1
|
Udayantha HMV, Samaraweera AV, Liyanage DS, Sandamalika WMG, Lim C, Yang H, Lee JH, Lee S, Lee J. Molecular characterization, antiviral activity, and UV-B damage responses of Caspase-9 from Amphiprion clarkii. FISH & SHELLFISH IMMUNOLOGY 2022; 125:247-257. [PMID: 35588907 DOI: 10.1016/j.fsi.2022.05.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 04/18/2022] [Accepted: 05/11/2022] [Indexed: 06/15/2023]
Abstract
Apoptosis plays a vital role in maintaining cellular homeostasis in multicellular organisms. Caspase-9 (casp-9) is one of the major initiator caspases that induces apoptosis by activating downstream intrinsic apoptosis pathway genes. Here, we isolated the cDNA sequence (1992 bp) of caspase-9 from Amphiprion clarkii (Accasp-9) that consists of a 1305 bp coding region and encodes a 434 aa protein. In silico analysis showed that Accasp-9 has a theoretical isoelectric point of 5.81 and a molecular weight of 48.45 kDa. Multiple sequence alignment revealed that the CARD domain is located at the N-terminus, whereas the large P-20 and small P-10 domains are located at the C-terminus. Moreover, a highly conserved pentapeptide active site (296QACGG301), as well as histidine and cysteine active sites, are also retained at the C-terminus. In phylogenetic analysis, Accasp-9 formed a clade with casp-9 from different species, distinct from other caspases. Accasp-9 was highly expressed in the gill and intestine compared with other tissues analyzed in healthy A. clarkii. Accasp-9 expression was significantly elevated in the blood after stimulation with Vibrio harveyi and polyinosinic:polycytidylic acid (poly I:C; 12-48 h), but not with lipopolysaccharide. The nucleoprotein expression of the viral hemorrhagic septicemia virus was significantly reduced in Accasp-9 overexpressed fathead minnow (FHM) cells compared with that in the control. In addition, other in vitro assays revealed that cell apoptosis was significantly elevated in poly I:C and UV-B-treated Accasp-9 transfected FHM cells. However, H248P or C298S mutated Accasp-9 significantly reduced apoptosis in UV-B irradiated cells. Collectively, our results show that Accasp-9 might play a defensive role against invading pathogens and UV-B radiation and H248 and C298 active residues are significantly involved in apoptosis in teleosts.
Collapse
Affiliation(s)
- H M V Udayantha
- Department of Marine Life Sciences & Fish Vaccine Research Center, Jeju National University, Jeju, 63243, Republic of Korea
| | - Anushka Vidurangi Samaraweera
- Department of Marine Life Sciences & Fish Vaccine Research Center, Jeju National University, Jeju, 63243, Republic of Korea
| | - D S Liyanage
- Department of Marine Life Sciences & Fish Vaccine Research Center, Jeju National University, Jeju, 63243, Republic of Korea
| | - W M Gayashani Sandamalika
- Department of Marine Life Sciences & Fish Vaccine Research Center, Jeju National University, Jeju, 63243, Republic of Korea
| | - Chaehyeon Lim
- Department of Marine Life Sciences & Fish Vaccine Research Center, Jeju National University, Jeju, 63243, Republic of Korea
| | - Hyerim Yang
- Department of Marine Life Sciences & Fish Vaccine Research Center, Jeju National University, Jeju, 63243, Republic of Korea
| | - Ji Hun Lee
- Department of Marine Life Sciences & Fish Vaccine Research Center, Jeju National University, Jeju, 63243, Republic of Korea
| | - Sukkyoung Lee
- Department of Marine Life Sciences & Fish Vaccine Research Center, Jeju National University, Jeju, 63243, Republic of Korea; Marine Science Institute, Jeju National University, Jeju, 63333, Republic of Korea
| | - Jehee Lee
- Department of Marine Life Sciences & Fish Vaccine Research Center, Jeju National University, Jeju, 63243, Republic of Korea; Marine Science Institute, Jeju National University, Jeju, 63333, Republic of Korea.
| |
Collapse
|
2
|
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.
Collapse
|
3
|
Gachpazan M, Kashani H, Khazaei M, Hassanian SM, Rezayi M, Asgharzadeh F, Ghayour-Mobarhan M, Ferns GA, Avan A. The Impact of Statin Therapy on the Survival of Patients with Gastrointestinal Cancer. Curr Drug Targets 2020; 20:738-747. [PMID: 30539694 DOI: 10.2174/1389450120666181211165449] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 10/25/2018] [Accepted: 12/05/2018] [Indexed: 12/13/2022]
Abstract
Statins are 3-hydroxy-3-methylglutaryl coenzyme A (HMG-CoA) reductase inhibitors that may play an important role in the evolution of cancers, due to their effects on cancer cell metabolism. Statins affect several potential pathways, including cell proliferation, angiogenesis, apoptosis and metastasis. The number of trials assessing the putative clinical benefits of statins in cancer is increasing. Currently, there are several trials listed on the global trial identifier website clinicaltrials.gov. Given the compelling evidence from these trials in a variety of clinical settings, there have been calls for a clinical trial of statins in the adjuvant gastrointestinal cancer setting. However, randomized controlled trials on specific cancer types in relation to statin use, as well as studies on populations without a clinical indication for using statins, have elucidated some potential underlying biological mechanisms, and the investigation of different statins is probably warranted. It would be useful for these trials to incorporate the assessment of tumour biomarkers predictive of statin response in their design. This review summarizes the recent preclinical and clinical studies that assess the application of statins in the treatment of gastrointestinal cancers with particular emphasize on their association with cancer risk.
Collapse
Affiliation(s)
- Meysam Gachpazan
- Metabolic syndrome Research center, Mashhad University of Medical Sciences, Mashhad, Iran.,Department of Modern Sciences and Technologies; Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Hoda Kashani
- Department of Modern Sciences and Technologies; Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Majid Khazaei
- Metabolic syndrome Research center, Mashhad University of Medical Sciences, Mashhad, Iran.,Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Seyed Mahdi Hassanian
- Metabolic syndrome Research center, Mashhad University of Medical Sciences, Mashhad, Iran.,Department of Medical Biochemistry; Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Majid Rezayi
- Metabolic syndrome Research center, Mashhad University of Medical Sciences, Mashhad, Iran.,Department of Modern Sciences and Technologies; Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Fereshteh Asgharzadeh
- Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Majid Ghayour-Mobarhan
- Metabolic syndrome Research center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Gordon A Ferns
- Brighton & Sussex Medical School, Division of Medical Education, Falmer, Brighton, Sussex BN1 9PH, United Kingdom
| | - Amir Avan
- Metabolic syndrome Research center, Mashhad University of Medical Sciences, Mashhad, Iran.,Department of Modern Sciences and Technologies; Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Cancer Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| |
Collapse
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
Saikia S, Bordoloi M, Sarmah R. Established and In-trial GPCR Families in Clinical Trials: A Review for Target Selection. Curr Drug Targets 2020; 20:522-539. [PMID: 30394207 DOI: 10.2174/1389450120666181105152439] [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: 06/18/2018] [Revised: 08/28/2018] [Accepted: 10/22/2018] [Indexed: 12/14/2022]
Abstract
The largest family of drug targets in clinical trials constitute of GPCRs (G-protein coupled receptors) which accounts for about 34% of FDA (Food and Drug Administration) approved drugs acting on 108 unique GPCRs. Factors such as readily identifiable conserved motif in structures, 127 orphan GPCRs despite various de-orphaning techniques, directed functional antibodies for validation as drug targets, etc. has widened their therapeutic windows. The availability of 44 crystal structures of unique receptors, unexplored non-olfactory GPCRs (encoded by 50% of the human genome) and 205 ligand receptor complexes now present a strong foundation for structure-based drug discovery and design. The growing impact of polypharmacology for complex diseases like schizophrenia, cancer etc. warrants the need for novel targets and considering the undiscriminating and selectivity of GPCRs, they can fulfill this purpose. Again, natural genetic variations within the human genome sometimes delude the therapeutic expectations of some drugs, resulting in medication response differences and ADRs (adverse drug reactions). Around ~30 billion US dollars are dumped annually for poor accounting of ADRs in the US alone. To curb such undesirable reactions, the knowledge of established and currently in clinical trials GPCRs families can offer huge understanding towards the drug designing prospects including "off-target" effects reducing economical resource and time. The druggability of GPCR protein families and critical roles played by them in complex diseases are explained. Class A, class B1, class C and class F are generally established family and GPCRs in phase I (19%), phase II(29%), phase III(52%) studies are also reviewed. From the phase I studies, frizzled receptors accounted for the highest in trial targets, neuropeptides in phase II and melanocortin in phase III studies. Also, the bioapplications for nanoparticles along with future prospects for both nanomedicine and GPCR drug industry are discussed. Further, the use of computational techniques and methods employed for different target validations are also reviewed along with their future potential for the GPCR based drug discovery.
Collapse
Affiliation(s)
- Surovi Saikia
- Natural Products Chemistry Group, CSIR North East Institute of Science & Technology, Jorhat-785006, Assam, India
| | - Manobjyoti Bordoloi
- Natural Products Chemistry Group, CSIR North East Institute of Science & Technology, Jorhat-785006, Assam, India
| | - Rajeev Sarmah
- Allied Health Sciences, Assam Down Town University, Panikhaiti, Guwahati 781026, Assam, India
| |
Collapse
|
6
|
Malik N, Dhiman P, Khatkar A. In Silico Design and Synthesis of Targeted Curcumin Derivatives as Xanthine Oxidase Inhibitors. Curr Drug Targets 2020; 20:593-603. [PMID: 30465499 DOI: 10.2174/1389450120666181122100511] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 09/24/2018] [Accepted: 11/02/2018] [Indexed: 12/11/2022]
Abstract
BACKGROUND Curcumin is a well-known pharmacophore and some of its derivatives are shown to target xanthine oxidase (XO) to alleviate disorders caused by the excess production of uric acid. OBJECTIVE Curcumin based derivatives were designed, synthesized and evaluated for their antioxidant and xanthine oxidase inhibitory potential. METHOD In this report, we designed and synthesized two series of curcumin derivatives modified by inserting pyrazole and pyrimidine ring to central keto group. The synthesized compounds were evaluated for their antioxidant and xanthine oxidase inhibitory potential. RESULTS Results showed that pyrazole analogues of curcumin produced excellent XO inhibitory potency with the IC50 values varying from 06.255 µM to 10.503 µM. Among pyrimidine derivatives compound CU3a1 having ortho nitro substitution exhibited more potent xanthine oxidase inhibitory activity than any other curcumin derivative of this series. CONCLUSION Curcumin derivatives CU5b1, CU5b2, CU5b3, and CU3a1 showed a potent inhibitory activity against xanthine oxidase along with good antioxidant potential.
Collapse
Affiliation(s)
- Neelam Malik
- Laboratory for Preservation Technology and Enzyme Inhibition Studies, Department of Pharmaceutical Sciences, M.D.University, Rohtak, Haryana, India
| | - Priyanka Dhiman
- Laboratory for Preservation Technology and Enzyme Inhibition Studies, Department of Pharmaceutical Sciences, M.D.University, Rohtak, Haryana, India
| | - Anurag Khatkar
- Laboratory for Preservation Technology and Enzyme Inhibition Studies, Department of Pharmaceutical Sciences, M.D.University, Rohtak, Haryana, India
| |
Collapse
|
7
|
Hu Y, Lu Y, Wang S, Zhang M, Qu X, Niu B. Application of Machine Learning Approaches for the Design and Study of Anticancer Drugs. Curr Drug Targets 2020; 20:488-500. [PMID: 30091413 DOI: 10.2174/1389450119666180809122244] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 06/19/2018] [Accepted: 06/25/2018] [Indexed: 12/14/2022]
Abstract
BACKGROUND Globally the number of cancer patients and deaths are continuing to increase yearly, and cancer has, therefore, become one of the world's highest causes of morbidity and mortality. In recent years, the study of anticancer drugs has become one of the most popular medical topics. OBJECTIVE In this review, in order to study the application of machine learning in predicting anticancer drugs activity, some machine learning approaches such as Linear Discriminant Analysis (LDA), Principal components analysis (PCA), Support Vector Machine (SVM), Random forest (RF), k-Nearest Neighbor (kNN), and Naïve Bayes (NB) were selected, and the examples of their applications in anticancer drugs design are listed. RESULTS Machine learning contributes a lot to anticancer drugs design and helps researchers by saving time and is cost effective. However, it can only be an assisting tool for drug design. CONCLUSION This paper introduces the application of machine learning approaches in anticancer drug design. Many examples of success in identification and prediction in the area of anticancer drugs activity prediction are discussed, and the anticancer drugs research is still in active progress. Moreover, the merits of some web servers related to anticancer drugs are mentioned.
Collapse
Affiliation(s)
- Yan Hu
- School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Yi Lu
- School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Shuo Wang
- School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Mengying Zhang
- School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Xiaosheng Qu
- National Engineering Laboratory of Southwest Endangered Medicinal Resources Development, Guangxi Botanical Garden of Medicinal Plants, 530023,Nanning, China
| | - Bing Niu
- School of Life Sciences, Shanghai University, Shanghai 200444, China
| |
Collapse
|
8
|
|
9
|
Zheng L, Huang S, Mu N, Zhang H, Zhang J, Chang Y, Yang L, Zuo Y. RAACBook: a web server of reduced amino acid alphabet for sequence-dependent inference by using Chou's five-step rule. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2020; 2019:5650975. [PMID: 31802128 PMCID: PMC6893003 DOI: 10.1093/database/baz131] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 10/16/2019] [Accepted: 10/17/2019] [Indexed: 12/12/2022]
Abstract
By reducing amino acid alphabet, the protein complexity can be significantly simplified, which could improve computational efficiency, decrease information redundancy and reduce chance of overfitting. Although some reduced alphabets have been proposed, different classification rules could produce distinctive results for protein sequence analysis. Thus, it is urgent to construct a systematical frame for reduced alphabets. In this work, we constructed a comprehensive web server called RAACBook for protein sequence analysis and machine learning application by integrating reduction alphabets. The web server contains three parts: (i) 74 types of reduced amino acid alphabet were manually extracted to generate 673 reduced amino acid clusters (RAACs) for dealing with unique protein problems. It is easy for users to select desired RAACs from a multilayer browser tool. (ii) An online tool was developed to analyze primary sequence of protein. The tool could produce K-tuple reduced amino acid composition by defining three correlation parameters (K-tuple, g-gap, λ-correlation). The results are visualized as sequence alignment, mergence of RAA composition, feature distribution and logo of reduced sequence. (iii) The machine learning server is provided to train the model of protein classification based on K-tuple RAAC. The optimal model could be selected according to the evaluation indexes (ROC, AUC, MCC, etc.). In conclusion, RAACBook presents a powerful and user-friendly service in protein sequence analysis and computational proteomics. RAACBook can be freely available at http://bioinfor.imu.edu.cn/raacbook. Database URL: http://bioinfor.imu.edu.cn/raacbook
Collapse
Affiliation(s)
- Lei Zheng
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Zhaojun Road No.24, Hohhot, 010070, China
| | - Shenghui Huang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Zhaojun Road No.24, Hohhot, 010070, China
| | - Nengjiang Mu
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Zhaojun Road No.24, Hohhot, 010070, China
| | - Haoyue Zhang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Zhaojun Road No.24, Hohhot, 010070, China
| | - Jiayu Zhang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Zhaojun Road No.24, Hohhot, 010070, China
| | - Yu Chang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Zhaojun Road No.24, Hohhot, 010070, China
| | - Lei Yang
- College of Bioinformatics Science and Technology, Harbin Medical University, Baojian Road No.157, Harbin 150081, China
| | - Yongchun Zuo
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Zhaojun Road No.24, Hohhot, 010070, China
| |
Collapse
|
10
|
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]
|
11
|
Zhou GP, Liao SM, Chen D, Huang RB. The Cooperative Effect between Polybasic Region (PBR) and Polysialyltransferase Domain (PSTD) within Tumor-Target Polysialyltranseferase ST8Sia II. Curr Top Med Chem 2020; 19:2831-2841. [PMID: 31755393 DOI: 10.2174/1568026619666191121145924] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2019] [Revised: 10/16/2019] [Accepted: 10/20/2019] [Indexed: 12/29/2022]
Abstract
ST8Sia II (STX) is a highly homologous mammalian polysialyltransferase (polyST), which is a validated tumor-target in the treatment of cancer metastasis reliant on tumor cell polysialylation. PolyST catalyzes the synthesis of α2,8-polysialic acid (polySia) glycans by carrying out the activated CMP-Neu5Ac (Sia) to N- and O-linked oligosaccharide chains on acceptor glycoproteins. In this review article, we summarized the recent studies about intrinsic correlation of two polybasic domains, Polysialyltransferase domain (PSTD) and Polybasic region (PBR) within ST8Sia II molecule, and suggested that the critical amino acid residues within the PSTD and PBR motifs of ST8Sia II for polysialylation of Neural cell adhesion molecules (NCAM) are related to ST8Sia II activity. In addition, the conformational changes of the PSTD domain due to point mutations in the PBR or PSTD domain verified an intramolecular interaction between the PBR and the PSTD. These findings have been incorporated into Zhou's NCAM polysialylation/cell migration model, which will provide new perspectives on drug research and development related to the tumor-target ST8Sia II.
Collapse
Affiliation(s)
- Guo-Ping Zhou
- National Engineering Research Center for Non-Food Biorefinery, State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Key Laboratory of Bio-refinery, Guangxi Academy of Sciences, 98 Daling Road, Nanning, 530007, China.,Gordon Life Science Institute, NC 27804, United States
| | - Si-Ming Liao
- National Engineering Research Center for Non-Food Biorefinery, State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Key Laboratory of Bio-refinery, Guangxi Academy of Sciences, 98 Daling Road, Nanning, 530007, China
| | - Dong Chen
- National Engineering Research Center for Non-Food Biorefinery, State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Key Laboratory of Bio-refinery, Guangxi Academy of Sciences, 98 Daling Road, Nanning, 530007, China
| | - Ri-Bo Huang
- National Engineering Research Center for Non-Food Biorefinery, State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Key Laboratory of Bio-refinery, Guangxi Academy of Sciences, 98 Daling Road, Nanning, 530007, China
| |
Collapse
|
12
|
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.
Collapse
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
| |
Collapse
|
13
|
Lu B, Liu XH, Liao SM, Lu ZL, Chen D, Troy Ii FA, Huang RB, Zhou GP. A Possible Modulation Mechanism of Intramolecular and Intermolecular Interactions for NCAM Polysialylation and Cell Migration. Curr Top Med Chem 2019; 19:2271-2282. [PMID: 31648641 DOI: 10.2174/1568026619666191018094805] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 08/01/2019] [Accepted: 08/06/2019] [Indexed: 12/31/2022]
Abstract
Polysialic acid (polySia) is a novel glycan that posttranslationally modifies neural cell adhesion molecules (NCAMs) in mammalian cells. Up-regulation of polySia-NCAM expression or NCAM polysialylation is associated with tumor cell migration and progression in many metastatic cancers and neurocognition. It has been known that two highly homologous mammalian polysialyltransferases (polySTs), ST8Sia II (STX) and ST8Sia IV (PST), can catalyze polysialylation of NCAM, and two polybasic domains, polybasic region (PBR) and polysialyltransferase domain (PSTD) in polySTs play key roles in affecting polyST activity or NCAM polysialylation. However, the molecular mechanisms of NCAM polysialylation and cell migration are still not entirely clear. In this minireview, the recent research results about the intermolecular interactions between the PBR and NCAM, the PSTD and cytidine monophosphate-sialic acid (CMP-Sia), the PSTD and polySia, and as well as the intramolecular interaction between the PBR and the PSTD within the polyST, are summarized. Based on these cooperative interactions, we have built a novel model of NCAM polysialylation and cell migration mechanisms, which may be helpful to design and develop new polysialyltransferase inhibitors.
Collapse
Affiliation(s)
- Bo Lu
- The National Engineering Research Center for Non-Food Biorefinery, Guangxi Academy of Sciences, Nanning, Guangxi 530007, China
| | - Xue-Hui Liu
- Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Si-Ming Liao
- The National Engineering Research Center for Non-Food Biorefinery, Guangxi Academy of Sciences, Nanning, Guangxi 530007, China
| | - Zhi-Long Lu
- The National Engineering Research Center for Non-Food Biorefinery, Guangxi Academy of Sciences, Nanning, Guangxi 530007, China
| | - Dong Chen
- The National Engineering Research Center for Non-Food Biorefinery, Guangxi Academy of Sciences, Nanning, Guangxi 530007, China
| | - Frederic A Troy Ii
- Department of Biochemistry and Molecular Medicine, University of California School of Medicine, Davis, CA, 95817, United States
| | - Ri-Bo Huang
- The National Engineering Research Center for Non-Food Biorefinery, Guangxi Academy of Sciences, Nanning, Guangxi 530007, China.,Life Science and Biotechnology College, Guangxi University, Nanning, Guangxi 530004, China
| | - Guo-Ping Zhou
- The National Engineering Research Center for Non-Food Biorefinery, Guangxi Academy of Sciences, Nanning, Guangxi 530007, China
| |
Collapse
|
14
|
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.
Collapse
Affiliation(s)
- Kuo-Chen Chou
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, 610054, China
| |
Collapse
|
15
|
Xie NZ, Li JX, Huang RB. Biological Production of (S)-acetoin: A State-of-the-Art Review. Curr Top Med Chem 2019; 19:2348-2356. [PMID: 31648637 DOI: 10.2174/1568026619666191018111424] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 08/28/2019] [Accepted: 09/02/2019] [Indexed: 12/24/2022]
Abstract
Acetoin is an important four-carbon compound that has many applications in foods, chemical synthesis, cosmetics, cigarettes, soaps, and detergents. Its stereoisomer (S)-acetoin, a high-value chiral compound, can also be used to synthesize optically active drugs, which could enhance targeting properties and reduce side effects. Recently, considerable progress has been made in the development of biotechnological routes for (S)-acetoin production. In this review, various strategies for biological (S)- acetoin production are summarized, and their constraints and possible solutions are described. Furthermore, future prospects of biological production of (S)-acetoin are discussed.
Collapse
Affiliation(s)
- Neng-Zhong Xie
- National Engineering Research Center for Non-Food Biorefinery, State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Key Laboratory of Bio-refinery, Guangxi Biomass Engineering Technology Research Center, Guangxi Academy of Sciences, 98 Daling Road, Nanning, 530007, China
| | - Jian-Xiu Li
- National Engineering Research Center for Non-Food Biorefinery, State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Key Laboratory of Bio-refinery, Guangxi Biomass Engineering Technology Research Center, Guangxi Academy of Sciences, 98 Daling Road, Nanning, 530007, China
| | - Ri-Bo Huang
- National Engineering Research Center for Non-Food Biorefinery, State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Key Laboratory of Bio-refinery, Guangxi Biomass Engineering Technology Research Center, Guangxi Academy of Sciences, 98 Daling Road, Nanning, 530007, China.,State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, 530004, China
| |
Collapse
|
16
|
Kang C. 19F-NMR in Target-based Drug Discovery. Curr Med Chem 2019; 26:4964-4983. [PMID: 31187703 DOI: 10.2174/0929867326666190610160534] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Revised: 08/14/2018] [Accepted: 03/13/2019] [Indexed: 02/06/2023]
Abstract
Solution NMR spectroscopy plays important roles in understanding protein structures, dynamics and protein-protein/ligand interactions. In a target-based drug discovery project, NMR can serve an important function in hit identification and lead optimization. Fluorine is a valuable probe for evaluating protein conformational changes and protein-ligand interactions. Accumulated studies demonstrate that 19F-NMR can play important roles in fragment- based drug discovery (FBDD) and probing protein-ligand interactions. This review summarizes the application of 19F-NMR in understanding protein-ligand interactions and drug discovery. Several examples are included to show the roles of 19F-NMR in confirming identified hits/leads in the drug discovery process. In addition to identifying hits from fluorinecontaining compound libraries, 19F-NMR will play an important role in drug discovery by providing a fast and robust way in novel hit identification. This technique can be used for ranking compounds with different binding affinities and is particularly useful for screening competitive compounds when a reference ligand is available.
Collapse
Affiliation(s)
- CongBao Kang
- Experimental Drug Development Centre (EDDC), Agency for Science, Technology and Research (A*STAR), 10 Biopolis Road, #05-01, Singapore, 138670, Singapore
| |
Collapse
|
17
|
Identifying DNase I hypersensitive sites using multi-features fusion and F-score features selection via Chou's 5-steps rule. Biophys Chem 2019; 253:106227. [DOI: 10.1016/j.bpc.2019.106227] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 07/04/2019] [Accepted: 07/10/2019] [Indexed: 01/12/2023]
|
18
|
FKRR-MVSF: A Fuzzy Kernel Ridge Regression Model for Identifying DNA-Binding Proteins by Multi-View Sequence Features via Chou's Five-Step Rule. Int J Mol Sci 2019; 20:ijms20174175. [PMID: 31454964 PMCID: PMC6747228 DOI: 10.3390/ijms20174175] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 08/10/2019] [Accepted: 08/19/2019] [Indexed: 12/22/2022] Open
Abstract
DNA-binding proteins play an important role in cell metabolism. In biological laboratories, the detection methods of DNA-binding proteins includes yeast one-hybrid methods, bacterial singles and X-ray crystallography methods and others, but these methods involve a lot of labor, material and time. In recent years, many computation-based approachs have been proposed to detect DNA-binding proteins. In this paper, a machine learning-based method, which is called the Fuzzy Kernel Ridge Regression model based on Multi-View Sequence Features (FKRR-MVSF), is proposed to identifying DNA-binding proteins. First of all, multi-view sequence features are extracted from protein sequences. Next, a Multiple Kernel Learning (MKL) algorithm is employed to combine multiple features. Finally, a Fuzzy Kernel Ridge Regression (FKRR) model is built to detect DNA-binding proteins. Compared with other methods, our model achieves good results. Our method obtains an accuracy of 83.26% and 81.72% on two benchmark datasets (PDB1075 and compared with PDB186), respectively.
Collapse
|
19
|
|
20
|
Liao SM, Shen NK, Liang G, Lu B, Lu ZL, Peng LX, Zhou F, Du LQ, Wei YT, Zhou GP, Huang RB. Inhibition of α-amylase Activity by Zn2+: Insights from Spectroscopy and Molecular Dynamics Simulations. Med Chem 2019; 15:510-520. [DOI: 10.2174/1573406415666181217114101] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 10/23/2018] [Accepted: 12/12/2018] [Indexed: 02/08/2023]
Abstract
Background:Inhibition of α-amylase activity is an important strategy in the treatment of diabetes mellitus. An important treatment for diabetes mellitus is to reduce the digestion of carbohydrates and blood glucose concentrations. Inhibiting the activity of carbohydrate-degrading enzymes such as α-amylase and glucosidase significantly decreases the blood glucose level. Most inhibitors of α-amylase have serious adverse effects, and the α-amylase inactivation mechanisms for the design of safer inhibitors are yet to be revealed.Objective:In this study, we focused on the inhibitory effect of Zn2+ on the structure and dynamic characteristics of α-amylase from Anoxybacillus sp. GXS-BL (AGXA), which shares the same catalytic residues and similar structures as human pancreatic and salivary α-amylase (HPA and HSA, respectively).Methods:Circular dichroism (CD) spectra of the protein (AGXA) in the absence and presence of Zn2+ were recorded on a Chirascan instrument. The content of different secondary structures of AGXA in the absence and presence of Zn2+ was analyzed using the online SELCON3 program. An AGXA amino acid sequence similarity search was performed on the BLAST online server to find the most similar protein sequence to use as a template for homology modeling. The pocket volume measurer (POVME) program 3.0 was applied to calculate the active site pocket shape and volume, and molecular dynamics simulations were performed with the Amber14 software package.Results:According to circular dichroism experiments, upon Zn2+ binding, the protein secondary structure changed obviously, with the α-helix content decreasing and β-sheet, β-turn and randomcoil content increasing. The structural model of AGXA showed that His217 was near the active site pocket and that Phe178 was at the outer rim of the pocket. Based on the molecular dynamics trajectories, in the free AGXA model, the dihedral angle of C-CA-CB-CG displayed both acute and planar orientations, which corresponded to the open and closed states of the active site pocket, respectively. In the AGXA-Zn model, the dihedral angle of C-CA-CB-CG only showed the planar orientation. As Zn2+ was introduced, the metal center formed a coordination interaction with H217, a cation-π interaction with W244, a coordination interaction with E242 and a cation-π interaction with F178, which prevented F178 from easily rotating to the open state and inhibited the activity of the enzyme.Conclusion:This research may have uncovered a subtle mechanism for inhibiting the activity of α-amylase with transition metal ions, and this finding will help to design more potent and specific inhibitors of α-amylases.
Collapse
Affiliation(s)
- Si-Ming Liao
- Department of Bioengineering, College of Life Science and Technology, Guangxi University, Nanning, Guangxi, 530004, China
| | - Nai-Kun Shen
- School of Marine Sciences and Biotechnology, Guangxi University for Nationalities, Nanning, Guangxi, 530008, China
| | - Ge Liang
- State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Academy of Sciences, Nanning, Guangxi, 530007, China
| | - Bo Lu
- State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Academy of Sciences, Nanning, Guangxi, 530007, China
| | - Zhi-Long Lu
- Department of Bioengineering, College of Life Science and Technology, Guangxi University, Nanning, Guangxi, 530004, China
| | - Li-Xin Peng
- Department of Bioengineering, College of Life Science and Technology, Guangxi University, Nanning, Guangxi, 530004, China
| | - Feng Zhou
- State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Academy of Sciences, Nanning, Guangxi, 530007, China
| | - Li-Qin Du
- Department of Bioengineering, College of Life Science and Technology, Guangxi University, Nanning, Guangxi, 530004, China
| | - Yu-Tuo Wei
- Department of Bioengineering, College of Life Science and Technology, Guangxi University, Nanning, Guangxi, 530004, China
| | - Guo-Ping Zhou
- State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Academy of Sciences, Nanning, Guangxi, 530007, China
| | - Ri-Bo Huang
- Department of Bioengineering, College of Life Science and Technology, Guangxi University, Nanning, Guangxi, 530004, China
| |
Collapse
|
21
|
Razzaq A, Shamsi S, Ali A, Ali Q, Sajjad M, Malik A, Ashraf M. Microbial Proteases Applications. Front Bioeng Biotechnol 2019; 7:110. [PMID: 31263696 PMCID: PMC6584820 DOI: 10.3389/fbioe.2019.00110] [Citation(s) in RCA: 170] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 05/01/2019] [Indexed: 11/13/2022] Open
Abstract
The use of chemicals around the globe in different industries has increased tremendously, affecting the health of people. The modern world intends to replace these noxious chemicals with environmental friendly products for the betterment of life on the planet. Establishing enzymatic processes in spite of chemical processes has been a prime objective of scientists. Various enzymes, specifically microbial proteases, are the most essentially used in different corporate sectors, such as textile, detergent, leather, feed, waste, and others. Proteases with respect to physiological and commercial roles hold a pivotal position. As they are performing synthetic and degradative functions, proteases are found ubiquitously, such as in plants, animals, and microbes. Among different producers of proteases, Bacillus sp. are mostly commercially exploited microbes for proteases. Proteases are successfully considered as an alternative to chemicals and an eco-friendly indicator for nature or the surroundings. The evolutionary relationship among acidic, neutral, and alkaline proteases has been analyzed based on their protein sequences, but there remains a lack of information that regulates the diversity in their specificity. Researchers are looking for microbial proteases as they can tolerate harsh conditions, ways to prevent autoproteolytic activity, stability in optimum pH, and substrate specificity. The current review focuses on the comparison among different proteases and the current problems faced during production and application at the industrial level. Deciphering these issues would enable us to promote microbial proteases economically and commercially around the world.
Collapse
Affiliation(s)
- Abdul Razzaq
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Sadia Shamsi
- School of Medicine, Medical Sciences and Nutrition, The Institute of Medical Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Arfan Ali
- 1-FB, Genetics, Four Brothers Group, Lahore, Pakistan
| | - Qurban Ali
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore, Pakistan
| | - Muhammad Sajjad
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore, Pakistan
| | - Arif Malik
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore, Pakistan
| | - Muhammad Ashraf
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore, Pakistan
| |
Collapse
|
22
|
Identification and characterization of WD40 superfamily genes in peach. Gene 2019; 710:291-306. [PMID: 31185283 DOI: 10.1016/j.gene.2019.06.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 04/25/2019] [Accepted: 06/05/2019] [Indexed: 01/16/2023]
Abstract
The WD40 transcription factor family is a superfamily found in all eukaryotes that plays important roles in regulating growth and development. To our knowledge, to date, WD40 superfamily genes have been identified and characterized in several plant species, but little information is available on the WD40 superfamily genes in peach. In this study, we identified 220 members of the WD40 superfamily in the peach genome, and these members were further classified into five subfamilies based on phylogenetic comparison with those in Arabidopsis. The members within each subfamily had conserved motifs and gene structures. The WD40 genes were unevenly distributed on chromosomes 1 to 8 of the peach genome. Additionally, 58 pairs of paralog WD40 members were found on eight chromosomes in peach, and 242 pairs of orthologous WD40 genes in peach and Arabidopsis were matched. The 54 selected putative WD40 genes in peach had diverse expression patterns in red-fleshed and white-fleshed peach fruits at five developmental stages. Prupe.6G211800.1 was located only on the cytomembrane, while Prupe.1G428200.1 and Prupe.I003200.1 were located on both the cytomembrane and in the nucleus; Prupe.1G558700.1 was densely localized around the nuclear rim but relatively faintly localized in the nucleoplasm; Prupe.5G116300.1 was located in the nucleus and cytomembrane with strong signals but showed weak signals in the cytoplasm; and Prupe.8G212400.1 and Prupe.1G053600.1 were located mainly in the nuclear envelope and cytomembrane but relatively faintly in the nucleoplasm. This study provides a foundation for the further functional verification of WD40 genes in peach.
Collapse
|
23
|
The preliminary efficacy evaluation of the CTLA-4-Ig treatment against Lupus nephritis through in-silico analyses. J Theor Biol 2019; 471:74-81. [DOI: 10.1016/j.jtbi.2019.03.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 03/22/2019] [Indexed: 01/04/2023]
|
24
|
Messerli MA, Sarkar A. Advances in Electrochemistry for Monitoring Cellular Chemical Flux. Curr Med Chem 2019; 26:4984-5002. [PMID: 31057100 DOI: 10.2174/0929867326666190506111629] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 03/06/2019] [Accepted: 03/12/2019] [Indexed: 11/22/2022]
Abstract
The transport of organic and inorganic molecules, along with inorganic ions across the plasma membrane results in chemical fluxes that reflect the cellular function in healthy and diseased states. Measurement of these chemical fluxes enables the characterization of protein function and transporter stoichiometry, characterization of a single cell and embryo viability prior to implantation, and screening of pharmaceutical agents. Electrochemical sensors emerge as sensitive and non-invasive tools for measuring chemical fluxes immediately outside the cells in the boundary layer, that are capable of monitoring a diverse range of transported analytes including inorganic ions, gases, neurotransmitters, hormones, and pharmaceutical agents. Used on their own or in combination with other methods, these sensors continue to expand our understanding of the function of rare cells and small tissues. Advances in sensor construction and detection strategies continue to improve sensitivity under physiological conditions, diversify analyte detection, and increase throughput. These advances will be discussed in the context of addressing technical challenges to measuring chemical flux in the boundary layer of cells and measuring the resultant changes to the chemical concentration in the bulk media.
Collapse
Affiliation(s)
- Mark A Messerli
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD. United States
| | - Anyesha Sarkar
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD. United States
| |
Collapse
|
25
|
Le NQK, Yapp EKY, Ou YY, Yeh HY. iMotor-CNN: Identifying molecular functions of cytoskeleton motor proteins using 2D convolutional neural network via Chou's 5-step rule. Anal Biochem 2019; 575:17-26. [PMID: 30930199 DOI: 10.1016/j.ab.2019.03.017] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 03/24/2019] [Accepted: 03/25/2019] [Indexed: 12/12/2022]
Abstract
Motor proteins are the driving force behind muscle contraction and are responsible for the active transportation of most proteins and vesicles in the cytoplasm. There are three superfamilies of cytoskeletal motor proteins with various molecular functions and structures: dynein, kinesin, and myosin. The functional loss of a specific motor protein molecular function has linked to a variety of human diseases, e.g., Charcot-Marie-Tooth disease, kidney disease. Therefore, creating a precise model to classify motor proteins is essential for helping biologists understand their molecular functions and design drug targets according to their impact on human diseases. Here we attempt to classify cytoskeleton motor proteins using deep learning, which has been increasingly and widely used to address numerous problems in a variety of fields resulting in state-of-the-art results. Our effective deep convolutional neural network is able to achieve an independent test accuracy of 97.5%, 96.4%, and 96.1% for each superfamily, respectively. Compared to other state-of-the-art methods, our approach showed a significant improvement in performance across a range of evaluation metrics. Through the proposed study, we provide an effective model for classifying motor proteins and a basis for further research that can enhance the performance of protein function classification using deep learning.
Collapse
Affiliation(s)
- Nguyen Quoc Khanh Le
- Medical Humanities Research Cluster, School of Humanities, Nanyang Technological University, 48 Nanyang Ave, 639798, Singapore.
| | - Edward Kien Yee Yapp
- Singapore Institute of Manufacturing Technology, 2 Fusionopolis Way, #08-04, Innovis, 138634, Singapore
| | - Yu-Yen Ou
- Department of Computer Science and Engineering, Yuan Ze University, 32003, Taiwan
| | - Hui-Yuan Yeh
- Medical Humanities Research Cluster, School of Humanities, Nanyang Technological University, 48 Nanyang Ave, 639798, Singapore.
| |
Collapse
|
26
|
Han Q, Yang C, Lu J, Zhang Y, Li J. Metabolism of Oxalate in Humans: A Potential Role Kynurenine Aminotransferase/Glutamine Transaminase/Cysteine Conjugate Beta-lyase Plays in Hyperoxaluria. Curr Med Chem 2019; 26:4944-4963. [PMID: 30907303 DOI: 10.2174/0929867326666190325095223] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 02/17/2019] [Accepted: 02/22/2019] [Indexed: 11/22/2022]
Abstract
Hyperoxaluria, excessive urinary oxalate excretion, is a significant health problem worldwide. Disrupted oxalate metabolism has been implicated in hyperoxaluria and accordingly, an enzymatic disturbance in oxalate biosynthesis can result in the primary hyperoxaluria. Alanine glyoxylate aminotransferase-1 and glyoxylate reductase, the enzymes involving glyoxylate (precursor for oxalate) metabolism, have been related to primary hyperoxalurias. Some studies suggest that other enzymes such as glycolate oxidase and alanine glyoxylate aminotransferase-2 might be associated with primary hyperoxaluria as well, but evidence of a definitive link is not strong between the clinical cases and gene mutations. There are still some idiopathic hyperoxalurias, which require a further study for the etiologies. Some aminotransferases, particularly kynurenine aminotransferases, can convert glyoxylate to glycine. Based on biochemical and structural characteristics, expression level, subcellular localization of some aminotransferases, a number of them appear able to catalyze the transamination of glyoxylate to glycine more efficiently than alanine glyoxylate aminotransferase-1. The aim of this minireview is to explore other undermining causes of primary hyperoxaluria and stimulate research toward achieving a comprehensive understanding of underlying mechanisms leading to the disease. Herein, we reviewed all aminotransferases in the liver for their functions in glyoxylate metabolism. Particularly, kynurenine aminotransferase-I and III were carefully discussed regarding their biochemical and structural characteristics, cellular localization, and enzyme inhibition. Kynurenine aminotransferase-III is, so far, the most efficient putative mitochondrial enzyme to transaminate glyoxylate to glycine in mammalian livers, might be an interesting enzyme to look over in hyperoxaluria etiology of primary hyperoxaluria and should be carefully investigated for its involvement in oxalate metabolism.
Collapse
Affiliation(s)
- Qian Han
- Key Laboratory of Tropical Biological Resources of Ministry of Education, Hainan University, Haikou, Hainan 570228. China
| | - Cihan Yang
- Key Laboratory of Tropical Biological Resources of Ministry of Education, Hainan University, Haikou, Hainan 570228. China
| | - Jun Lu
- Central South University Xiangya School of Medicine Affiliated Haikou People's Hospital, Haikou, Hainan 570208. China
| | - Yinai Zhang
- Central South University Xiangya School of Medicine Affiliated Haikou People's Hospital, Haikou, Hainan 570208. China
| | - Jianyong Li
- Department of Biochemistry, Virginia Tech, Blacksburg, VA 24061. United States
| |
Collapse
|
27
|
Pires ÁS, Rigueiras PO, Dohms SM, Porto WF, Franco OL. Structure-guided identification of antimicrobial peptides in the spathe transcriptome of the non-model plant, arum lily (Zantedeschia aethiopica
). Chem Biol Drug Des 2019; 93:1265-1275. [DOI: 10.1111/cbdd.13498] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 12/29/2018] [Accepted: 01/31/2019] [Indexed: 11/26/2022]
Affiliation(s)
- Állan S. Pires
- Centro de Análises Proteômicas e Bioquímicas; Pós-Graduação em Ciências Genômicas e Biotecnologia; Universidade Católica de Brasília; Brasília Brazil
| | - Pietra O. Rigueiras
- Centro de Análises Proteômicas e Bioquímicas; Pós-Graduação em Ciências Genômicas e Biotecnologia; Universidade Católica de Brasília; Brasília Brazil
| | - Stephan M. Dohms
- Centro de Análises Proteômicas e Bioquímicas; Pós-Graduação em Ciências Genômicas e Biotecnologia; Universidade Católica de Brasília; Brasília Brazil
| | - William F. Porto
- Porto Reports; Brasília Brazil
- S-Inova Biotech; Programa de Pós-Graduação em Biotecnologia; Universidade Católica Dom Bosco; Campo Grande Brazil
| | - Octavio L. Franco
- Centro de Análises Proteômicas e Bioquímicas; Pós-Graduação em Ciências Genômicas e Biotecnologia; Universidade Católica de Brasília; Brasília Brazil
- S-Inova Biotech; Programa de Pós-Graduação em Biotecnologia; Universidade Católica Dom Bosco; Campo Grande Brazil
| |
Collapse
|
28
|
Acylguanidine-BACE1 complex: Insights of intermolecular interactions and dynamics. J Theor Biol 2019; 464:33-49. [DOI: 10.1016/j.jtbi.2018.12.020] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 12/09/2018] [Accepted: 12/15/2018] [Indexed: 12/14/2022]
|
29
|
Rout S, Mahapatra RK. In silico analysis of plasmodium falciparum CDPK5 protein through molecular modeling, docking and dynamics. J Theor Biol 2019; 461:254-267. [DOI: 10.1016/j.jtbi.2018.10.045] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 10/15/2018] [Accepted: 10/22/2018] [Indexed: 10/28/2022]
|
30
|
Xu P, Ning P, Wang J, Qin Y, Liang F, Cheng Y. Precise control of apoptosis via gold nanostars for dose dependent photothermal therapy of melanoma. J Mater Chem B 2019; 7:6934-6944. [DOI: 10.1039/c9tb01956a] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Precise induction and monitoring of cell apoptosis are significant for cancer treatment.
Collapse
Affiliation(s)
- Peng Xu
- The State Key Laboratory of Refractories and Metallurgy
- Coal Conversion and New Carbon Materials Hubei Key Laboratory
- School of Chemistry and Chemical Engineering
- Wuhan University of Science and Technology
- Wuhan
| | - Peng Ning
- Institute for Regenerative Medicine
- Institute for Translational Nanomedicine
- Shanghai East Hospital
- Tongji University School of Medicine
- Shanghai
| | - Jingjing Wang
- Institute for Regenerative Medicine
- Institute for Translational Nanomedicine
- Shanghai East Hospital
- Tongji University School of Medicine
- Shanghai
| | - Yao Qin
- Institute for Regenerative Medicine
- Institute for Translational Nanomedicine
- Shanghai East Hospital
- Tongji University School of Medicine
- Shanghai
| | - Feng Liang
- The State Key Laboratory of Refractories and Metallurgy
- Coal Conversion and New Carbon Materials Hubei Key Laboratory
- School of Chemistry and Chemical Engineering
- Wuhan University of Science and Technology
- Wuhan
| | - Yu Cheng
- Institute for Regenerative Medicine
- Institute for Translational Nanomedicine
- Shanghai East Hospital
- Tongji University School of Medicine
- Shanghai
| |
Collapse
|
31
|
Shin WJ, Seong BL. Novel antiviral drug discovery strategies to tackle drug-resistant mutants of influenza virus strains. Expert Opin Drug Discov 2018; 14:153-168. [PMID: 30585088 DOI: 10.1080/17460441.2019.1560261] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
INTRODUCTION The emergence of drug-resistant influenza virus strains highlights the need for new antiviral therapeutics to combat future pandemic outbreaks as well as continuing seasonal cycles of influenza. Areas covered: This review summarizes the mechanisms of current FDA-approved anti-influenza drugs and patterns of resistance to those drugs. It also discusses potential novel targets for broad-spectrum antiviral drugs and recent progress in novel drug design to overcome drug resistance in influenza. Expert opinion: Using the available structural information about drug-binding pockets, research is currently underway to identify molecular interactions that can be exploited to generate new antiviral drugs. Despite continued efforts, antivirals targeting viral surface proteins like HA, NA, and M2, are all susceptible to developing resistance. Structural information on the internal viral polymerase complex (PB1, PB2, and PA) provides a new avenue for influenza drug discovery. Host factors, either at the initial step of viral infection or at the later step of nuclear trafficking of viral RNP complex, are being actively pursued to generate novel drugs with new modes of action, without resulting in drug resistance.
Collapse
Affiliation(s)
- Woo-Jin Shin
- a Department of Molecular Microbiology and Immunology, Keck School of Medicine , University of Southern California , Los Angeles , CA , USA
| | - Baik L Seong
- b Department of Biotechnology , College of Life Science and Biotechnology, Yonsei University , Seoul , South Korea.,c Vaccine Translational Research Center , Yonsei University , Seoul , South Korea
| |
Collapse
|
32
|
Ghosh A, Yan H. Hydrogen bond analysis of the EGFR-ErbB3 heterodimer related to non-small cell lung cancer and drug resistance. J Theor Biol 2018; 464:63-71. [PMID: 30593826 DOI: 10.1016/j.jtbi.2018.12.035] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2018] [Revised: 12/19/2018] [Accepted: 12/24/2018] [Indexed: 01/25/2023]
Abstract
Lung cancer is the predominant cause of cancer deaths on a worldwide scale. A mutation in the epidermal growth factor receptor (EGFR) can cause non-small cell lung cancer (NSCLC). The L858R one-point mutation in exon 21 in EGFR is the most prevalent in NSCLC. For over 60% of EGFR-muted NSCLC, another mutation T790M can cause drug resistance. In this paper, we consider EGFR and ErbB3 heterodimers involving three structures of EGFR, wild-type, with L858R mutation, and with L858R and T790M mutations. We perform molecular dynamics (MD) simulations to analyze hydrogen bonds in all three instances. The hydrogen bonds contribute to the conformational stability of the protein and molecular recognition. Several other parameters are also investigated in the present study, which reveals significant changes in the dimer at different levels of mutation. The knowledge and results obtained from this study lead to useful insight into the mechanism of NSCLC drug resistance.
Collapse
Affiliation(s)
- Avirup Ghosh
- Department of Electronics Engineering, City University of Hong Kong, Kowloon, Hong Kong.
| | - Hong Yan
- Department of Electronics Engineering, City University of Hong Kong, Kowloon, Hong Kong
| |
Collapse
|
33
|
Chen W, Liang X, Nong Z, Li Y, Pan X, Chen C, Huang L. The Multiple Applications and Possible Mechanisms of the Hyperbaric Oxygenation Therapy. Med Chem 2018; 15:459-471. [PMID: 30569869 DOI: 10.2174/1573406415666181219101328] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 10/23/2018] [Accepted: 12/12/2018] [Indexed: 12/18/2022]
Abstract
Hyperbaric Oxygenation Therapy (HBOT) is used as an adjunctive method for multiple diseases. The method meets the routine treating and is non-invasive, as well as provides 100% pure oxygen (O2), which is at above-normal atmospheric pressure in a specialized chamber. It is well known that in the condition of O2 deficiency, it will induce a series of adverse events. In order to prevent the injury induced by anoxia, the capability of offering pressurized O2 by HBOT seems involuntary and significant. In recent years, HBOT displays particular therapeutic efficacy in some degree, and it is thought to be beneficial to the conditions of angiogenesis, tissue ischemia and hypoxia, nerve system disease, diabetic complications, malignancies, Carbon monoxide (CO) poisoning and chronic radiation-induced injury. Single and combination HBOT are both applied in previous studies, and the manuscript is to review the current applications and possible mechanisms of HBOT. The applicability and validity of HBOT for clinical treatment remain controversial, even though it is regarded as an adjunct to conventional medical treatment with many other clinical benefits. There also exists a negative side effect of accepting pressurized O2, such as oxidative stress injury, DNA damage, cellular metabolic, activating of coagulation, endothelial dysfunction, acute neurotoxicity and pulmonary toxicity. Then it is imperative to comprehensively consider the advantages and disadvantages of HBOT in order to obtain a satisfying therapeutic outcome.
Collapse
Affiliation(s)
- Wan Chen
- Department of Emergency, the People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, Guangxi 530021, China
| | - Xingmei Liang
- Department of Pharmacy, Guangxi Medical College, Nanning, Guangxi 530021, China
| | - Zhihuan Nong
- Department of Pharmacology, Guangxi Institute of Chinese Medicine and Pharmaceutical Science, Nanning 530022, China
| | - Yaoxuan Li
- Department of Neurology, the People's Hospital of Guangxi Zhuang Autonomous Region, Nanning 530022, China
| | - Xiaorong Pan
- Department of Hyperbaric oxygen, the People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, Guangxi 530021, China
| | - Chunxia Chen
- Department of Hyperbaric oxygen, the People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, Guangxi 530021, China
| | - Luying Huang
- Department of Respiratory Medicine, the People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, Guangxi 530021, China
| |
Collapse
|
34
|
Zhu Y, Bian Y, Zhang Q, Hu J, Li L, Yang M, Qian H, Yu L, Liu B, Qian X. Construction and analysis of dysregulated lncRNA-associated ceRNA network in colorectal cancer. J Cell Biochem 2018; 120:9250-9263. [PMID: 30525245 DOI: 10.1002/jcb.28201] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 11/15/2018] [Indexed: 12/26/2022]
Abstract
Colorectal cancer (CRC) is one of the most frequently diagnosed digestive system cancer. The aim of the present study was to investigate the interactions among messenger RNAs (mRNAs), microRNAs (miRNAs), and long noncoding RNAs (lncRNAs) in CRC to reveal the mechanisms of CRC. Differentially expressed genes (DEGs) were identified from public gene expression data sets. One thousand eighty-one common dysregulated mRNAs in two data sets were identified. Gene function analysis and protein-protein interaction network analysis indicated that these DEGs might play important roles in CRC. LINC00365 was selected through coding- noncoding network analysis and its expression was validated upregulated in 22 paired clinical samples and four CRC cell lines. A competing endogenous RNA network composed of 70 miRNAs, nine mRNAs, and LINC00365 was constructed. Eight of nine mRNAs were validated upregulated in The Cancer Genome Atlas data set. Our results suggested that LINC00365 was an oncogene in CRC and it could regulate the expression of several mRNAs through sponging miRNAs.
Collapse
Affiliation(s)
- Yiping Zhu
- Comprehensive Cancer Center, Nanjing Drum Tower Hospital, Clinical College of Nanjing Medical University, Nanjing, Jiangsu, China.,Department of Oncology, Yijishan Hospital, Wannan Medical College, Wuhu, Anhui, China
| | - Yinzhu Bian
- Department of Oncology, The First People's Hospital of Yancheng, Yancheng, Jiangsu, China
| | - Qun Zhang
- Comprehensive Cancer Center, Nanjing Drum Tower Hospital, Medical School of Nanjing University, Clinical Cancer Institute of Nanjing University, Nanjing, Jiangsu, China
| | - Jing Hu
- Comprehensive Cancer Center, Nanjing Drum Tower Hospital, Medical School of Nanjing University, Clinical Cancer Institute of Nanjing University, Nanjing, Jiangsu, China
| | - Li Li
- Comprehensive Cancer Center, Nanjing Drum Tower Hospital, Medical School of Nanjing University, Clinical Cancer Institute of Nanjing University, Nanjing, Jiangsu, China
| | - Mi Yang
- Comprehensive Cancer Center, Nanjing Drum Tower Hospital, Medical School of Nanjing University, Clinical Cancer Institute of Nanjing University, Nanjing, Jiangsu, China
| | - Hanqing Qian
- Comprehensive Cancer Center, Nanjing Drum Tower Hospital, Medical School of Nanjing University, Clinical Cancer Institute of Nanjing University, Nanjing, Jiangsu, China
| | - Lixia Yu
- Comprehensive Cancer Center, Nanjing Drum Tower Hospital, Medical School of Nanjing University, Clinical Cancer Institute of Nanjing University, Nanjing, Jiangsu, China
| | - Baorui Liu
- Comprehensive Cancer Center, Nanjing Drum Tower Hospital, Clinical College of Nanjing Medical University, Nanjing, Jiangsu, China.,Comprehensive Cancer Center, Nanjing Drum Tower Hospital, Medical School of Nanjing University, Clinical Cancer Institute of Nanjing University, Nanjing, Jiangsu, China
| | - Xiaoping Qian
- Comprehensive Cancer Center, Nanjing Drum Tower Hospital, Clinical College of Nanjing Medical University, Nanjing, Jiangsu, China.,Comprehensive Cancer Center, Nanjing Drum Tower Hospital, Medical School of Nanjing University, Clinical Cancer Institute of Nanjing University, Nanjing, Jiangsu, China
| |
Collapse
|
35
|
Exploration of synthetic multifunctional amides as new therapeutic agents for Alzheimer's disease through enzyme inhibition, chemoinformatic properties, molecular docking and dynamic simulation insights. J Theor Biol 2018; 458:169-183. [PMID: 30243565 DOI: 10.1016/j.jtbi.2018.09.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 09/06/2018] [Accepted: 09/17/2018] [Indexed: 12/12/2022]
Abstract
A new series of multifunctional amides has been synthesized having moderate enzyme inhibitory potentials and mild cytotoxicity. 2-Furyl(1-piperazinyl)methanone (1) was coupled with 3,5-dichloro-2-hydroxybenzenesulfonyl chloride (2) to form {4-[(3,5-dichloro-2-hydroxyphenyl)sulfonyl]-1-piperazinyl}(2-furyl)methanone (3). Different elecrophiles were synthesized by the reaction of various un/substituted anilines (4a-o) with 2-bromoacetylbromide (5), 2‑bromo‑N-(un/substituted-phenyl)acetamides (6a-o). Further, equimolar ratios of 3 and 6a-o were allowed to react in the presence of K2CO3 in acetonitrile to form desired multifunctional amides (7a-o). The structural confirmation of all the synthesized compounds was carried out by their EI-MS, IR, 1H NMR and 13C NMR spectral data. Enzyme inhibition activity was performed against acetyl and butyrylcholinestrase enzymes, whereby 7e showed very good activity having IC50 value of 5.54 ± 0.03 and 9.15 ± 0.01 μM, respectively, relative to eserine, a reference standard. Hemolytic activity of the molecules was checked to asertain their cytotoxicity towards red blood cell membrance and it was observed that most of the compounds were not toxic up to certain range. Moreover, chemoinformatic protepties and docking simulation results also showed the significance of 7e as compared to other compounds. Based on in vitro and in silico analysis 7e could be used as a template for the development of new drugs against Alzheimer's disease.
Collapse
|
36
|
Wang MY, Liang JW, Olounfeh KM, Sun Q, Zhao N, Meng FH. A Comprehensive In Silico Method to Study the QSTR of the Aconitine Alkaloids for Designing Novel Drugs. Molecules 2018; 23:E2385. [PMID: 30231506 PMCID: PMC6225272 DOI: 10.3390/molecules23092385] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 09/11/2018] [Accepted: 09/12/2018] [Indexed: 12/22/2022] Open
Abstract
A combined in silico method was developed to predict potential protein targets that are involved in cardiotoxicity induced by aconitine alkaloids and to study the quantitative structure⁻toxicity relationship (QSTR) of these compounds. For the prediction research, a Protein-Protein Interaction (PPI) network was built from the extraction of useful information about protein interactions connected with aconitine cardiotoxicity, based on nearly a decade of literature and the STRING database. The software Cytoscape and the PharmMapper server were utilized to screen for essential proteins in the constructed network. The Calcium-Calmodulin-Dependent Protein Kinase II alpha (CAMK2A) and gamma (CAMK2G) were identified as potential targets. To obtain a deeper insight on the relationship between the toxicity and the structure of aconitine alkaloids, the present study utilized QSAR models built in Sybyl software that possess internal robustness and external high predictions. The molecular dynamics simulation carried out here have demonstrated that aconitine alkaloids possess binding stability for the receptor CAMK2G. In conclusion, this comprehensive method will serve as a tool for following a structural modification of the aconitine alkaloids and lead to a better insight into the cardiotoxicity induced by the compounds that have similar structures to its derivatives.
Collapse
Affiliation(s)
- Ming-Yang Wang
- School of Pharmacy, China Medical University, Shenyang 110122, Liaoning, China.
| | - Jing-Wei Liang
- School of Pharmacy, China Medical University, Shenyang 110122, Liaoning, China.
| | | | - Qi Sun
- School of Pharmacy, China Medical University, Shenyang 110122, Liaoning, China.
| | - Nan Zhao
- School of Pharmacy, China Medical University, Shenyang 110122, Liaoning, China.
| | - Fan-Hao Meng
- School of Pharmacy, China Medical University, Shenyang 110122, Liaoning, China.
| |
Collapse
|
37
|
pLoc_bal-mGpos: Predict subcellular localization of Gram-positive bacterial proteins by quasi-balancing training dataset and PseAAC. Genomics 2018; 111:886-892. [PMID: 29842950 DOI: 10.1016/j.ygeno.2018.05.017] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 05/14/2018] [Accepted: 05/18/2018] [Indexed: 12/12/2022]
Abstract
Knowledge of protein subcellular localization is vitally important for both basic research and drug development. With the avalanche of protein sequences emerging in the post-genomic age, it is highly desired to develop computational tools for timely and effectively identifying their subcellular localization purely based on the sequence information alone. Recently, a predictor called "pLoc-mGpos" was developed for identifying the subcellular localization of Gram-positive bacterial proteins. Its performance is overwhelmingly better than that of the other predictors for the same purpose, particularly in dealing with multi-label systems in which some proteins, called "multiplex proteins", may simultaneously occur in two or more subcellular locations. Although it is indeed a very powerful predictor, more efforts are definitely needed to further improve it. This is because pLoc-mGpos was trained by an extremely skewed dataset in which some subset (subcellular location) was over 11 times the size of the other subsets. Accordingly, it cannot avoid the bias consequence caused by such an uneven training dataset. To alleviate such bias consequence, we have developed a new and bias-reducing predictor called pLoc_bal-mGpos by quasi-balancing the training dataset. Rigorous target jackknife tests on exactly the same experiment-confirmed dataset have indicated that the proposed new predictor is remarkably superior to pLoc-mGpos, the existing state-of-the-art predictor in identifying the subcellular localization of Gram-positive bacterial proteins. To maximize the convenience for most experimental scientists, a user-friendly web-server for the new predictor has been established at http://www.jci-bioinfo.cn/pLoc_bal-mGpos/, by which users can easily get their desired results without the need to go through the detailed mathematics.
Collapse
|
38
|
Agrahari AK, Kumar A, R S, Zayed H, C GPD. Substitution impact of highly conserved arginine residue at position 75 in GJB1 gene in association with X-linked Charcot-Marie-tooth disease: A computational study. J Theor Biol 2018; 437:305-317. [PMID: 29111421 DOI: 10.1016/j.jtbi.2017.10.028] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 10/23/2017] [Accepted: 10/26/2017] [Indexed: 10/18/2022]
Abstract
X-linked Charcot-Marie-Tooth type 1 X (CMTX1) disease is a subtype of Charcot-Marie-Tooth (CMT), which is mainly caused by mutations in the GJB1 gene. It is also known as connexin 32 (Cx32) that leads to Schwann cell abnormalities and peripheral neuropathy. CMTX1 is considered as the second most common form of CMT disease. The aim of this study is to computationally predict the potential impact of different single amino acid substitutions at position 75 of Cx32, from arginine (R) to proline (P), glutamine (Q) and tryptophan (W). This position is known to be highly conserved among the family of connexin. To understand the structural and functional changes due to these single amino acid substitutions, we employed a homology-modeling technique to build the three-dimensional structure models for the native and mutant proteins. The protein structures were further embedded into a POPC lipid bilayer, inserted into a water box, and subjected to molecular dynamics simulation for 50 ns. Our results show that the mutants R75P, R75Q and R75W display variable structural conformation and dynamic behavior compared to the native protein. Our data proves useful in predicting the potential pathogenicity of the mutant proteins and is expected to serve as a platform for drug discovery for patients with CMT.
Collapse
Affiliation(s)
| | - Amit Kumar
- Department of Mechanical, Chemical and Materials Engineering, University of Cagliari, via Marengo 2, 09123 Cagliari, Italy; Biosciences Sector, Center for advanced study research and development in Sardinia (CRS4), Loc. Piscina Manna, 09010 Pula, Italy
| | - Siva R
- School of Biosciences and Technology, VIT University, Vellore, Tamil Nadu, India
| | - Hatem Zayed
- Department of Biomedical Sciences, College of Health and Sciences, Qatar University, Doha, Qatar
| | - George Priya Doss C
- School of Biosciences and Technology, VIT University, Vellore, Tamil Nadu, India.
| |
Collapse
|
39
|
Niu B, Zhang M, Du P, Jiang L, Qin R, Su Q, Chen F, Du D, Shu Y, Chou KC. Small molecular floribundiquinone B derived from medicinal plants inhibits acetylcholinesterase activity. Oncotarget 2017; 8:57149-57162. [PMID: 28915661 PMCID: PMC5593632 DOI: 10.18632/oncotarget.19169] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2017] [Accepted: 06/28/2017] [Indexed: 12/12/2022] Open
Abstract
Being a neurodegenerative disorder, Alzheimer's disease (AD) is the one of the most terrible diseases. And acetylcholinesterase (AChE) is considered as an important target for treating AD. Acetylcholinesterase inhibitors (AChEI) are considered to be one of the effective drugs for the treatment of AD. The aim of this study is to find a novel potential AChEI as a drug for the treatment of AD. In this study, instead of using the synthetic compounds, we used those extracted from plants to investigate the interaction between floribundiquinone B (FB) and AChE by means of both the experimental approach such as fluorescence spectra, ultraviolet-visible (UV-vis) absorption spectrometry, circular dichroism (CD) and the theoretical approaches such as molecular docking. The findings reported here have provided many useful clues and hints for designing more effective and less toxic drugs against Alzheimer's disease.
Collapse
Affiliation(s)
- Bing Niu
- Shanghai Key Laboratory of Bio-Energy Crops, College of Life Science, Shanghai University, Shanghai, 200444, China.,Gordon Life Science Institute, Boston, MA 02478, USA
| | - Mengying Zhang
- Shanghai Key Laboratory of Bio-Energy Crops, College of Life Science, Shanghai University, Shanghai, 200444, China
| | - Pu Du
- Department of Neurology, The First People's Hospital of Foshan, Foshan, 528000, China
| | - Li Jiang
- Shanghai Key Laboratory of Bio-Energy Crops, College of Life Science, Shanghai University, Shanghai, 200444, China
| | - Rui Qin
- Department of Gynecology, Affiliated Minzu Hospital of Guangxi Medical University, Minzu Hospital of Guangxi Zhuang Autonomous Region, Nanning, 530001, China
| | - Qiang Su
- Shanghai Key Laboratory of Bio-Energy Crops, College of Life Science, Shanghai University, Shanghai, 200444, China
| | - Fuxue Chen
- Shanghai Key Laboratory of Bio-Energy Crops, College of Life Science, Shanghai University, Shanghai, 200444, China
| | - Dongshu Du
- Shanghai Key Laboratory of Bio-Energy Crops, College of Life Science, Shanghai University, Shanghai, 200444, China.,Department of Life Science, Heze University, Heze, Shandong, 274500, China
| | - Yilai Shu
- Department of Otolaryngology-Head and Neck Surgery, Eye and Ear, Nose, Throat, Hospital, Shanghai Medical College, Fudan University, Shanghai, 200031, China
| | - Kuo-Chen Chou
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, 610054, China.,Gordon Life Science Institute, Boston, MA 02478, USA
| |
Collapse
|
40
|
Nitric oxide-mediated apoptosis of neutrophils through caspase-8 and caspase-3-dependent mechanism. Cell Death Dis 2016; 7:e2348. [PMID: 27584786 PMCID: PMC5059853 DOI: 10.1038/cddis.2016.248] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Revised: 06/20/2016] [Accepted: 07/13/2016] [Indexed: 11/08/2022]
Abstract
Neutrophils play an indispensable role in killing of invading pathogens by enhancing reactive oxygen species (ROS) and NO generation, and subsequently undergoing apoptosis. Unlike ROS/NOX2, role of NO/NOS still remains undefined in the apoptosis of neutrophils (PMNs) and the present study attempts to decipher the importance of NO/NOS in the neutrophil apoptosis. Prolonged treatment of human PMNs or mice bone marrow derived neutrophils (BMDN) with NO led to enhanced ROS generation, caspase-8/caspase-3 cleavage, reduced mitochondrial membrane potential and finally cellular apoptosis. NO-induced ROS generation led to caspase-8 deglutathionylation and activation, which subsequently activated mitochondrial death pathway via BID (Bcl-2 family protein) cleavage. NO-mediated augmentation of caspase-8 and BID cleavage was significantly prevented in BMDN from neutrophil cytosolic factor-1 (NCF-1) knockout (KO) mice, implying the involvement of NOX2 in NO-induced apoptosis of PMNs. Furthermore, ROS, NO generation and inducible nitric oxide synthase (iNOS) expression were enhanced in a time-dependent manner in human PMNs and mice BMDN undergoing spontaneous apoptosis. Pharmacological and genetic ablation of iNOS in human PMNs and mice BMDN significantly reduced the levels of apoptosis. Impaired apoptosis of BMDN from iNOS KO mice was due to reduced caspase-8 activity which subsequently prevented caspase-3 and -9 activation. Altogether, our results suggest a crucial role of NO/iNOS in neutrophil apoptosis via enhanced ROS generation and caspase-8 mediated activation of mitochondrial death pathway.
Collapse
|
41
|
Likhachev IV, Balabaev NK, Galzitskaya OV. Available Instruments for Analyzing Molecular Dynamics Trajectories. Open Biochem J 2016; 10:1-11. [PMID: 27053964 PMCID: PMC4797681 DOI: 10.2174/1874091x01610010001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Revised: 02/05/2015] [Accepted: 04/07/2015] [Indexed: 11/22/2022] Open
Abstract
Molecular dynamics trajectories are the result of molecular dynamics simulations. Trajectories are sequential snapshots of simulated molecular system which represents atomic coordinates at specific time periods. Based on the definition, in a text format trajectory files are characterized by their simplicity and uselessness. To obtain information from such files, special programs and information processing techniques are applied: from molecular dynamics animation to finding characteristics along the trajectory (versus time). In this review, we describe different programs for processing molecular dynamics trajectories. The performance of these programs, usefulness for analyses of molecular dynamics trajectories, strong and weak aspects are discussed.
Collapse
Affiliation(s)
- I V Likhachev
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia; Institute of Mathematical Problems of Biology, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia
| | - N K Balabaev
- Institute of Mathematical Problems of Biology, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia
| | - O V Galzitskaya
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia
| |
Collapse
|
42
|
iPPBS-Opt: A Sequence-Based Ensemble Classifier for Identifying Protein-Protein Binding Sites by Optimizing Imbalanced Training Datasets. Molecules 2016; 21:E95. [PMID: 26797600 PMCID: PMC6274413 DOI: 10.3390/molecules21010095] [Citation(s) in RCA: 136] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Revised: 12/18/2015] [Accepted: 01/07/2016] [Indexed: 12/25/2022] Open
Abstract
Knowledge of protein-protein interactions and their binding sites is indispensable for in-depth understanding of the networks in living cells. With the avalanche of protein sequences generated in the postgenomic age, it is critical to develop computational methods for identifying in a timely fashion the protein-protein binding sites (PPBSs) based on the sequence information alone because the information obtained by this way can be used for both biomedical research and drug development. To address such a challenge, we have proposed a new predictor, called iPPBS-Opt, in which we have used: (1) the K-Nearest Neighbors Cleaning (KNNC) and Inserting Hypothetical Training Samples (IHTS) treatments to optimize the training dataset; (2) the ensemble voting approach to select the most relevant features; and (3) the stationary wavelet transform to formulate the statistical samples. Cross-validation tests by targeting the experiment-confirmed results have demonstrated that the new predictor is very promising, implying that the aforementioned practices are indeed very effective. Particularly, the approach of using the wavelets to express protein/peptide sequences might be the key in grasping the problem's essence, fully consistent with the findings that many important biological functions of proteins can be elucidated with their low-frequency internal motions. To maximize the convenience of most experimental scientists, we have provided a step-by-step guide on how to use the predictor's web server (http://www.jci-bioinfo.cn/iPPBS-Opt) to get the desired results without the need to go through the complicated mathematical equations involved.
Collapse
|
43
|
Fayaz SM, Rajanikant GK. Modelling the molecular mechanism of protein-protein interactions and their inhibition: CypD-p53 case study. Mol Divers 2015; 19:931-43. [PMID: 26170095 DOI: 10.1007/s11030-015-9612-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Accepted: 07/01/2015] [Indexed: 02/06/2023]
Abstract
Cyclophilin D (CypD) is an important regulatory protein involved in mitochondrial membrane permeability transition and cell death. Further, the mitochondrial CypD-p53 axis is an important contributor to necroptosis, a form of programmed necrosis, involved in various cardiovascular and neurological disorders. The CypD ligand, Cyclosporin A (CsA), was identified as an inhibitor of this interaction. In this study, using computational methods, we have attempted to model the CypD-p53 interaction in order to delineate their mode of binding and also to disclose the molecular mechanism, by means of which CsA interferes with this interaction. It was observed that p53 binds at the CsA-binding site of CypD. The knowledge obtained from this modelling was employed to identify novel CypD inhibitors through structure-based methods. Further, the identified compounds were tested by a similar strategy, adopted during the modelling process. This strategy could be applied to study the mechanism of protein-protein interaction (PPI) inhibition and to identify novel PPI inhibitors.
Collapse
Affiliation(s)
- S M Fayaz
- School of Biotechnology, National Institute of Technology Calicut, Calicut, 673601, India
| | - G K Rajanikant
- School of Biotechnology, National Institute of Technology Calicut, Calicut, 673601, India.
| |
Collapse
|
44
|
ProTSAV: A protein tertiary structure analysis and validation server. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1864:11-9. [PMID: 26478257 DOI: 10.1016/j.bbapap.2015.10.004] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Revised: 09/26/2015] [Accepted: 10/14/2015] [Indexed: 01/06/2023]
Abstract
Quality assessment of predicted model structures of proteins is as important as the protein tertiary structure prediction. A highly efficient quality assessment of predicted model structures directs further research on function. Here we present a new server ProTSAV, capable of evaluating predicted model structures based on some popular online servers and standalone tools. ProTSAV furnishes the user with a single quality score in case of individual protein structure along with a graphical representation and ranking in case of multiple protein structure assessment. The server is validated on ~64,446 protein structures including experimental structures from RCSB and predicted model structures for CASP targets and from public decoy sets. ProTSAV succeeds in predicting quality of protein structures with a specificity of 100% and a sensitivity of 98% on experimentally solved structures and achieves a specificity of 88%and a sensitivity of 91% on predicted protein structures of CASP11 targets under 2Å.The server overcomes the limitations of any single server/method and is seen to be robust in helping in quality assessment. ProTSAV is freely available at http://www.scfbio-iitd.res.in/software/proteomics/protsav.jsp.
Collapse
|
45
|
Protein cold adaptation: Role of physico-chemical parameters in adaptation of proteins to low temperatures. J Theor Biol 2015; 383:130-7. [DOI: 10.1016/j.jtbi.2015.07.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Revised: 06/21/2015] [Accepted: 07/16/2015] [Indexed: 11/21/2022]
|
46
|
Agrahari A, George Priya Doss C. Impact of I30T and I30M substitution in MPZ gene associated with Dejerine–Sottas syndrome type B (DSSB): A molecular modeling and dynamics. J Theor Biol 2015; 382:23-33. [DOI: 10.1016/j.jtbi.2015.06.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Revised: 05/21/2015] [Accepted: 06/10/2015] [Indexed: 11/28/2022]
|
47
|
Rodríguez DC, Ocampo M, Reyes C, Arévalo‐Pinzón G, Munoz M, Patarroyo MA, Patarroyo ME. Cell‐Peptide Specific Interaction Can Inhibit
Mycobacterium tuberculosis H37Rv
Infection. J Cell Biochem 2015; 117:946-58. [DOI: 10.1002/jcb.25379] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Accepted: 09/14/2015] [Indexed: 11/10/2022]
Affiliation(s)
- Deisy Carolina Rodríguez
- Fundacion Instituto de Inmunología de Colombia (FIDIC)BogotáColombia
- Universidad del RosarioBogotáColombia
| | - Marisol Ocampo
- Fundacion Instituto de Inmunología de Colombia (FIDIC)BogotáColombia
- Universidad del RosarioBogotáColombia
| | - Cesar Reyes
- Fundacion Instituto de Inmunología de Colombia (FIDIC)BogotáColombia
- Universidad del RosarioBogotáColombia
| | - Gabriela Arévalo‐Pinzón
- Fundacion Instituto de Inmunología de Colombia (FIDIC)BogotáColombia
- Universidad del RosarioBogotáColombia
| | - Marina Munoz
- Fundacion Instituto de Inmunología de Colombia (FIDIC)BogotáColombia
- Universidad del RosarioBogotáColombia
| | - Manuel Alfonso Patarroyo
- Fundacion Instituto de Inmunología de Colombia (FIDIC)BogotáColombia
- Universidad del RosarioBogotáColombia
| | - Manuel Elkin Patarroyo
- Fundacion Instituto de Inmunología de Colombia (FIDIC)BogotáColombia
- Universidad Nacional de ColombiaBogotáColombia
| |
Collapse
|
48
|
Ganguly B, Tewari K, Singh R. Homology modeling, functional annotation and comparative genomics of outer membrane protein H of Pasteurella multocida. J Theor Biol 2015; 386:18-24. [PMID: 26362105 DOI: 10.1016/j.jtbi.2015.08.028] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Revised: 08/29/2015] [Accepted: 08/31/2015] [Indexed: 11/18/2022]
Abstract
Pasteurella multocida is an important pathogen of animals and humans. Outer Membrane Protein (Omp) H is a major conserved protein in the envelope of P. multocida and has been commonly targeted as a protective antigen. However, not much is known about its structure and function due to the difficulties that are typically associated with obtaining sufficient amounts of purified prokaryotic transmembrane proteins. The present work is aimed at studying the OmpH using an in silico approach and consolidate the findings in light of existing experimental evidences. Our study describes the first 3D model of the P. multocida OmpH obtained through a combination of several in silico modeling approaches. From our results, OmpH of P. multocida could be classified as a homotrimeric, 16 stranded, β-barrel porin involved in the non-specific transport of small, hydrophilic molecules, serving essential osmoregulatory function. Moreover, very small homologous sequences could be identified in the host proteome, strengthening the probability of a successful OmpH-based vaccine against the pathogen with remote chances of cross-reaction to host proteins.
Collapse
Affiliation(s)
- Bhaskar Ganguly
- Animal Biotechnology Center, Department of Veterinary Physiology and Biochemistry, College of Veterinary and Animal Sciences, G. B. Pant University of Agriculture and Technology, Pantnagar 263145, India; Department of Veterinary Microbiology, College of Veterinary and Animal Sciences, G. B. Pant University of Agriculture and Technology, Pantnagar 263145, India.
| | - Kamal Tewari
- Department of Veterinary Microbiology, College of Veterinary and Animal Sciences, G. B. Pant University of Agriculture and Technology, Pantnagar 263145, India
| | - Rashmi Singh
- Department of Veterinary Microbiology, College of Veterinary and Animal Sciences, G. B. Pant University of Agriculture and Technology, Pantnagar 263145, India
| |
Collapse
|
49
|
Thai KM, Le DP, Tran NVK, Nguyen TTH, Tran TD, Le MT. Computational assay of Zanamivir binding affinity with original and mutant influenza neuraminidase 9 using molecular docking. J Theor Biol 2015; 385:31-9. [PMID: 26341387 DOI: 10.1016/j.jtbi.2015.08.019] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Revised: 08/13/2015] [Accepted: 08/14/2015] [Indexed: 01/26/2023]
Abstract
Based upon molecular docking, this study aimed to find notable in silico neuraminidase 9 (NA9) point mutations of the avian influenza A H7N9 virus that possess a Zanamivir resistant property and to determine the lead compound capable of inhibiting these NA9 mutations. Seven amino acids (key residues) at the binding site of neuraminidase 9 responsible for Zanamivir-NA9 direct interactions were identified and 72 commonly occurring mutant NA9 versions were created using the Sybyl-X 2.0 software. The docking scores obtained after Zanamivir was bound to all mutant molecules of NA9 revealed 3 notable mutations R292W, R118P, and R292K that could greatly reduce the binding affinity of the medicine. These 3 mutant NA9 versions were then bound to each of 154 different molecules chosen from 5 groups of compounds to determine which molecule(s) might be capable of inhibiting mutant neuraminidase 9, leading to the discovery of the lead compound of potent mutant NA9 inhibitors. This compound, together with other mutations occurring to NA9 identified in the study, would be used as data for further research regarding neuraminidase inhibitors and synthesizing new viable medications used in the fight against the virus.
Collapse
Affiliation(s)
- Khac-Minh Thai
- Department of Medicinal Chemistry, Faculty of Pharmacy, University of Medicine and Pharmacy, 41 Dinh Tien Hoang St, Dist 1, Ho Chi Minh City, Viet Nam.
| | - Duy-Phong Le
- Department of Medicinal Chemistry, Faculty of Pharmacy, University of Medicine and Pharmacy, 41 Dinh Tien Hoang St, Dist 1, Ho Chi Minh City, Viet Nam
| | - Nguyen-Viet-Khoa Tran
- Department of Medicinal Chemistry, Faculty of Pharmacy, University of Medicine and Pharmacy, 41 Dinh Tien Hoang St, Dist 1, Ho Chi Minh City, Viet Nam
| | - Thi-Thu-Ha Nguyen
- Department of Medicinal Chemistry, Faculty of Pharmacy, University of Medicine and Pharmacy, 41 Dinh Tien Hoang St, Dist 1, Ho Chi Minh City, Viet Nam
| | - Thanh-Dao Tran
- Department of Medicinal Chemistry, Faculty of Pharmacy, University of Medicine and Pharmacy, 41 Dinh Tien Hoang St, Dist 1, Ho Chi Minh City, Viet Nam
| | - Minh-Tri Le
- Department of Medicinal Chemistry, Faculty of Pharmacy, University of Medicine and Pharmacy, 41 Dinh Tien Hoang St, Dist 1, Ho Chi Minh City, Viet Nam
| |
Collapse
|
50
|
Yuan J, Xue B. Role of structural flexibility in the evolution of emerin. J Theor Biol 2015; 385:102-11. [PMID: 26319992 DOI: 10.1016/j.jtbi.2015.08.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Revised: 08/07/2015] [Accepted: 08/17/2015] [Indexed: 02/07/2023]
Abstract
Emerin is a short inner nuclear membrane protein with an LEM-domain at the N-terminal end and a transmembrane domain at the C-terminal end. The middle region of human emerin contains multiple binding motifs. Since emerin is often found in evolutionarily newer species, the functional conservation of emerin becomes an interesting topic. In this study, we have demonstrated that most of the functional motifs of emerin are intrinsically disordered or highly flexible. Many post-translational modification sites and mutation sites are associated with these disordered regions. The averaged substitution rates of most functional motifs between species correlate positively with the averaged disorder scores of those functional motifs. Human emerin sequence may have acquired new functions on protein-protein interaction through the formation of hydrophobic motifs in the middle region, which is resulted from accumulated mutations during the evolution process.
Collapse
Affiliation(s)
- Jia Yuan
- Department of Cell Biology, Microbiology and Molecular Biology, School of Natural Sciences and Mathematics, College of Arts and Sciences, University of South Florida, 4202 E. Fowler Ave, ISA 2015, Tampa, FL 33620, USA
| | - Bin Xue
- Department of Cell Biology, Microbiology and Molecular Biology, School of Natural Sciences and Mathematics, College of Arts and Sciences, University of South Florida, 4202 E. Fowler Ave, ISA 2015, Tampa, FL 33620, USA.
| |
Collapse
|