews EJ. (2014) Regul Toxicol Pharmacol. pii: S0273-2300(14)00286-4

Estimation of the chemical-induced eye injury using a Weight-of-Evidence (WoE) battery of 21 artificial neural network (ANN) c-QSAR models (QSAR-21): Part II: Corrosion potential.
Verma RP, Matthews EJ. (2014) Regul Toxicol Pharmacol. pii: S0273-2300(14)00297-9

Isoxazolotacrines as non-toxic and selective butyrylcholinesterase inhibitors for Alzheimer's disease.
Cherif O, Allouche F, Chabchoub F, Chioua M, Soriano E, Yañez M, Cacabelos R, Romero A, López MG, Marco-Contelles J. (2014) Future Med Chem. 6(17):1883-91.

Xyloketal B, a marine compound, acts on a network of molecular proteins and regulates the activity and expression of rat cytochrome P450 3a: a bioinformatic and animal study.

Su J, Chang C, Xiang Q, Zhou ZW, Luo R, Yang L, He ZX, Yang H, Li J, Bei Y, Xu J, Zhang M, Zhang Q, Su Z, Huang Y, Pang J, Zhou SF. (2014) Drug Des Devel Ther. 8:2555-602.

Best of Both Worlds: Combining Pharma Data and State of the Art Modeling Technology to Improve in silico pKa Prediction.

Fraczkiewicz R, Lobell M, Göller AH, Krenz U, Schoenneis R, Clark RD, Hillisch A. (2014) J. Chem. Inf. Model. (Just Accepted Manuscript)

Formulation of the Microbicide INP0341 for In Vivo Protection against a Vaginal Challenge by Chlamydia trachomatis.
Pedersen C, Slepenkin A, Andersson SB, Fagerberg JH, Bergström CA, Peterson EM. (2014) PLoS One. Oct 30;9(10)

Relationships between the antidotal efficacy and structure, PK/PD parameters and bio-relevant molecular descriptors of AChE reactivating oximes: inclusion and integration to biopharmaceutical classification systems.
Voicu V, Radulescu FS, Medvedovici A. (2014) Expert Opin Drug Metab Toxicol. Nov 6:1-15

Three-Dimensional Quantitative Structure-Activity Relationship Analysis for Human Pregnane X Receptor for the Prediction of CYP3A4 Induction in Human Hepatocytes: Structure-Based Comparative Molecular Field Analysis.
Handa K, Nakagome I, Yamaotsu N, Gouda H, Hirono S. (2014) J Pharm Sci. Nov 7

A combination of pharmacophore modeling, molecular docking, and virtual screening for P2Y12 receptor antagonists from Chinese herbs.
He Y, Jiang L, Yang Z, Qiao Y, Zhang YL. (2014) Canadian J. Chem. Nov 18

Ranking the binding energies of p53 mutant activators and their ADMET properties.
Omar SI, Tuszynski J. (2014) Chem Biol Drug Des. Nov 19.

Concomitant intake of alcohol may increase the absorption of poorly soluble drugs.
Fagerberg JH, Sjögren E, Bergström CAS. (2014) Eur. J. Pharm. Sci. 67:12-20

Imidazole aldoximes effective in assisting butyrylcholinesterase catalysis of organophosphate detoxification.
Sit RK, Fokin VV, Amitai G, Sharpless KB, Taylor P, Radic Z. (2014) J Med Chem. Feb 27;57(4):1378-89.

Improving genetic programming for the prediction of pharmacokinetic parameters.
Vanneschi L. (2014) Memetic Computing Oct 26

A new in vitro system for evaluation of passive intestinal drug absorption: Establishment of a double artificial membrane permeation assay.
Kataoka M, Tsuneishi S, Maeda Y, Masaoka Y, Sakuma S, Yamashita S. (2014) Eur J Pharm Biopharm. Oct 7

Eslicarbazepine and the enhancement of slow inactivation of voltage-gated sodium channels: A comparison with carbamazepine, oxcarbazepine and lacosamide.
Hebeisen S, Pires N, Loureiro AI, Bonifácio MJ, Palma N, Whyment A, Spanswick D, Soares-da-Silva P. (2014) Neuropharmacology. Sep 19;89C:122-135

The Poorly Membrane Permeable Antipsychotic Drugs Amisulpride and Sulpiride Are Substrates of the Organic Cation Transporters from the SLC22 Family.
Dos Santos Pereira JN, Tadjerpisheh S, Abed MA, Saadatmand AR, Weksler B, Romero IA, Couraud PO, Brockmöller J, Tzvetkov MV. (2014) AAPS J. Aug 26.

In Silico Prediction of Major Drug Clearance Pathways by Support Vector Machines with Feature-Selected Descriptors.
Toshimoto K, Wakayama N, Kusama M, Maeda K, Sugiyama Y, Akiyama Y. (2014) Drug Metab Dispos. Aug 14

Synthesis of a novel universal opioid receptor agonist with the 1,3,5-trioxazatriquinane skeleton and its pharmacologies.
Hirayamaa S, Wadaa N, Kurodaa N, Iwaia T, Yamaotsua N, Hironoa S, Fujiia H, Nagasea H. (2014) Bioorganic Med. Chem. Lett. Aug 12

Discovery of furan-2-carbohydrazides as orally active glucagon receptor antagonists.
Hasegawa F, Niidome K, Migihashi C, Murata M, Negoro T, Matsumoto T, Kato K, Fujii A. (2014) Bioorg Med Chem Lett. Jul 24

The acute effects of daily nicotine intake on heart rate - A toxicokinetic and toxicodynamic modelling study.

Gajewska M, Worth A, Urani C, Briesen H, Schramm KW. (2014) Regul Toxicol Pharmacol. Jul 24;70(1):312-324

Physiologically based pharmacokinetic modeling for assessing the clinical drug-drug interaction of alisporivir.

Xia B, Barve A, Heimbach T, Zhang T, Gu H, Wang L, Einolf H, Alexander N, Hanna I, Ke J, Mangold JB, He H, Sunkara G. (2014) Eur J Pharm Sci. Jul 4

Maximum Entropy in Drug Discovery.
Tseng CY, Tuszynski J. (2014) Entropy 16:3754-3768

Predicting when Biliary Excretion of Parent Drug is a Major Route of Elimination in Humans.
Hosey CM, Broccatelli F, Benet LZ. (2014) AAPS J. Jul 9.

Computational Predictions of Glass-Forming Ability and Crystallization Tendency of Drug Molecules.
Alhalaweh A, Alzghoul A, Kaialy W, Mahlin D, Bergström CA. (2014) Mol Pharm. Jul 11.

Synthesis and Antioxidant Activity Evaluation of New Compounds from Hydrazinecarbothioamide and 1,2,4-Triazole Class Containing Diarylsulfone and 2,4-Difluorophenyl Moieties.
Barbuceanu SF, Ilies DC, Saramet G, Uivarosi V, Draghici C, Radulescu V. (2014) Int. J. Mol. Sciences 15:10908-10925

Comparison of in silico models for prediction of Daphnia magna acute toxicity.
Golbamaki A, Cassano A, Lombardo A, Moggio Y, Colafranceschi M, Benfenati E. (2014) SAR QSAR Environ Res. Jun 9:1-22.

Non-linear assessment of anticancer activity of 17-picolyl and 17-picolinylidene androstane derivatives - Chemometric guidelines for further syntheses.
Kovacevic SZ, Podunavac-Kuzmanovic SO, Jevric LR, Djurendic EA, Ajdukovic JJ. (2014) Eur J Pharm Sci. Jun 11.

A tutorial for analysing the cost-effectiveness of alternative methods for assessing chemical toxicity: the case of acute oral toxicity prediction.
Norlen H, Worth AP, Gabbert S. (2014) Altern Lab Anim. May;42(2):115-27.

Using beta binomials to estimate classification uncertainty for ensemble models.
Clark RD, Liang W, Lee AC, Lawless MS, Fraczkiewicz R, Waldman M. (2014) J. of Cheminfo. 6:34

BU08073 a Buprenorphine Analog with Partial Agonist Activity at mu Receptors in vitro but Long-Lasting Opioid Antagonist Activity in vivo in Mice.
Khroyan TV, Wu J, Polgar WE, Cami-Kobeci G, Fotaki N, Husbands SM, Toll L. (2014) Br J Pharmacol. Jun 5

N-(furan-2-ylmethyl)-N-methylprop-2-yn-1-amine (F2MPA): A Potential Cognitive Enhancer with MAO Inhibitor Properties.
Di Giovanni G, García I, Colangeli R, Pierucci M, Rivadulla ML, Soriano E, Chioua M, Della Corte L, Yáñez M, De Deurwaerdère P, Fall Y, Marco-Contelles J. (2014) CNS Neurosci Ther. May 21

Synthesis and in silico studies of pyrrolidine sulfonamide based dipeptides as ß-gluscosidase inhibitors.
Santosh Kumara B, Guru Prasad AR, Madhu G, Raveendra Reddy P, Ravindranath LK. (2014) Annales Pharmaceutiques Françaises Mar. 27

Differential effects of methoxy group on the interaction of curcuminoids with two major ligand binding sites of human serum albumin.
Sato H, Chuang VT, Yamasaki K, Yamaotsu N, Watanabe H, Nagumo K, Anraku M, Kadowaki D, Ishima Y, Hirono S, Otagiri M, Maruyama T. (2014) PLoS One, Feb 3;9(2):e87919

Lipophilicity indices derived from the liquid chromatographic behavior observed under bimodal retention conditions (reversed phase/hydrophilic interaction): Application to a representative set of pyridinium oximes.
Voicu V, Sârbu C, Tache F, Micale F, Radulescu SF, Sakurada K, Ohta H, Medvedovici A. (2014) Talanta 122:172-179

Metabolism and physiologically based pharmacokinetic modeling of flumioxazin in pregnant animals.
Takaku T, Nagahori H, Sogame Y. (2014) Toxicol Appl Pharmacol. Apr 6

Lipophilicity indices derived from the liquid chromatographic behavior observed under bimodal retention conditions (reversed phase/hydrophilic interaction): Application to a representative set of pyridinium oximes.

Voicu V, Sârbu C, Tache F, Micale F, Radulescu SF, Sakurada K, Ohta H, Medvedovici A. (2014) Talanta 122:172-179

Differential effects of methoxy group on the interaction of curcuminoids with two major ligand binding sites of human serum albumin.
Sato H, Chuang VT, Yamasaki K, Yamaotsu N, Watanabe H, Nagumo K, Anraku M, Kadowaki D, Ishima Y, Hirono S, Otagiri M, Maruyama T. (2014) PLoS One, Feb 3;9(2):e87919

Synthesis and in silico studies of pyrrolidine sulfonamide based dipeptides as ß-gluscosidase inhibitors.
Santosh Kumara B, Guru Prasad AR, Madhu G, Raveendra Reddy P, Ravindranath LK. (2014) Annales Pharmaceutiques Françaises Mar. 27  

Diaromatic sulfur-containing ‘naphthenic’ acids in process waters.
Westa CE, Scarlett AG, Tonkina A, O’Carroll-Fitzpatricka D, Pureveenb J, Tegelaarb E, Gieleciakc R, Hagerc D, Petersene K, Tollefsene KE, Rowlanda SJ. (2013) Water Research Nov. 1

Purely in-silico BCS classification: Science based quality standards for the world's drugs.
Dahan A, Wolk O, Kim YH, Ramachandran C, Crippen GM, Takagi T, Bermejo M, Amidon GL. (2013) Mol Pharm. Oct 4

Bioisosteric approach in designing new monastrol derivatives: An investigation on their ADMET prediction using in silico derived parameters.
Hassan SF, Rashid U, Ansari FL, Ul-Haq Z. (2013) J Mol Graph Model. 45C:202-210

Is the full potential of the Biopharmaceutics Classification System reached?
Bergström CA, Andersson SB, Fagerberg JH, Ragnarsson G, Lindahl A. (2013) Eur J Pharm Sci. Sept. 25

Validation of quantitative structure–activity relationship models to predict water-solubility of organic compounds.
Cappelli CI, Manganelli S, Lombardo A, Gissi A, Benfenati E. (2013) Science of the Total Environment 463-64:781-89

Dendritic Cell Immunoreceptor Is a New Target for Anti-AIDS Drug Development: Identification of DCIR/HIV-1 Inhibitors.
Lambert AA, Azzi A, Lin SX, Allaire G, St-Gelais KP, Tremblay MJ, Gilbert C. (2013) PLOS ONE

Evaluation and Optimisation of Current Milrinone Prescribing for the Treatment and Prevention of Low Cardiac Output Syndrome in Paediatric Patients After Open Heart Surgery Using a Physiology-Based Pharmacokinetic Drug-Disease Model.
Vogt W. (2013) Clin Pharmacokinet. Jul 10

Similarity-based virtual screening for microtubule stabilizers reveals novel antimitotic scaffold.
Ayouba AT, Klobukowskia M, Tuszynski J. (2013) J. of Mol. Graphics and Model. June 25

Oral delivery of anticancer drugs: Challenges and opportunities.
Thanki K, Gangwal RP, Sangamwar AT, Jain S. (2013) J. Control. Release 170(1):15-40

A Computational Drug-Target Network for Yuanhu Zhitong Prescription.
Xu H, Tao Y, Lu P, Wang P, Zhang F, Yuan Y, Wang S, Xiao X, Yang H, Huang L. (2013) Evidence-Based Complementary and Alternative Medicine, Article ID 658531

Docking and in silico ADMET studies of noraristeromycin, curcumin and its derivatives with Plasmodium falciparum SAH hydrolase: A molecular drug target against malaria.
Singh DB, Gupta MK, Singh DV, Singh SK, Misra K. (2013) Interdiscip Sci. Mar;5(1):1-12

Interaction of Silymarin Flavonolignans with Organic Anion-Transporting Polypeptides.
Köck K, Xie Y, Hawke RL, Oberlies NH, Brouwer KL. (2013) Drug Metab Dispos. May;41(5):958-65

Three-Dimensional Quantitative Structure–Activity Relationship Analysis of Inhibitors of Human and Rat Cytochrome P4503A Enzymes.
Handa K, Nakagome I, Yamaotsu N, Gouda H, Hirono S. (2013) Drug Metab Pharmacokinet. Jan. 29

Interactions of laulimalide, peloruside, and their derivatives with the isoforms of ß-tubulin.
Gajewski MM, Tuszynski JA, Barakat K, Huzil JT, Klobukowskia M. (2013) Canadian J. Chem. Apr 2

In silico modeling to predict drug-induced phospholipidosis
Choi SS, Kim JS, Valerio Jr. LG, Sadrieh N. Toxicol. Appl. Pharmacol. 2013, in press

Optimizing Solubility and Permeability of a Biopharmaceutics Classification System (BCS) Class 4 Antibiotic Drug using Lipophilic Fragments Disturbing the Crystal Lattice.
Tehler U, Fagerberg JH, Svensson R, Larhed M, Artursson P, Bergström CA. (2013) J. Med. Chem. Feb. 25

Interaction of Silymarin Flavonolignans with Organic Anion Transporting Polypeptides (OATPs).
Kock K, Xie1 Y, Oberlies NH, Hawke RL, Brouwer KL. (2013) Drug Metab. Dispos. Feb. 11

Virtual Screening and Biological Evaluation of Inhibitors Targeting the XPA-ERCC1 Interaction.
Barakat KH, Jordheim LP, Perez-Pineiro R, Wishart D, Dumontet C, Tuszynski JA. (2012) PLoS ONE 7(12): e51329

Simulation of the pharmacokinetics of bisoprolol in healthy adults and patients with impaired renal function using whole-body physiologically based pharmacokinetic modeling
Li, G.-f., Wang, K., Chen, R., Zhao, H.-r., Yang, J., and Zheng, Q.-s. Acta Pharmacol. Sin., 33: 1359-1371, 2012.

Nilotinib preclinical pharmacokinetics and practical application toward clinical projections of oral absorption and systemic availability
Xia, B., Heimbach, T., He, H., and Lin, T.-h. Biopharmaceutics & Drug Disposition, web edition, 2012

Regioselective oxidation of phospho-NSAIDs by human cytochrome P450 and flavin monooxygenase isoforms: implications for their pharmacokinetic properties and safety.
Xie G, Wong CC, Cheng KW, Huang L, Constantinides PP, Rigas B. (2012) Br J Pharmacol. 167(1):222-32

Integrated Pharmacokinetic-Driven Approach to Screen Candidate Anticancer Drugs for Brain Tumor Chemotherapy.
Lv H, Zhang X, Sharma J, Reddy MVR, Reddy EP, Gallo JM. (2012) AAPS J. Nov. 22

Toxicological considerations of acetylcholinesterase reactivators.
Voicu V, Radulescu FS, Medvedovici A. (2012) Expert Opinion Drug Metab. and Toxicol. Nov. 24

Dynamic Change of Heme Environment in Soluble Guanylate Cyclase and Complexation of NO-Independent Drug Agents with H-NOX Domain.
Alisaraie L, Fu Y, A Tuszynski J. (2012) Chem Biol Drug Des. Oct. 24

Ethanol Effects on Apparent Solubility of Poorly Soluble Drugs in Simulated Intestinal Fluid.
Fagerberg JH, Al-Tikriti Y, Ragnarsson G, Bergström CA. (2012) Mol. Pharm. June 20

Classification of Inhibitors of Hepatic Organic Anion Transporting Polypeptides (OATPs): Influence of Protein Expression on Drug- Drug Interactions.
Karlgren M, Vildhede A, Norinder U, Wisniewski JR, Kimoto E, Lai Y, Haglund U, Artursson P. (2012) J. Med. Chem. 55(10):4740-63

Parameters for pyrethroid insecticide QSAR and PBPK/PD models for human risk assessment.
Knaak JB, Dary CC, Zhang X, Gerlach RW, Tornero-Velez R, Chang DT, Goldsmith R, Blancato JN. (2012) Rev. Environ. Contam. Toxicol. 219:1-114

Provisional Biopharmaceutical Classification of Some Common Herbs Used in Western Medicine.
Waldmann S, Almukainzi M, Chacra NB, Amidon GL, Lee BJ, Feng J, Kanfer I, Zuo JZ, Wei H, Bolger MB, Löbenberg R. (2012) Mol. Pharm. Feb. 18

In Vitro and In Silico Strategies to Identify OATP1B1 Inhibitors and Predict Clinical Drug–Drug Interactions
Karlgren M, Ahlin G, Bergstrom CAS, Svensson R, Palm J, Artursson P. (2012) Pharm. Res. 29:2, 411-426

Use of structure-activity landscape index curves and curve integrals to evaluate the performance of multiple machine learning prediction models
LeDonne Jr NC, Rissolo K, Bulgarelli J, Tini L. (2011) J. Cheminformatics 3:7

Quantitative Prediction of Regioselectivity Toward Cytochrome P450/3A4 Using Machine Learning Approaches
Hasegawa K, Koyama M, Funatsu K, (2010) Mol. Inf. 29, 243-249

In Silico Classification of Major Clearance Pathways of Drugs with Their Physiochemical Parameters
Kusama M, Toshimoto K, Maeda K, Hirai Y, Imai S, Chiba K, Akiyama Y, Sugiyama Y. (2010) Drug Metab Dispos. 38, 1362-1370

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