1
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Nguyen TTD, Ho QT, Le NQK, Phan VD, Ou YY. Use Chou's 5-Steps Rule With Different Word Embedding Types to Boost Performance of Electron Transport Protein Prediction Model. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2022; 19:1235-1244. [PMID: 32750894 DOI: 10.1109/tcbb.2020.3010975] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Living organisms receive necessary energy substances directly from cellular respiration. The completion of electron storage and transportation requires the process of cellular respiration with the aid of electron transport chains. Therefore, the work of deciphering electron transport proteins is inevitably needed. The identification of these proteins with high performance has a prompt dependence on the choice of methods for feature extraction and machine learning algorithm. In this study, protein sequences served as natural language sentences comprising words. The nominated word embedding-based feature sets, hinged on the word embedding modulation and protein motif frequencies, were useful for feature choosing. Five word embedding types and a variety of conjoint features were examined for such feature selection. The support vector machine algorithm consequentially was employed to perform classification. The performance statistics within the 5-fold cross-validation including average accuracy, specificity, sensitivity, as well as MCC rates surpass 0.95. Such metrics in the independent test are 96.82, 97.16, 95.76 percent, and 0.9, respectively. Compared to state-of-the-art predictors, the proposed method can generate more preferable performance above all metrics indicating the effectiveness of the proposed method in determining electron transport proteins. Furthermore, this study reveals insights about the applicability of various word embeddings for understanding surveyed sequences.
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2
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Khalid M, Ali A, Haq S, Tahir MN, Iqbal J, Braga AA, Ashfaq M, Akhtar SUH. O-4-Acetylamino-benzenesulfonylated pyrimidine derivatives: synthesis, SC-XRD, DFT analysis and electronic behaviour investigation. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2020.129308] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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3
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Ali A, Khalid M, Rehman MFU, Haq S, Ali A, Tahir MN, Ashfaq M, Rasool F, Braga AA. Efficient Synthesis, SC-XRD, and Theoretical Studies of O-Benzenesulfonylated Pyrimidines: Role of Noncovalent Interaction Influence in Their Supramolecular Network. ACS OMEGA 2020; 5:15115-15128. [PMID: 32637784 PMCID: PMC7331070 DOI: 10.1021/acsomega.0c00975] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 06/04/2020] [Indexed: 05/29/2023]
Abstract
Crystalline organic compounds, 2-amino-6-methylpyrimidin-4-yl benzenesulfonate (AMPBS) and 2,6-diaminopyrimidin-4-yl benzenesulfonate (DAPBS), were prepared via O-benzenesulfonylation of 2-amino-6-methylpyrimidin-4-ol 1 and 2,6-diaminopyrimidin-4-ol 2, respectively. The structural interpretations were achieved unambiguously by single-crystal X-ray diffraction (SC-XRD) analysis. The Hirshfeld surface study showed that C-H···O, N-H···N, and especially C-H···C hydrogen bond interactions are the key contributors to the intermolecular stabilization in the crystal. Density functional theory (DFT) studies were used to obtain a better understanding of natural bond orbitals (NBOs) and nonlinear optical (NLO) analysis for AMPBS and DAPBS at the B3LYP/6-311G(d,p) level. The time-dependent density functional theory (TD-DFT)/CAM-B3LYP/6-311G(d,p) level was employed for frontier molecular orbital analysis of both compounds. DFT-based vibrations for C-H, C=N, N-H, and stretching for C-C were found to be in good agreement with the experimental data. Overall, the theoretical findings were acquired in correspondence to the SC-XRD-based parameters. Intracharge transfer occurred in AMPBS and DAPBS compounds, which was evaluated through FMO activity. Global reactivity indices had been acquired utilizing energies of HOMO-LUMO orbitals. Overall, the theoretical findings related to AMPBS and DAPBS consist of promising correspondence to experimental findings. The theoretical-based study also exhibited that both AMPBS and DAPBS compounds contain promising NLO features.
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Affiliation(s)
- Akbar Ali
- Department
of Chemistry, University of Sargodha, Sargodha 40100, Pakistan
| | - Muhammad Khalid
- Department
of Chemistry, Khwaja Fareed University of
Engineering & Information Technology, Rahim Yar Khan 64200, Pakistan
| | | | - Sadia Haq
- Department
of Chemistry, Khwaja Fareed University of
Engineering & Information Technology, Rahim Yar Khan 64200, Pakistan
| | - Arif Ali
- Department
of Physics, University of Sargodha, Sargodha 40100, Pakistan
| | | | - Muhammad Ashfaq
- Department
of Physics, University of Sargodha, Sargodha 40100, Pakistan
| | - Faiz Rasool
- Department
of Chemistry, Khwaja Fareed University of
Engineering & Information Technology, Rahim Yar Khan 64200, Pakistan
| | - Ataualpa Albert
Carmo Braga
- Departamento
de Química Fundamental, Instituto de Química, Universidade de São Paulo, Avenida Professor Lineu Prestes, 748, São Paulo 05508-000, Brazil
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4
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Abstract
During the last three decades or so, many efforts have been made to study the protein cleavage
sites by some disease-causing enzyme, such as HIV (Human Immunodeficiency Virus) protease
and SARS (Severe Acute Respiratory Syndrome) coronavirus main proteinase. It has become increasingly
clear <i>via</i> this mini-review that the motivation driving the aforementioned studies is quite wise,
and that the results acquired through these studies are very rewarding, particularly for developing peptide
drugs.
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Affiliation(s)
- Kuo-Chen Chou
- Gordon Life Science Institute, Boston, MA 02478, United States
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5
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Chou KC. An Insightful 10-year Recollection Since the Emergence of the 5-steps Rule. Curr Pharm Des 2020; 25:4223-4234. [PMID: 31782354 DOI: 10.2174/1381612825666191129164042] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 11/25/2019] [Indexed: 11/22/2022]
Abstract
OBJECTIVE One of the most challenging and also the most difficult problems is how to formulate a biological sequence with a vector but considerably keep its sequence order information. METHODS To address such a problem, the approach of Pseudo Amino Acid Components or PseAAC has been developed. RESULTS AND CONCLUSION It has become increasingly clear via the 10-year recollection that the aforementioned proposal has been indeed very powerful.
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Affiliation(s)
- Kuo-Chen Chou
- Gordon Life Science Institute, Boston, Massachusetts 02478, United States.,Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
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6
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7
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8
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Identifying FL11 subtype by characterizing tumor immune microenvironment in prostate adenocarcinoma via Chou's 5-steps rule. Genomics 2020; 112:1500-1515. [DOI: 10.1016/j.ygeno.2019.08.021] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 08/03/2019] [Accepted: 08/26/2019] [Indexed: 12/14/2022]
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9
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Zheng H, Yang H, Gong D, Mai L, Qiu X, Chen L, Su X, Wei R, Zeng Z. Progress in the Mechanism and Clinical Application of Cilostazol. Curr Top Med Chem 2020; 19:2919-2936. [PMID: 31763974 DOI: 10.2174/1568026619666191122123855] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 07/27/2019] [Accepted: 08/02/2019] [Indexed: 12/20/2022]
Abstract
Cilostazol is a unique platelet inhibitor that has been used clinically for more than 20 years. As a phosphodiesterase type III inhibitor, cilostazol is capable of reversible inhibition of platelet aggregation and vasodilation, has antiproliferative effects, and is widely used in the treatment of peripheral arterial disease, cerebrovascular disease, percutaneous coronary intervention, etc. This article briefly reviews the pharmacological mechanisms and clinical application of cilostazol.
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Affiliation(s)
- Huilei Zheng
- Department of Medical Examination & Health Management, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China.,Guangxi Key Laboratory of Precision Medicine in Cardio-cerebrovascular Diseases Control and Prevention,Nanning, Guangxi, China.,Guangxi Clinical Research Center for Cardio-cerebrovascular Diseases, Nanning, Guangxi, China
| | - Hua Yang
- Guangxi Key Laboratory of Precision Medicine in Cardio-cerebrovascular Diseases Control and Prevention,Nanning, Guangxi, China.,Guangxi Clinical Research Center for Cardio-cerebrovascular Diseases, Nanning, Guangxi, China.,Department of Critical Care Medicine, Second People's Hospital of Nanning, Nanning, Guangxi, China
| | - Danping Gong
- Guangxi Key Laboratory of Precision Medicine in Cardio-cerebrovascular Diseases Control and Prevention,Nanning, Guangxi, China.,Guangxi Clinical Research Center for Cardio-cerebrovascular Diseases, Nanning, Guangxi, China.,Elderly Cardiology Ward, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Lanxian Mai
- Guangxi Key Laboratory of Precision Medicine in Cardio-cerebrovascular Diseases Control and Prevention,Nanning, Guangxi, China.,Guangxi Clinical Research Center for Cardio-cerebrovascular Diseases, Nanning, Guangxi, China.,Disciplinary Construction Office, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Xiaoling Qiu
- Guangxi Key Laboratory of Precision Medicine in Cardio-cerebrovascular Diseases Control and Prevention,Nanning, Guangxi, China.,Guangxi Clinical Research Center for Cardio-cerebrovascular Diseases, Nanning, Guangxi, China
| | - Lidai Chen
- Guangxi Key Laboratory of Precision Medicine in Cardio-cerebrovascular Diseases Control and Prevention,Nanning, Guangxi, China.,Guangxi Clinical Research Center for Cardio-cerebrovascular Diseases, Nanning, Guangxi, China
| | - Xiaozhou Su
- Guangxi Key Laboratory of Precision Medicine in Cardio-cerebrovascular Diseases Control and Prevention,Nanning, Guangxi, China.,Guangxi Clinical Research Center for Cardio-cerebrovascular Diseases, Nanning, Guangxi, China
| | - Ruoqi Wei
- Department of Computer Science and Engineering, University of Bridgeport,126 Park Ave, BRIDGEPORT, CT 06604, United States
| | - Zhiyu Zeng
- Guangxi Key Laboratory of Precision Medicine in Cardio-cerebrovascular Diseases Control and Prevention,Nanning, Guangxi, China.,Guangxi Clinical Research Center for Cardio-cerebrovascular Diseases, Nanning, Guangxi, China.,Elderly Cardiology Ward, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
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10
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Chou KC. Impacts of Pseudo Amino Acid Components and 5-steps Rule to Proteomics and Proteome Analysis. Curr Top Med Chem 2019; 19:2283-2300. [DOI: 10.2174/1568026619666191018100141] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 08/18/2019] [Accepted: 08/26/2019] [Indexed: 01/27/2023]
Abstract
Stimulated by the 5-steps rule during the last decade or so, computational proteomics has achieved remarkable progresses in the following three areas: (1) protein structural class prediction; (2) protein subcellular location prediction; (3) post-translational modification (PTM) site prediction. The results obtained by these predictions are very useful not only for an in-depth study of the functions of proteins and their biological processes in a cell, but also for developing novel drugs against major diseases such as cancers, Alzheimer’s, and Parkinson’s. Moreover, since the targets to be predicted may have the multi-label feature, two sets of metrics are introduced: one is for inspecting the global prediction quality, while the other for the local prediction quality. All the predictors covered in this review have a userfriendly web-server, through which the majority of experimental scientists can easily obtain their desired data without the need to go through the complicated mathematics.
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Affiliation(s)
- Kuo-Chen Chou
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, 610054, China
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11
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Chou KC. Proposing Pseudo Amino Acid Components is an Important Milestone for Proteome and Genome Analyses. Int J Pept Res Ther 2019. [DOI: 10.1007/s10989-019-09910-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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12
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Jiang QX. Structural Variability in the RLR-MAVS Pathway and Sensitive Detection of Viral RNAs. Med Chem 2019; 15:443-458. [PMID: 30569868 DOI: 10.2174/1573406415666181219101613] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 10/23/2018] [Accepted: 12/12/2018] [Indexed: 12/25/2022]
Abstract
Cells need high-sensitivity detection of non-self molecules in order to fight against pathogens. These cellular sensors are thus of significant importance to medicinal purposes, especially for treating novel emerging pathogens. RIG-I-like receptors (RLRs) are intracellular sensors for viral RNAs (vRNAs). Their active forms activate mitochondrial antiviral signaling protein (MAVS) and trigger downstream immune responses against viral infection. Functional and structural studies of the RLR-MAVS signaling pathway have revealed significant supramolecular variability in the past few years, which revealed different aspects of the functional signaling pathway. Here I will discuss the molecular events of RLR-MAVS pathway from the angle of detecting single copy or a very low copy number of vRNAs in the presence of non-specific competition from cytosolic RNAs, and review key structural variability in the RLR / vRNA complexes, the MAVS helical polymers, and the adapter-mediated interactions between the active RLR / vRNA complex and the inactive MAVS in triggering the initiation of the MAVS filaments. These structural variations may not be exclusive to each other, but instead may reflect the adaptation of the signaling pathways to different conditions or reach different levels of sensitivity in its response to exogenous vRNAs.
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Affiliation(s)
- Qiu-Xing Jiang
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, United States
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13
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14
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Khan S, Khan M, Iqbal N, Hussain T, Khan SA, Chou KC. A Two-Level Computation Model Based on Deep Learning Algorithm for Identification of piRNA and Their Functions via Chou’s 5-Steps Rule. Int J Pept Res Ther 2019. [DOI: 10.1007/s10989-019-09887-3] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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15
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Qiu WR, Sun BQ, Xiao X, Xu ZC, Chou KC. iHyd-PseCp: Identify hydroxyproline and hydroxylysine in proteins by incorporating sequence-coupled effects into general PseAAC. Oncotarget 2018; 7:44310-44321. [PMID: 27322424 PMCID: PMC5190098 DOI: 10.18632/oncotarget.10027] [Citation(s) in RCA: 141] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 05/29/2016] [Indexed: 12/30/2022] Open
Abstract
Protein hydroxylation is a posttranslational modification (PTM), in which a CH group in Pro (P) or Lys (K) residue has been converted into a COH group, or a hydroxyl group (−OH) is converted into an organic compound. Closely associated with cellular signaling activities, this type of PTM is also involved in some major diseases, such as stomach cancer and lung cancer. Therefore, from the angles of both basic research and drug development, we are facing a challenging problem: for an uncharacterized protein sequence containing many residues of P or K, which ones can be hydroxylated, and which ones cannot? With the explosive growth of protein sequences in the post-genomic age, the problem has become even more urgent. To address such a problem, we have developed a predictor called iHyd-PseCp by incorporating the sequence-coupled information into the general pseudo amino acid composition (PseAAC) and introducing the “Random Forest” algorithm to operate the calculation. Rigorous jackknife tests indicated that the new predictor remarkably outperformed the existing state-of-the-art prediction method for the same purpose. For the convenience of most experimental scientists, a user-friendly web-server for iHyd-PseCp has been established at http://www.jci-bioinfo.cn/iHyd-PseCp, by which users can easily obtain their desired results without the need to go through the complicated mathematical equations involved.
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Affiliation(s)
- Wang-Ren Qiu
- Computer Department, Jingdezhen Ceramic Institute, Jingdezhen, China.,Department of Computer Science and Bond Life Science Center, University of Missouri, Columbia, MO, USA
| | - Bi-Qian Sun
- Computer Department, Jingdezhen Ceramic Institute, Jingdezhen, China
| | - Xuan Xiao
- Computer Department, Jingdezhen Ceramic Institute, Jingdezhen, China.,Gordon Life Science Institute, Boston, MA, USA
| | - Zhao-Chun Xu
- Computer Department, Jingdezhen Ceramic Institute, Jingdezhen, China
| | - Kuo-Chen Chou
- Gordon Life Science Institute, Boston, MA, USA.,Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah, Saudi Arabia.,Center of Bioinformatics, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
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16
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Prediction of HIV-1 and HIV-2 proteins by using Chou's pseudo amino acid compositions and different classifiers. Sci Rep 2018; 8:2359. [PMID: 29402983 PMCID: PMC5799304 DOI: 10.1038/s41598-018-20819-x] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 01/24/2018] [Indexed: 01/02/2023] Open
Abstract
Human immunodeficiency virus (HIV) is the retroviral agent that causes acquired immune deficiency syndrome (AIDS). The number of HIV caused deaths was about 4 million in 2016 alone; it was estimated that about 33 million to 46 million people worldwide living with HIV. The HIV disease is especially harmful because the progressive destruction of the immune system prevents the ability of forming specific antibodies and to maintain an efficacious killer T cell activity. Successful prediction of HIV protein has important significance for the biological and pharmacological functions. In this study, based on the concept of Chou’s pseudo amino acid (PseAA) composition and increment of diversity (ID), support vector machine (SVM), logisitic regression (LR), and multilayer perceptron (MP) were presented to predict HIV-1 proteins and HIV-2 proteins. The results of the jackknife test indicated that the highest prediction accuracy and CC values were obtained by the SVM and MP were 0.9909 and 0.9763, respectively, indicating that the classifiers presented in this study were suitable for predicting two groups of HIV proteins.
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17
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iACP: a sequence-based tool for identifying anticancer peptides. Oncotarget 2017; 7:16895-909. [PMID: 26942877 PMCID: PMC4941358 DOI: 10.18632/oncotarget.7815] [Citation(s) in RCA: 296] [Impact Index Per Article: 42.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 02/11/2016] [Indexed: 02/07/2023] Open
Abstract
Cancer remains a major killer worldwide. Traditional methods of cancer treatment are expensive and have some deleterious side effects on normal cells. Fortunately, the discovery of anticancer peptides (ACPs) has paved a new way for cancer treatment. With the explosive growth of peptide sequences generated in the post genomic age, it is highly desired to develop computational methods for rapidly and effectively identifying ACPs, so as to speed up their application in treating cancer. Here we report a sequence-based predictor called iACP developed by the approach of optimizing the g-gap dipeptide components. It was demonstrated by rigorous cross-validations that the new predictor remarkably outperformed the existing predictors for the same purpose in both overall accuracy and stability. For the convenience of most experimental scientists, a publicly accessible web-server for iACP has been established at http://lin.uestc.edu.cn/server/iACP, by which users can easily obtain their desired results.
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18
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Anharmonic vibrational and electronic spectral study of 2-amino-4-hydroxy-6–methylpyrimidine: A combined experimental (FTIR, FT-Raman, UV–Vis) and theoretical (DFT, MP2) approach. J Mol Struct 2017. [DOI: 10.1016/j.molstruc.2017.07.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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19
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Prabavathi N, Nilufer A. Quantum chemical calculations on elucidation of molecular structure and spectroscopic insights on 2-amino-4-methoxy-6-methylpyrimidine and 2-amino-5-bromo-6-methyl-4-pyrimidinol--a comparative study. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2015; 136 Pt B:192-204. [PMID: 25440582 DOI: 10.1016/j.saa.2014.09.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Revised: 09/04/2014] [Accepted: 09/10/2014] [Indexed: 06/04/2023]
Abstract
The FTIR and FT-Raman spectra of 2-amino-4-methoxy-6-methylpyrimidine (AMMP) and 2-amino-5-bromo-6-methyl-4-pyrimidinol (ABMP) have been recorded in the region 4000-450 and 4000-100 cm(-1), respectively. The optimized geometry, frequency and intensity of the vibrational bands of AMMP and ABMP were obtained by the density functional theory (DFT) using 6-311++G(∗∗) basis set. The harmonic vibrational frequencies were calculated and the scaled values have been compared with experimental FTIR and FT-Raman spectra. The observed and the calculated frequencies are found to be in good agreement. The (1)H and (13)C NMR spectra have been recorded. The (1)H and (13)C nuclear magnetic resonance chemical shifts of the molecule were also calculated using the gauge independent atomic orbital (GIAO) method. The theoretical UV-visible spectrum of the compound using TD-DFT method and the electronic properties, such as HOMO and LUMO energies, are performed by time-dependent DFT (TD-DFT) approach. The calculated HOMO and LUMO energies show that charge transfer occurs within molecule. The first order hyperpolarizability (β0) and its related components of AMMP and ABMP are calculated using DFT/6-311++G(∗∗) method on the finite-field approach. The natural atomic charges of the molecules were also discussed. The change in electron density (ED) in the σ(∗) antibonding orbitals and stabilization energies E(2) have been calculated by natural bond orbital (NBO) analysis to give clear evidence of stabilization originating in the hyper conjugation of hydrogen-bonded interactions.
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Affiliation(s)
- N Prabavathi
- Department of Physics, Sri Sarada College for Women (Autonomous), Salem 636 016, India.
| | - A Nilufer
- Department of Physics, Sri Sarada College for Women (Autonomous), Salem 636 016, India
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20
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Fatemi MH, Heidari A, Gharaghani S. QSAR prediction of HIV-1 protease inhibitory activities using docking derived molecular descriptors. J Theor Biol 2015; 369:13-22. [PMID: 25600056 DOI: 10.1016/j.jtbi.2015.01.008] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Revised: 01/10/2015] [Accepted: 01/12/2015] [Indexed: 01/30/2023]
Abstract
In this study, application of a new hybrid docking-quantitative structure activity relationship (QSAR) methodology to model and predict the HIV-1 protease inhibitory activities of a series of newly synthesized chemicals is reported. This hybrid docking-QSAR approach can provide valuable information about the most important chemical and structural features of the ligands that affect their inhibitory activities. Docking studies were used to find the actual conformations of chemicals in active site of HIV-1 protease. Then the molecular descriptors were calculated from these conformations. Multiple linear regression (MLR) and least square support vector machine (LS-SVM) were used as QSAR models, respectively. The obtained results reveal that statistical parameters of the LS-SVM model are better than the MLR model, which indicate that there are some non-linear relations between selected molecular descriptors and anti-HIV activities of interested chemicals. The correlation coefficient (R), root mean square error (RMSE) and average absolute error (AAE) for LS-SVM are: R=0.988, RMSE=0.207 and AAE=0.145 for the training set, and R=0.965, RMSE=0.403 and AAE=0.338 for the test set. Leave one out cross validation test was used for assessment of the predictive power and validity of models which led to cross-validation correlation coefficient QUOTE of 0.864 and 0.850 and standardized predicted relative error sum of squares (SPRESS) of 0.553 and 0.581 for LS-SVM and MLR models, respectively.
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Affiliation(s)
- Mohammad H Fatemi
- Chemometrics Laboratory, Faculty of Chemistry, University of Mazandaran, Babolsar 47416-95447, Iran.
| | - Afsane Heidari
- Chemometrics Laboratory, Faculty of Chemistry, University of Mazandaran, Babolsar 47416-95447, Iran
| | - Sajjad Gharaghani
- Department of Bioinformatics, Laboratory of Chemoinformatics, Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
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21
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iSS-PseDNC: identifying splicing sites using pseudo dinucleotide composition. BIOMED RESEARCH INTERNATIONAL 2014; 2014:623149. [PMID: 24967386 PMCID: PMC4055483 DOI: 10.1155/2014/623149] [Citation(s) in RCA: 97] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Revised: 04/22/2014] [Accepted: 04/23/2014] [Indexed: 11/17/2022]
Abstract
In eukaryotic genes, exons are generally interrupted by introns. Accurately removing introns and joining exons together are essential processes in eukaryotic gene expression. With the avalanche of genome sequences generated in the postgenomic age, it is highly desired to develop automated methods for rapid and effective detection of splice sites that play important roles in gene structure annotation and even in RNA splicing. Although a series of computational methods were proposed for splice site identification, most of them neglected the intrinsic local structural properties. In the present study, a predictor called “iSS-PseDNC” was developed for identifying splice sites. In the new predictor, the sequences were formulated by a novel feature-vector called “pseudo dinucleotide composition” (PseDNC) into which six DNA local structural properties were incorporated. It was observed by the rigorous cross-validation tests on two benchmark datasets that the overall success rates achieved by iSS-PseDNC in identifying splice donor site and splice acceptor site were 85.45% and 87.73%, respectively. It is anticipated that iSS-PseDNC may become a useful tool for identifying splice sites and that the six DNA local structural properties described in this paper may provide novel insights for in-depth investigations into the mechanism of RNA splicing.
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22
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Ivetac A, Swift SE, Boyer PL, Diaz A, Naughton J, Young JAT, Hughes SH, McCammon JA. Discovery of novel inhibitors of HIV-1 reverse transcriptase through virtual screening of experimental and theoretical ensembles. Chem Biol Drug Des 2014; 83:521-31. [PMID: 24405985 DOI: 10.1111/cbdd.12277] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Accepted: 12/16/2013] [Indexed: 12/31/2022]
Abstract
Non-nucleoside reverse transcriptase inhibitors (NNRTIs) are potent anti-HIV chemotherapeutics. Although there are FDA-approved NNRTIs, challenges such as the development of resistance have limited their utility. Here, we describe the identification of novel NNRTIs through a combination of computational and experimental approaches. Based on the known plasticity of the NNRTI binding pocket (NNIBP), we adopted an ensemble-based virtual screening strategy: coupling receptor conformations from 10 X-ray crystal structures with 120 snapshots from a total of 480 ns of molecular dynamics (MD) trajectories. A screening library of 2864 National Cancer Institute (NCI) compounds was built and docked against the ensembles in a hierarchical fashion. Sixteen diverse compounds were tested for their ability to block HIV infection in human tissue cultures using a luciferase-based reporter assay. Three promising compounds were further characterized, using a HIV-1 RT-based polymerase assay, to determine the specific mechanism of inhibition. We found that 2 of the three compounds inhibited the polymerase activity of RT (with potency similar to the positive control, the FDA-approved drug nevirapine). Through a computational approach, we were able to discover two compounds which inhibit HIV replication and block the activity of RT, thus offering the potential for optimization into mature inhibitors.
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Affiliation(s)
- Anthony Ivetac
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, CA, 92093-0365, USA
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Fernández-Blanco E, Aguiar-Pulido V, Munteanu CR, Dorado J. Random Forest classification based on star graph topological indices for antioxidant proteins. J Theor Biol 2013; 317:331-7. [DOI: 10.1016/j.jtbi.2012.10.006] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2012] [Revised: 09/17/2012] [Accepted: 10/02/2012] [Indexed: 10/27/2022]
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24
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Genc M, Yılmaz E, Ilhan S, Karagoz Z. Synthesis, antihistaminic action and theoretical studies of (4-methoxybenzyl)(1,4,5,6-tetrahydropirimidin-2-yl)amine hydroiodide. RESEARCH ON CHEMICAL INTERMEDIATES 2012. [DOI: 10.1007/s11164-012-0813-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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25
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Fernandez-Blanco E, Rivero D, Rabuñal J, Dorado J, Pazos A, Munteanu CR. Automatic seizure detection based on star graph topological indices. J Neurosci Methods 2012; 209:410-9. [DOI: 10.1016/j.jneumeth.2012.07.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2012] [Revised: 06/28/2012] [Accepted: 07/10/2012] [Indexed: 11/27/2022]
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Aguiar-Pulido V, Munteanu CR, Seoane JA, Fernández-Blanco E, Pérez-Montoto LG, González-Díaz H, Dorado J. Naïve Bayes QSDR classification based on spiral-graph Shannon entropies for protein biomarkers in human colon cancer. MOLECULAR BIOSYSTEMS 2012; 8:1716-22. [PMID: 22466084 DOI: 10.1039/c2mb25039j] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Fast cancer diagnosis represents a real necessity in applied medicine due to the importance of this disease. Thus, theoretical models can help as prediction tools. Graph theory representation is one option because it permits us to numerically describe any real system such as the protein macromolecules by transforming real properties into molecular graph topological indices. This study proposes a new classification model for proteins linked with human colon cancer by using spiral graph topological indices of protein amino acid sequences. The best quantitative structure-disease relationship model is based on eleven Shannon entropy indices. It was obtained with the Naïve Bayes method and shows excellent predictive ability (90.92%) for new proteins linked with this type of cancer. The statistical analysis confirms that this model allows diagnosing the absence of human colon cancer obtaining an area under receiver operating characteristic of 0.91. The methodology presented can be used for any type of sequential information such as any protein and nucleic acid sequence.
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Affiliation(s)
- Vanessa Aguiar-Pulido
- Department of Information and Communications Technologies, University of A Coruña, A Coruña, Spain
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27
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Zhan P, Chen X, Li D, Fang Z, De Clercq E, Liu X. HIV-1 NNRTIs: structural diversity, pharmacophore similarity, and implications for drug design. Med Res Rev 2011; 33 Suppl 1:E1-72. [PMID: 21523792 DOI: 10.1002/med.20241] [Citation(s) in RCA: 152] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Nonnucleoside reverse transcriptase inhibitors (NNRTIs) nowadays represent very potent and most promising anti-AIDS agents that specifically target the HIV-1 reverse transcriptase (RT). However, the effectiveness of NNRTI drugs can be hampered by rapid emergence of drug-resistant viruses and severe side effects upon long-term use. Therefore, there is an urgent need to develop novel, highly potent NNRTIs with broad spectrum antiviral activity and improved pharmacokinetic properties, and more efficient strategies that facilitate and shorten the drug discovery process would be extremely beneficial. Fortunately, the structural diversity of NNRTIs provided a wide space for novel lead discovery, and the pharmacophore similarity of NNRTIs gave valuable hints for lead discovery and optimization. More importantly, with the continued efforts in the development of computational tools and increased crystallographic information on RT/NNRTI complexes, structure-based approaches using a combination of traditional medicinal chemistry, structural biology, and computational chemistry are being used increasingly in the design of NNRTIs. First, this review covers two decades of research and development for various NNRTI families based on their chemical scaffolds, and then describes the structural similarity of NNRTIs. We have attempted to assemble a comprehensive overview of the general approaches in NNRTI lead discovery and optimization reported in the literature during the last decade. The successful applications of medicinal chemistry strategies, crystallography, and computational tools for designing novel NNRTIs are highlighted. Future directions for research are also outlined.
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Affiliation(s)
- Peng Zhan
- Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Shandong University, Jinan, Shandong, PR China
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28
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Wyrzykiewicz E, Mielcarek S, Migoń A, Badura J. Thio Analogs of Pyrimidine Bases: Syntheses, EIMS and 13 C NMR Study of New Ortho -( Meta - and Para -) Substituted Derivatives of 2-benzylthio-5-bromo-6-methyluracils. PHOSPHORUS SULFUR 2010. [DOI: 10.1080/10426500210677] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
| | | | - Anna Migoń
- a Faculty of Chemistry , Adam Mickiewicz University , Poznań, Poland
| | - Jolanta Badura
- a Faculty of Chemistry , Adam Mickiewicz University , Poznań, Poland
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El-Shafei A, Fadda AA, Bondock S, Khalil AM, Tawfik EH. Facile Synthesis, Pure DFT Calculations, and PM3 Semiempirical MO Method Validation of Regiospecificity of Novel 1,4-Dihydropyrido[2,3-d]pyrimidine Derivatives. SYNTHETIC COMMUN 2010. [DOI: 10.1080/00397910903534015] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- A. El-Shafei
- a Fiber and Polymer Chemistry Program, North Carolina State University , Raleigh, North Carolina, USA
| | - A. A. Fadda
- b Faculty of Science, Department of Chemistry , Mansoura University , Mansoura, Egypt
| | - S. Bondock
- b Faculty of Science, Department of Chemistry , Mansoura University , Mansoura, Egypt
| | - A. M. Khalil
- b Faculty of Science, Department of Chemistry , Mansoura University , Mansoura, Egypt
| | - Eman H. Tawfik
- b Faculty of Science, Department of Chemistry , Mansoura University , Mansoura, Egypt
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Pérez-Montoto LG, Santana L, González-Díaz H. Scoring function for DNA-drug docking of anticancer and antiparasitic compounds based on spectral moments of 2D lattice graphs for molecular dynamics trajectories. Eur J Med Chem 2009; 44:4461-9. [PMID: 19604606 PMCID: PMC7127518 DOI: 10.1016/j.ejmech.2009.06.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2009] [Revised: 06/04/2009] [Accepted: 06/05/2009] [Indexed: 02/02/2023]
Abstract
We introduce here a new class of invariants for MD trajectories based on the spectral moments pi(k)(L) of the Markov matrix associated to lattice network-like (LN) graph representations of Molecular Dynamics (MD) trajectories. The procedure embeds the MD energy profiles on a 2D Cartesian coordinates system using simple heuristic rules. At the same time, we associate the LN with a Markov matrix that describes the probabilities of passing from one state to other in the new 2D space. We construct this type of LNs for 422 MD trajectories obtained in DNA-drug docking experiments of 57 furocoumarins. The combined use of psoralens+ultraviolet light (UVA) radiation is known as PUVA therapy. PUVA is effective in the treatment of skin diseases such as psoriasis and mycosis fungoides. PUVA is also useful to treat human platelet (PTL) concentrates in order to eliminate Leishmania spp. and Trypanosoma cruzi. Both are parasites that cause Leishmaniosis (a dangerous skin and visceral disease) and Chagas disease, respectively; and may circulate in blood products collected from infected donors. We included in this study both lineal (psoralens) and angular (angelicins) furocoumarins. In the study, we grouped the LNs on two sets; set1: DNA-drug complex MD trajectories for active compounds and set2: MD trajectories of non-active compounds or no-optimal MD trajectories of active compounds. We calculated the respective pi(k)(L) values for all these LNs and used them as inputs to train a new classifier that discriminate set1 from set2 cases. In training series the model correctly classifies 79 out of 80 (specificity=98.75%) set1 and 226 out of 238 (Sensitivity=94.96%) set2 trajectories. In independent validation series the model correctly classifies 26 out of 26 (specificity=100%) set1 and 75 out of 78 (sensitivity=96.15%) set2 trajectories. We propose this new model as a scoring function to guide DNA-docking studies in the drug design of new coumarins for anticancer or antiparasitic PUVA therapy.
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Affiliation(s)
- Lázaro G. Pérez-Montoto
- Department of Microbiology & Parasitology, and Department of Organic Chemistry
- Faculty of Pharmacy, University of Santiago de Compostela, 15782, Spain
| | - Lourdes Santana
- Faculty of Pharmacy, University of Santiago de Compostela, 15782, Spain
| | - Humberto González-Díaz
- Department of Microbiology & Parasitology, and Department of Organic Chemistry
- Faculty of Pharmacy, University of Santiago de Compostela, 15782, Spain
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31
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Munteanu CR, Vázquez JM, Dorado J, Sierra AP, Sánchez-González Á, Prado-Prado FJ, González-Díaz H. Complex Network Spectral Moments for ATCUN Motif DNA Cleavage: First Predictive Study on Proteins of Human Pathogen Parasites. J Proteome Res 2009; 8:5219-28. [DOI: 10.1021/pr900556g] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Cristian R. Munteanu
- Department of Information and Communication Technologies, Computer Science Faculty, University of A Coruña, Campus de Elviña, s/n 15071 A Coruña, Spain, Department of Inorganic Chemistry, Faculty of Pharmacy, University of Santiago de Compostela, Praza Seminario de Estudos Galegos, s/n. Campus sur, 15782 Santiago de Compostela, Spain, and Department of Microbiology & Parasitology, Faculty of Pharmacy, University of Santiago de Compostela, Praza Seminario de Estudos Galegos, s/n. Campus sur, 15782
| | - José M. Vázquez
- Department of Information and Communication Technologies, Computer Science Faculty, University of A Coruña, Campus de Elviña, s/n 15071 A Coruña, Spain, Department of Inorganic Chemistry, Faculty of Pharmacy, University of Santiago de Compostela, Praza Seminario de Estudos Galegos, s/n. Campus sur, 15782 Santiago de Compostela, Spain, and Department of Microbiology & Parasitology, Faculty of Pharmacy, University of Santiago de Compostela, Praza Seminario de Estudos Galegos, s/n. Campus sur, 15782
| | - Julián Dorado
- Department of Information and Communication Technologies, Computer Science Faculty, University of A Coruña, Campus de Elviña, s/n 15071 A Coruña, Spain, Department of Inorganic Chemistry, Faculty of Pharmacy, University of Santiago de Compostela, Praza Seminario de Estudos Galegos, s/n. Campus sur, 15782 Santiago de Compostela, Spain, and Department of Microbiology & Parasitology, Faculty of Pharmacy, University of Santiago de Compostela, Praza Seminario de Estudos Galegos, s/n. Campus sur, 15782
| | - Alejandro Pazos Sierra
- Department of Information and Communication Technologies, Computer Science Faculty, University of A Coruña, Campus de Elviña, s/n 15071 A Coruña, Spain, Department of Inorganic Chemistry, Faculty of Pharmacy, University of Santiago de Compostela, Praza Seminario de Estudos Galegos, s/n. Campus sur, 15782 Santiago de Compostela, Spain, and Department of Microbiology & Parasitology, Faculty of Pharmacy, University of Santiago de Compostela, Praza Seminario de Estudos Galegos, s/n. Campus sur, 15782
| | - Ángeles Sánchez-González
- Department of Information and Communication Technologies, Computer Science Faculty, University of A Coruña, Campus de Elviña, s/n 15071 A Coruña, Spain, Department of Inorganic Chemistry, Faculty of Pharmacy, University of Santiago de Compostela, Praza Seminario de Estudos Galegos, s/n. Campus sur, 15782 Santiago de Compostela, Spain, and Department of Microbiology & Parasitology, Faculty of Pharmacy, University of Santiago de Compostela, Praza Seminario de Estudos Galegos, s/n. Campus sur, 15782
| | - Francisco J. Prado-Prado
- Department of Information and Communication Technologies, Computer Science Faculty, University of A Coruña, Campus de Elviña, s/n 15071 A Coruña, Spain, Department of Inorganic Chemistry, Faculty of Pharmacy, University of Santiago de Compostela, Praza Seminario de Estudos Galegos, s/n. Campus sur, 15782 Santiago de Compostela, Spain, and Department of Microbiology & Parasitology, Faculty of Pharmacy, University of Santiago de Compostela, Praza Seminario de Estudos Galegos, s/n. Campus sur, 15782
| | - Humberto González-Díaz
- Department of Information and Communication Technologies, Computer Science Faculty, University of A Coruña, Campus de Elviña, s/n 15071 A Coruña, Spain, Department of Inorganic Chemistry, Faculty of Pharmacy, University of Santiago de Compostela, Praza Seminario de Estudos Galegos, s/n. Campus sur, 15782 Santiago de Compostela, Spain, and Department of Microbiology & Parasitology, Faculty of Pharmacy, University of Santiago de Compostela, Praza Seminario de Estudos Galegos, s/n. Campus sur, 15782
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Generalized lattice graphs for 2D-visualization of biological information. J Theor Biol 2009; 261:136-47. [PMID: 19646452 PMCID: PMC7094121 DOI: 10.1016/j.jtbi.2009.07.029] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2009] [Revised: 07/18/2009] [Accepted: 07/20/2009] [Indexed: 01/09/2023]
Abstract
Several graph representations have been introduced for different data in theoretical biology. For instance, complex networks based on Graph theory are used to represent the structure and/or dynamics of different large biological systems such as protein–protein interaction networks. In addition, Randic, Liao, Nandy, Basak, and many others developed some special types of graph-based representations. This special type of graph includes geometrical constrains to node positioning in space and adopts final geometrical shapes that resemble lattice-like patterns. Lattice networks have been used to visually depict DNA and protein sequences but they are very flexible. However, despite the proved efficacy of new lattice-like graph/networks to represent diverse systems, most works focus on only one specific type of biological data. This work proposes a generalized type of lattice and illustrates how to use it in order to represent and compare biological data from different sources. We exemplify the following cases: protein sequence; mass spectra (MS) of protein peptide mass fingerprints (PMF); molecular dynamic trajectory (MDTs) from structural studies; mRNA microarray data; single nucleotide polymorphisms (SNPs); 1D or 2D-Electrophoresis study of protein polymorphisms and protein-research patent and/or copyright information. We used data available from public sources for some examples but for other, we used experimental results reported herein for the first time. This work may break new ground for the application of Graph theory in theoretical biology and other areas of biomedical sciences.
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Pérez-Montoto LG, Dea-Ayuela MA, Prado-Prado FJ, Bolas-Fernández F, Ubeira FM, González-Díaz H. Study of peptide fingerprints of parasite proteins and drug-DNA interactions with Markov-Mean-Energy invariants of biopolymer molecular-dynamic lattice networks. POLYMER 2009; 50:3857-3870. [PMID: 32287404 PMCID: PMC7111648 DOI: 10.1016/j.polymer.2009.05.055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2009] [Revised: 05/06/2009] [Accepted: 05/14/2009] [Indexed: 11/26/2022]
Abstract
Since the advent of Molecular Dynamics (MD) in biopolymers science with the study by Karplus et al. on protein dynamics, MD has become the by foremost well established, computational technique to investigate structure and function of biomolecules and their respective complexes and interactions. The analysis of the MD trajectories (MDTs) remains, however, the greatest challenge and requires a great deal of insight, experience, and effort. Here, we introduce a new class of invariants for MDTs based on the spatial distribution of Mean-Energy values ξk (L) on a 2D Euclidean space representation of the MDTs. The procedure forces one MD trajectory to fold into a 2D Cartesian coordinates system using a step-by-step procedure driven by simple rules. The ξk (L) values are invariants of a Markov matrix (1 Π), which describes the probabilities of transition between two states in the new 2D space; which is associated to a graph representation of MDTs similar to the lattice networks (LNs) of DNA and protein sequences. We also introduce a new algorithm to perform phylogenetic analysis of peptides based on MDTs instead of the sequence of the polypeptide. In a first experiment, we illustrate this algorithm for 35 peptides present on the Peptide Mass Fingerprint (PMF) of a new protein of Leishmania infantum studied in this work. We report, by the first time, 2D Electrophoresis isolation, MALDI TOF Mass Spectroscopy characterization, and MASCOT search results for this PMF. In a second experiment, we construct the LNs for 422 MDTs obtained in DNA-Drug Docking simulations of the interaction of 57 anticancer furocoumarins with a DNA oligonucleotide. We calculated the respective ξk (L) values for all these LNs and used them as inputs to train a new classifier with Accuracy = 85.44% and 84.91% in training and validation respectively. The new model can be used as scoring function to guide DNA-Drug Docking studies in drug design of new coumarins for PUVA therapy. The new phylogenetics analysis algorithms encode information different from sequence similarity and may be used to analyze MDTs obtained in Docking or modeling experiments for any classes of biopolymers. The work opens new perspective on the analysis and applications of MD in polymer sciences.
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Affiliation(s)
- Lázaro Guillermo Pérez-Montoto
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain,Department of Organic Chemistry, Faculty of Pharmacy, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - María Auxiliadora Dea-Ayuela
- Departamento de Atención Sanitaria, Salud Pública y Sanidad Animal, Facultad CC Experimentales y de La Salud, Universidad CEU Cardenal Herrera, 46113 Moncada (Valencia), Spain
| | - Francisco J. Prado-Prado
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain,Department of Organic Chemistry, Faculty of Pharmacy, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | | | - Florencio M. Ubeira
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Humberto González-Díaz
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain,Corresponding author. Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain
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Prajapati DG, Ramajayam R, Yadav MR, Giridhar R. The search for potent, small molecule NNRTIs: A review. Bioorg Med Chem 2009; 17:5744-62. [PMID: 19632850 DOI: 10.1016/j.bmc.2009.06.060] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2009] [Revised: 06/22/2009] [Accepted: 06/23/2009] [Indexed: 11/29/2022]
Abstract
AIDS has become the leading pandemic disease, and is the cause of death worldwide. Presently, HAART treatment, a combination of reverse transcriptase (RT) and protease inhibitors is also unsuccessful due to the virus getting resistant to the drugs because of mutational changes. Two types of RT inhibitors exist namely nucleoside reverse transcriptase inhibitors (NRTIs) and non-nucleoside reverse transcriptase inhibitors (NNRTIs). The NNRTIs which bind to an allosteric site on RT are an important arsenal of drugs against HIV-1. The specificity of NNRTIs towards HIV-1 has led to extensive structural and molecular modelling studies of enzyme complexes and chemical synthesis of second and third-generation NNRTIs. The major drawbacks of NNRTIs are generation of resistance and pharmacokinetic problems. By mutational studies of non-nucleoside inhibitor binding pocket (NNIBP) some amino acids which were found to play an important role in proper binding resulted less prone to mutation. In this review we present a chronological history of NNRTI development, also highlighting the need for small molecules belonging to the NNRTI class for the management of AIDS.
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Affiliation(s)
- Dhaval G Prajapati
- Pharmacy Department, Kalabhavan, The M.S. University of Baroda, Vadodara, India
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Agüero-Chapin G, Varona-Santos J, de la Riva GA, Antunes A, González-Villa T, Uriarte E, González-Díaz H. Alignment-Free Prediction of Polygalacturonases with Pseudofolding Topological Indices: Experimental Isolation from Coffea arabica and Prediction of a New Sequence. J Proteome Res 2009; 8:2122-8. [DOI: 10.1021/pr800867y] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Guillermín Agüero-Chapin
- Unit of Bioinformatics & Connectivity Analysis (UBICA), Institute of Industrial Pharmacy, Department of Organic Chemistry, Faculty of Pharmacy, University of Santiago de Compostela, Santiago de Compostela (USC), 15782, Spain, CBQ, Central University of Las Villas, 54830, Santa Clara, Cuba, CIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Rua dos Bragas, 177, 4050-123 Porto, Portugal, Sylvester Comprehensive Cancer Center, University of Miami, Miami, Florida 33136
| | - Javier Varona-Santos
- Unit of Bioinformatics & Connectivity Analysis (UBICA), Institute of Industrial Pharmacy, Department of Organic Chemistry, Faculty of Pharmacy, University of Santiago de Compostela, Santiago de Compostela (USC), 15782, Spain, CBQ, Central University of Las Villas, 54830, Santa Clara, Cuba, CIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Rua dos Bragas, 177, 4050-123 Porto, Portugal, Sylvester Comprehensive Cancer Center, University of Miami, Miami, Florida 33136
| | - Gustavo A. de la Riva
- Unit of Bioinformatics & Connectivity Analysis (UBICA), Institute of Industrial Pharmacy, Department of Organic Chemistry, Faculty of Pharmacy, University of Santiago de Compostela, Santiago de Compostela (USC), 15782, Spain, CBQ, Central University of Las Villas, 54830, Santa Clara, Cuba, CIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Rua dos Bragas, 177, 4050-123 Porto, Portugal, Sylvester Comprehensive Cancer Center, University of Miami, Miami, Florida 33136
| | - Agostinho Antunes
- Unit of Bioinformatics & Connectivity Analysis (UBICA), Institute of Industrial Pharmacy, Department of Organic Chemistry, Faculty of Pharmacy, University of Santiago de Compostela, Santiago de Compostela (USC), 15782, Spain, CBQ, Central University of Las Villas, 54830, Santa Clara, Cuba, CIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Rua dos Bragas, 177, 4050-123 Porto, Portugal, Sylvester Comprehensive Cancer Center, University of Miami, Miami, Florida 33136
| | - Tomás González-Villa
- Unit of Bioinformatics & Connectivity Analysis (UBICA), Institute of Industrial Pharmacy, Department of Organic Chemistry, Faculty of Pharmacy, University of Santiago de Compostela, Santiago de Compostela (USC), 15782, Spain, CBQ, Central University of Las Villas, 54830, Santa Clara, Cuba, CIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Rua dos Bragas, 177, 4050-123 Porto, Portugal, Sylvester Comprehensive Cancer Center, University of Miami, Miami, Florida 33136
| | - Eugenio Uriarte
- Unit of Bioinformatics & Connectivity Analysis (UBICA), Institute of Industrial Pharmacy, Department of Organic Chemistry, Faculty of Pharmacy, University of Santiago de Compostela, Santiago de Compostela (USC), 15782, Spain, CBQ, Central University of Las Villas, 54830, Santa Clara, Cuba, CIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Rua dos Bragas, 177, 4050-123 Porto, Portugal, Sylvester Comprehensive Cancer Center, University of Miami, Miami, Florida 33136
| | - Humberto González-Díaz
- Unit of Bioinformatics & Connectivity Analysis (UBICA), Institute of Industrial Pharmacy, Department of Organic Chemistry, Faculty of Pharmacy, University of Santiago de Compostela, Santiago de Compostela (USC), 15782, Spain, CBQ, Central University of Las Villas, 54830, Santa Clara, Cuba, CIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Rua dos Bragas, 177, 4050-123 Porto, Portugal, Sylvester Comprehensive Cancer Center, University of Miami, Miami, Florida 33136
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Munteanu CR, Magalhães AL, Uriarte E, González-Díaz H. Multi-target QPDR classification model for human breast and colon cancer-related proteins using star graph topological indices. J Theor Biol 2008; 257:303-11. [PMID: 19111559 PMCID: PMC7094125 DOI: 10.1016/j.jtbi.2008.11.017] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2008] [Revised: 11/11/2008] [Accepted: 11/22/2008] [Indexed: 11/07/2022]
Abstract
The cancer diagnostic is a complex process and, sometimes, the specific markers can interfere or produce negative results. Thus, new simple and fast theoretical models are required. One option is the complex network graphs theory that permits us to describe any real system, from the small molecules to the complex genetic, neural or social networks by transforming real properties in topological indices. This work converts the protein primary structure data in specific Randic's star networks topological indices using the new sequence to star networks (S2SNet) application. A set of 1054 proteins were selected from previous works and contains proteins related or not with two types of cancer, human breast cancer (HBC) and human colon cancer (HCC). The general discriminant analysis method generates an input-coded multi-target classification model with the training/predicting set accuracies of 90.0% for the forward stepwise model type. In addition, a protein subset was modified by single amino acid mutations with higher log-odds PAM250 values and tested with the new classification if can be related with HBC or HCC. In conclusion, we shown that, using simple input data such is the primary protein sequence and the simples linear analysis, it is possible to obtain accurate classification models that can predict if a new protein related with two types of cancer. These results promote the use of the S2SNet in clinical proteomics.
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Munteanu CR, González-Díaz H, Borges F, de Magalhães AL. Natural/random protein classification models based on star network topological indices. J Theor Biol 2008; 254:775-83. [PMID: 18692072 PMCID: PMC7094162 DOI: 10.1016/j.jtbi.2008.07.018] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2008] [Revised: 07/09/2008] [Accepted: 07/15/2008] [Indexed: 11/18/2022]
Abstract
The development of the complex network graphs permits us to describe any real system such as social, neural, computer or genetic networks by transforming real properties in topological indices (TIs). This work uses Randic's star networks in order to convert the protein primary structure data in specific topological indices that are used to construct a natural/random protein classification model. The set of natural proteins contains 1046 protein chains selected from the pre-compiled CulledPDB list from PISCES Dunbrack's Web Lab. This set is characterized by a protein homology of 20%, a structure resolution of 1.6 Å and R-factor lower than 25%. The set of random amino acid chains contains 1046 sequences which were generated by Python script according to the same type of residues and average chain length found in the natural set. A new Sequence to Star Networks (S2SNet) wxPython GUI application (with a Graphviz graphics back-end) was designed by our group in order to transform any character sequence in the following star network topological indices: Shannon entropy of Markov matrices, trace of connectivity matrices, Harary number, Wiener index, Gutman index, Schultz index, Moreau–Broto indices, Balaban distance connectivity index, Kier–Hall connectivity indices and Randic connectivity index. The model was constructed with the General Discriminant Analysis methods from STATISTICA package and gave training/predicting set accuracies of 90.77% for the forward stepwise model type. In conclusion, this study extends for the first time the classical TIs to protein star network TIs by proposing a model that can predict if a protein/fragment of protein is natural or random using only the amino acid sequence data. This classification can be used in the studies of the protein functions by changing some fragments with random amino acid sequences or to detect the fake amino acid sequences or the errors in proteins. These results promote the use of the S2SNet application not only for protein structure analysis but also for mass spectroscopy, clinical proteomics and imaging, or DNA/RNA structure analysis.
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Affiliation(s)
- Cristian Robert Munteanu
- REQUIMTE-University of Porto, Faculty of Science, Chemistry Department, University of Porto 4169-007, Portugal.
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38
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Using ensemble of classifiers for predicting HIV protease cleavage sites in proteins. Amino Acids 2008; 36:409-16. [DOI: 10.1007/s00726-008-0076-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2008] [Accepted: 03/27/2008] [Indexed: 10/22/2022]
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39
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Mechanisms of telomerase-dimer catalysis. J Theor Biol 2007; 250:512-23. [PMID: 18054367 DOI: 10.1016/j.jtbi.2007.10.028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2007] [Revised: 10/20/2007] [Accepted: 10/25/2007] [Indexed: 11/22/2022]
Abstract
There is evidence that human telomerase acts as a dimer [Wenz, C., Enenkel, B., Amacker, M., Kelleher, C., Damm, K., Lingner, J., 2001. Human telomerase contains two cooperating telomerase RNA molecules. EMBO J. 20, 3526-3534]. Three possible mechanisms have been proposed. We translate those proposals into three detailed mechanistic models for telomerase action, also introducing optional isomerizations with equilibrium constants inversely related to the number of bound nucleotides. To distinguish between these models by in situ experiments we propose a microscopic system which uses two-photon excitation of fluorescence in a volume of about 0.5 microm(3). A variety of detection strategies and experimental designs are considered; we focus on those best suited to observation of a small volume under limitations imposed by diffusion to and from the reacting micro-volume, and consequently restrict ourselves to constant flow. Numerical simulation is used to help identify an optimal experimental design. The detection of mechanistic changes hinges on linking fluorescence reporters to selected reaction components, either directly (chemically) or indirectly (via an indicator reaction). We show that rapid mixing experiments are better than chemical relaxation experiments, as the statistics of single molecule kinetics affects the latter more than the former. However, some fast reaction steps can only be revealed by chemical relaxation coupled with mixing experiments. We explore connections between our methods and studies of HIV and other systems with RNA to DNA transcription.
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Du Q, Huang R, Wei Y, Wang C, Chou K. Peptide reagent design based on physical and chemical properties of amino acid residues. J Comput Chem 2007; 28:2043-50. [PMID: 17450553 PMCID: PMC7166493 DOI: 10.1002/jcc.20732] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
It has tremendous values for both drug discovery and basic research to develop a solid bioinformatical tool for guiding peptide reagent design. Based on the physical and chemical properties of amino acids, a new strategy for peptide reagent design, the so‐called AABPD (amino acid based‐peptide design), is proposed. The peptide samples in a training dataset are described by a series of HMLP (heuristic molecular lipophilicity potential) parameters and other physicochemical properties of amino acid residues that form a three‐dimensional data matrix where each component is defined by three indexes: the first index refers to the peptide samples, the second to the amino acid positions, and the third to the amino acid parameters. The binding free energy between a peptide ligand and its protein receptor is calculated by a linear free energy equation through the physicochemical parameters, resulting in a set of simultaneous linear equations between the bioactivity of the peptides and the physicochemical properties of amino acids. An iterative double least square technique is developed for the solution of the three‐dimensional simultaneous linear equation set to determine the amino acid position coefficients of peptide sequence and the physicochemical parameter coefficients of amino acid residues alternately. The two sets of coefficients thus obtained are used for predicting the bioactivity of other query peptide reagents. Two calculation examples, the peptide substrate specificity of the SARS coronavirus 3C‐like proteinase and the affinity prediction for epitope‐peptides with Class I MHC molecules are studied by using the peptide reagent design strategy. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2007
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Affiliation(s)
- Qi‐Shi Du
- Guangxi Key Laboratory of Subtropical Bioresource Conservation and Utilization, Guangxi University, Nanning, Guangxi, 530004, China
- Institute of Bioinformatics and Drug Discovery, Tianjin Normal University, Tianjin, 300074, China
- Gordon Life Science Institute, San Diego, California 92130, USA
| | - Ri‐Bo Huang
- Guangxi Key Laboratory of Subtropical Bioresource Conservation and Utilization, Guangxi University, Nanning, Guangxi, 530004, China
- Guangxi Academy of Sciences, 98 Daling Road, Nanning, Guangxi 530004, China
| | - Yu‐Tuo Wei
- Guangxi Key Laboratory of Subtropical Bioresource Conservation and Utilization, Guangxi University, Nanning, Guangxi, 530004, China
| | - Cheng‐Hua Wang
- Guangxi Key Laboratory of Subtropical Bioresource Conservation and Utilization, Guangxi University, Nanning, Guangxi, 530004, China
| | - Kuo‐Chen Chou
- Gordon Life Science Institute, San Diego, California 92130, USA
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41
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Bondock S, Tarhoni AEG, Fadda AA. Synthesis and Reactions of Some New Thiobarbituric Acid Derivatives. PHOSPHORUS SULFUR 2007. [DOI: 10.1080/10426500701415907] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Samir Bondock
- a Department of Chemistry, Faculty of Science , Mansoura University , Mansoura , Egypt
| | - Abd El-Gaber Tarhoni
- a Department of Chemistry, Faculty of Science , Mansoura University , Mansoura , Egypt
| | - Ahmed A. Fadda
- a Department of Chemistry, Faculty of Science , Mansoura University , Mansoura , Egypt
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Abdel-Latif E, Mustafa HM, Etman HA, Fadda AA. Synthesis of new purine, pteridine, and other pyrimidine derivatives. RUSSIAN JOURNAL OF ORGANIC CHEMISTRY 2007. [DOI: 10.1134/s1070428007030219] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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44
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Simulation of 13C Nuclear Magnetic Resonance Spectra for Derivatives of Bases and Nucleotides. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2006. [DOI: 10.1016/s1872-2040(06)60019-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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45
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Gao L, Ding YS, Dai H, Shao SH, Huang ZD, Chou KC. A novel fingerprint map for detecting SARS-CoV. J Pharm Biomed Anal 2005; 41:246-50. [PMID: 16289934 PMCID: PMC7127393 DOI: 10.1016/j.jpba.2005.09.031] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2005] [Revised: 09/20/2005] [Accepted: 09/24/2005] [Indexed: 01/15/2023]
Abstract
Spike (S) protein is the most important membrane protein on the surface of severe acute respiratory syndrome coronavirus (SARS-CoV). It associates with cellular receptors to mediate infection of their target cells. Inspired by such a mechanism, an in-depth investigation into the genome sequences of S protein of SARS-CoV and its receptor are conducted thru a mathematical transformation and graphic approach. As an outcome, a novel method for visualizing the characteristic of SARS-CoV is suggested. An extensive comparison among a large number of genome sequences has proved that the characteristic thus revealed is unique for SARS-CoV. As such, the characteristic can be regarded as the fingerprint map of SARS-CoV for diagnostic usage. Moreover, the conclusion has been further supported in a real case in Guangdong province of China. The fingerprint map proposed here has the merits of clear visibility and reliability that can serve as a complementary clinical tool for detecting SARS-CoV, particularly for the cases where the results obtained by the conventional methods are uncertain or conflicted with each other.
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Affiliation(s)
- Lei Gao
- Bio-Informatics Research Center, College of Information Sciences and Technology, Donghua University, Shanghai 200051, China
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Chandrasekaran S, Nagarajan S. Microwave-assisted synthesis and anti-bacterial activity of some 2-amino-6-aryl-4-(2-thienyl)pyrimidines. ACTA ACUST UNITED AC 2005; 60:279-82. [PMID: 15848201 DOI: 10.1016/j.farmac.2005.01.012] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2004] [Revised: 01/21/2005] [Accepted: 01/31/2005] [Indexed: 11/18/2022]
Abstract
Some novel 2-amino-6-aryl-4-(2-thienyl)pyrimidines were synthesized from 3-aryl-1-thien-2-ylprop-2-en-1-ones and guanidine hydrochloride in presence of alkali by conventional heating in alcoholic medium and microwave heating in solvent-free conditions. The compounds were evaluated for in vitro anti-bacterial activity. The anti-bacterial data revealed that compounds 5a-e had better activity against tested gram-positive organisms than the reference ciprofloxacin and norfloxacin. However, the compounds were nearly inactive against gram-negative bacteria. Compounds 5c and e were the most active compounds against gram-positive bacteria.
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Affiliation(s)
- S Chandrasekaran
- Department of Chemistry, Annamalai University, Annamalai Nagar-608 002, India
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48
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Du QS, Wang SQ, Zhu Y, Wei DQ, Guo H, Sirois S, Chou KC. Polyprotein cleavage mechanism of SARS CoV Mpro and chemical modification of the octapeptide. Peptides 2004; 25:1857-64. [PMID: 15501516 PMCID: PMC7115412 DOI: 10.1016/j.peptides.2004.06.018] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/01/2004] [Revised: 06/18/2004] [Accepted: 06/22/2004] [Indexed: 11/26/2022]
Abstract
The cleavage mechanism of severe acute respiratory syndrome (SARS) coronavirus main proteinase (M(pro) or 3CL(pro)) for the octapeptide AVLQSGFR is studied using molecular mechanics (MM) and quantum mechanics (QM). The catalytic dyad His-41 and Cys-145 in the active pocket between domain I and II seem to polarize the pi-electron density of the peptide bond between Gln and Ser in the octapeptide, leading to an increase of positive charge on C(CO) of Gln and negative charge on N(NH) of Ser. The possibility of enhancing the chemical bond between Gln and Ser based on the "distorted key" theory [Anal. Biochem. 233 (1996) 1] is examined. The scissile peptide bond between Gln and Ser is found to be solidified through "hybrid peptide bond" by changing the carbonyl group CO of Gln to CH(2) or CF(2). This leads to a break of the pi-bond system for the peptide bond, making the octapeptide (AVLQSGFR) a "distorted key" and a potential starting system for the design of anti SARS drugs.
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Affiliation(s)
- Qi-Shi Du
- Tianjin Normal University and Tianjin Institute of Bioinformatics and Drug Discovery (TIBDD), Tianjin 300074, China
- Institut Technologique de Montreal, Suite 168, 5253 Boul. Decarie, Montreal, Que., Canada H3W 3C3
| | - Shu-Qing Wang
- Tianjin Normal University and Tianjin Institute of Bioinformatics and Drug Discovery (TIBDD), Tianjin 300074, China
| | - Yu Zhu
- Tianjin Normal University and Tianjin Institute of Bioinformatics and Drug Discovery (TIBDD), Tianjin 300074, China
| | - Dong-Qing Wei
- Tianjin Normal University and Tianjin Institute of Bioinformatics and Drug Discovery (TIBDD), Tianjin 300074, China
- Institut Technologique de Montreal, Suite 168, 5253 Boul. Decarie, Montreal, Que., Canada H3W 3C3
- Center For Research in Molecular Modeling (CERMM), Concordia University, Montreal, Canada
| | - Hong Guo
- University of Tennessee, Department of Biochemistry, Cell and Molecular Biology, Knoxville, TN 37996-0840, USA
| | - Suzanne Sirois
- Institut Technologique de Montreal, Suite 168, 5253 Boul. Decarie, Montreal, Que., Canada H3W 3C3
| | - Kuo-Chen Chou
- Tianjin Normal University and Tianjin Institute of Bioinformatics and Drug Discovery (TIBDD), Tianjin 300074, China
- Institute of Image Processing and Pattern Recognition, Shanghai Jiaotong University, Shanghai 200030, China
- Gordon Life Science Institute, San Diego, CA 92130, USA
- Corresponding author.
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Wyrzykiewicz E, Szponar-Krajewicz A. Electron impact induced mass spectral study of new metameric 2-alkoxycarbonylalkylthio- and 1-alkoxycarbonylalkyl-2-alkoxycarbonylalkylthio-6-aminouracils. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2003; 17:1919-1923. [PMID: 12876694 DOI: 10.1002/rcm.1122] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
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50
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Wyrzykiewicz E, Szponar A. New isomeric 2-ortho-(meta- and para-) chloro-(bromo and nitro-)benzylthio-6-aminouracils. J Heterocycl Chem 2001. [DOI: 10.1002/jhet.5570380627] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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