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Shakour N, Hoseinpoor S, Rajabian F, Azimi SG, Iranshahi M, Sadeghi-Aliabadi H, Hadizadeh F. Discovery of non-peptide GLP-1r natural agonists for enhancing coronary safety in type 2 diabetes patients. J Biomol Struct Dyn 2024:1-18. [PMID: 38165453 DOI: 10.1080/07391102.2023.2298734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 12/17/2023] [Indexed: 01/03/2024]
Abstract
This study explores the computational discovery of non-peptide agonists targeting the Glucagon-Like Peptide-1 Receptor (GLP-1R) to enhance the safety of major coronary outcomes in individuals affected by Type 2 Diabetes. The objective is to identify novel compounds that can activate the GLP-1R pathway without the limitations associated with peptide agonists. Type 2 diabetes mellitus (T2DM) is associated with an increased risk of cardiovascular disease (CVD) and mortality, which is attributed to the accumulation of fat in organs, including the heart. Glucagon-like peptide-1 receptor agonists (GLP-1RAs) are frequently used to manage T2DM and could potentially offer cardiovascular benefits. Therefore, this study examines non-peptide agonists of GLP-1R to improve coronary safety in type 2 diabetes patients. After rigorous assessments, two standout candidates were identified, with natural compound 12 emerging as the most promising. This study represents a notable advancement in enhancing the management of coronary outcomes among individuals with type 2 diabetes. The computational methodology employed successfully pinpointed potential GLP-1R natural agonists, providing optimism for the development of safer and more effective therapeutic interventions. Although computational methodologies have provided crucial insights, realizing the full potential of these compounds requires extensive experimental investigations, crucial in advancing therapeutic strategies for this critical patient population.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Neda Shakour
- Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
- Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Saeideh Hoseinpoor
- Department of Biochemistry and Biophysics, Faculty of Sciences, Mashhad Branch, Islamic Azad University, Mashhad, Iran
- International UNESCO Center for Health-Related Basic Sciences and Human Nutrition, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Fatemeh Rajabian
- Department of Pharmacodynamics and Toxicology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Sabikeh G Azimi
- Department of Chemistry, Faculty of Sciences, University of Birjand, Birjand, Iran
| | - Mehrdad Iranshahi
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Hojjat Sadeghi-Aliabadi
- Department of Pharmaceutical Chemistry, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Farzin Hadizadeh
- Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
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Vijayakumar S, Kumar LL, Borkotoky S, Murali A. The Application of MD Simulation to Lead Identification, Vaccine Design, and Structural Studies in Combat against Leishmaniasis - A Review. Mini Rev Med Chem 2024; 24:1089-1111. [PMID: 37680156 DOI: 10.2174/1389557523666230901105231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 06/07/2023] [Accepted: 07/14/2023] [Indexed: 09/09/2023]
Abstract
Drug discovery, vaccine design, and protein interaction studies are rapidly moving toward the routine use of molecular dynamics simulations (MDS) and related methods. As a result of MDS, it is possible to gain insights into the dynamics and function of identified drug targets, antibody-antigen interactions, potential vaccine candidates, intrinsically disordered proteins, and essential proteins. The MDS appears to be used in all possible ways in combating diseases such as cancer, however, it has not been well documented as to how effectively it is applied to infectious diseases such as Leishmaniasis. As a result, this review aims to survey the application of MDS in combating leishmaniasis. We have systematically collected articles that illustrate the implementation of MDS in drug discovery, vaccine development, and structural studies related to Leishmaniasis. Of all the articles reviewed, we identified that only a limited number of studies focused on the development of vaccines against Leishmaniasis through MDS. Also, the PCA and FEL studies were not carried out in most of the studies. These two were globally accepted utilities to understand the conformational changes and hence it is recommended that this analysis should be taken up in similar approaches in the future.
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Affiliation(s)
| | | | - Subhomoi Borkotoky
- Department of Biotechnology, Invertis University, Bareilly, Uttar Pradesh, India
| | - Ayaluru Murali
- Department of Bioinformatics, Pondicherry University, Puducherry, India
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Ghosh S, Kumar V, Verma A, Sharma T, Pradhan D, Selvapandiyan A, Salotra P, Singh R. Genome-wide analysis reveals allelic variation and chromosome copy number variation in paromomycin-resistant Leishmania donovani. Parasitol Res 2022; 121:3121-3132. [PMID: 36056959 DOI: 10.1007/s00436-022-07645-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 08/24/2022] [Indexed: 11/30/2022]
Abstract
In the absence of adequate diagnosis and treatment, leishmaniasis remains a major public health concern on a global scale. Drug resistance remains a key obstacle in controlling and eliminating visceral leishmaniasis. The therapeutic gap due to lack of target-specific medicine and vaccine can be minimized by obtaining parasite's genomic information. This study compared whole-genome sequence of paromomycin-resistant parasite (K133PMM) developed through in vitro adaptation and selection with sensitive Leishmania clinical isolate (K133WT). We found a large number of upstream and intergenic gene variations in K133PMM. There were 259 single nucleotide polymorphisms (SNPs), 187 insertion-deletion (InDels), and 546 copy number variations (CNVs) identified. Most of the genomic variations were found in the gene's upstream and non-coding regions. Ploidy estimation revealed chromosome 5 in tetrasomy and 6, 9, and 12 in trisomy, uniquely in K133PMM. These contain the genes for protein degradation, parasite motility, autophagy, cell cycle maintenance, and drug efflux membrane transporters. Furthermore, we also observed reduction in ploidy of chromosomes 15, 20, and 23, in the resistant parasite containing mostly the genes for hypothetical proteins and membrane transporters. We chronicled correlated genomic conversion and aneuploidy in parasites and hypothesize that this led to rapid evolutionary changes in response to drug induced pressure, which causes them to become resistant.
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Affiliation(s)
- Sushmita Ghosh
- ICMR-National Institute of Pathology, Safdarjung Hospital Campus, New Delhi, 110029, India.,Department of Molecular Medicine, Jamia Hamdard, New Delhi, 110062, India
| | - Vinay Kumar
- ICMR-National Institute of Pathology, Safdarjung Hospital Campus, New Delhi, 110029, India
| | - Aditya Verma
- ICMR-National Institute of Pathology, Safdarjung Hospital Campus, New Delhi, 110029, India
| | - Tanya Sharma
- ICMR-AIIMS Computational Genomics Centre, Indian Council of Medical Research, New Delhi, 110029, India
| | - Dibyabhaba Pradhan
- ICMR-AIIMS Computational Genomics Centre, Indian Council of Medical Research, New Delhi, 110029, India
| | | | - Poonam Salotra
- ICMR-National Institute of Pathology, Safdarjung Hospital Campus, New Delhi, 110029, India
| | - Ruchi Singh
- ICMR-National Institute of Pathology, Safdarjung Hospital Campus, New Delhi, 110029, India.
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Jain S, Sahu U, Kumar A, Khare P. Metabolic Pathways of Leishmania Parasite: Source of Pertinent Drug Targets and Potent Drug Candidates. Pharmaceutics 2022; 14:pharmaceutics14081590. [PMID: 36015216 PMCID: PMC9416627 DOI: 10.3390/pharmaceutics14081590] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 07/22/2022] [Accepted: 07/25/2022] [Indexed: 02/04/2023] Open
Abstract
Leishmaniasis is a tropical disease caused by a protozoan parasite Leishmania that is transmitted via infected female sandflies. At present, leishmaniasis treatment mainly counts on chemotherapy. The currently available drugs against leishmaniasis are costly, toxic, with multiple side effects, and limitations in the administration route. The rapid emergence of drug resistance has severely reduced the potency of anti-leishmanial drugs. As a result, there is a pressing need for the development of novel anti-leishmanial drugs with high potency, low cost, acceptable toxicity, and good pharmacokinetics features. Due to the availability of preclinical data, drug repurposing is a valuable approach for speeding up the development of effective anti-leishmanial through pointing to new drug targets in less time, having low costs and risk. Metabolic pathways of this parasite play a crucial role in the growth and proliferation of Leishmania species during the various stages of their life cycle. Based on available genomics/proteomics information, known pathways-based (sterol biosynthetic pathway, purine salvage pathway, glycolysis, GPI biosynthesis, hypusine, polyamine biosynthesis) Leishmania-specific proteins could be targeted with known drugs that were used in other diseases, resulting in finding new promising anti-leishmanial therapeutics. The present review discusses various metabolic pathways of the Leishmania parasite and some drug candidates targeting these pathways effectively that could be potent drugs against leishmaniasis in the future.
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Affiliation(s)
- Surbhi Jain
- Department of Microbiology, All India Institute of Medical Sciences, Bhopal 462026, Madhya Pradesh, India; (S.J.); (U.S.)
| | - Utkarsha Sahu
- Department of Microbiology, All India Institute of Medical Sciences, Bhopal 462026, Madhya Pradesh, India; (S.J.); (U.S.)
- Division of Synthetic Biology, Absolute Foods, Plot 68, Sector 44, Gurugram 122003, Haryana, India
| | - Awanish Kumar
- Department of Biotechnology, National Institute of Technology, Raipur 492010, Chhattisgarh, India
- Correspondence: or (A.K.); (P.K.)
| | - Prashant Khare
- Department of Microbiology, All India Institute of Medical Sciences, Bhopal 462026, Madhya Pradesh, India; (S.J.); (U.S.)
- Division of Synthetic Biology, Absolute Foods, Plot 68, Sector 44, Gurugram 122003, Haryana, India
- Correspondence: or (A.K.); (P.K.)
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Shakour N, Sahebkar A, Karimi G, Paseban M, Tasbandi A, Mosaffa F, Tayarani-Najaran Z, Ghodsi R, Hadizadeh F. Design, synthesis and biological evaluation of novel 5-(imidazolyl-methyl) thiazolidinediones as antidiabetic agents. Bioorg Chem 2021; 115:105162. [PMID: 34314919 DOI: 10.1016/j.bioorg.2021.105162] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 07/05/2021] [Accepted: 07/08/2021] [Indexed: 12/31/2022]
Abstract
A newly designed series of imidazolyl-methyl- l-2,4-thiazolidinediones 9 (a-m) were synthesized and In Silico studies were carried out to rationalize their anti-diabetic activity. Generally, all newly synthesized thiazolidinediones had anti-hyperglycemic activity compared with a diabetic-control group, without toxicity in 3T3 cells (viability ≥ 90%). These studies revealed that the compounds 9e and 9b (11∗10-6mol/kg) lowered blood glucose more effectively when compared to pioglitazone at the same dose. Following the administration of compound 9e, no weight gains or any serious side effects on liver and pancreas were observed. Moreover, the glucose consumption assay results showed a significant glucose-lowering effect (p < 0.001) in HepG2 cells, which were exposed to 11 mM of glucose at concentrations of 1.25-10 mM of compound 9e. Also, the PPAR-γ gene expression study revealed that pioglitazone and 9e showed similar behavior relative to the control group.
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Affiliation(s)
- Neda Shakour
- Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran; Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Amirhossein Sahebkar
- School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran; Neurogenic Inflammation Research Center, Mashhad University of Medical Sciences, Mashhad, Iran; Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Gholamreza Karimi
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Pharmacodynamics and Toxicology, School Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Maryam Paseban
- Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Physiology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Aida Tasbandi
- Neurogenic Inflammation Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Fatemeh Mosaffa
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Zahra Tayarani-Najaran
- Department of Pharmacodynamics and Toxicology, School Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Razieh Ghodsi
- Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran; Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Farzin Hadizadeh
- Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran; Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran.
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Curcumin Can Bind and Interact with CRP: An in silico Study. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1308:91-100. [PMID: 33861438 DOI: 10.1007/978-3-030-64872-5_7] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Curcuminis a polyphenol with anti-inflammatory and antioxidative properties, found primarily in turmeric, a flowering plant of the ginger family. Among its numerous medical uses, curcumin has been used in the management of metabolic syndrome, and inflammatory conditions such as artrhritis, anxiety and hyperlipidemia. In this paper, we used molecular docking tools to assess the affinity of four curcumin derivatives (Curcumin, Cyclocurcumin, Demethoxycurcumin, Bisdemethoxycurcumin) as well as the endogenous ligand phosphorylcholine to C-reactive protein (CRP), a sensitive marker of systemic inflammation. Our results showed that curcumin interacts through H bond with CRP at GLN 150 and ASP 140. Similar H bond interactions were found for each of the four curcumin derivatives with CRP. Moreover, a molecular dynamic simulation were performed to further establish the interaction between CRP and the ligands in atomic details using the Nanoscale Molecular Dynamics (NAMD) and CHARMM27 force field. Importantly, our results suggest the possible interaction between curcumin and curcurmin related molecules with CRP, thus showing an important regulatory function with plausible applications in inflammatory and oxidative processes in diseases.
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Morotti ALM, Martins-Teixeira MB, Carvalho I. Protozoan Parasites Glycosylphosphatidylinositol Anchors: Structures, Functions and Trends for Drug Discovery. Curr Med Chem 2019; 26:4301-4322. [PMID: 28748758 DOI: 10.2174/0929867324666170727110801] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Revised: 07/12/2017] [Accepted: 07/12/2017] [Indexed: 11/22/2022]
Abstract
BACKGROUND Glycosylphosphatidylinositol (GPI) anchors are molecules located on cell membranes of all eukaryotic organisms. Proteins, enzymes, and other macromolecules which are anchored by GPIs are essential elements for interaction between cells, and are widely used by protozoan parasites when compared to higher eukaryotes. METHODS More than one hundred references were collected to obtain broad information about mammalian and protozoan parasites' GPI structures, biosynthetic pathways, functions and attempts to use these molecules as drug targets against parasitic diseases. Differences between GPI among species were compared and highlighted. Strategies for drug discovery and development against protozoan GPI anchors were discussed based on what has been reported on literature. RESULTS There are many evidences that GPI anchors are crucial for parasite's survival and interaction with hosts' cells. Despite all GPI anchors contain a conserved glycan core, they present variations regarding structural features and biosynthetic pathways between organisms, which could offer adequate selectivity to validate GPI anchors as drug targets. Discussion was developed with focus on the following parasites: Trypanosoma brucei, Trypanosoma cruzi, Leishmania, Plasmodium falciparum and Toxoplasma gondii, causative agents of tropical neglected diseases. CONCLUSION This review debates the main variances between parasitic and mammalian GPI anchor biosynthesis and structures, as well as clues for strategic development for new anti-parasitic therapies based on GPI anchors.
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Affiliation(s)
- Ana Luísa Malaco Morotti
- School of Pharmaceutical Sciences of Ribeirao Preto - University of Sao Paulo, Sao Paulo, Brazil
| | | | - Ivone Carvalho
- School of Pharmaceutical Sciences of Ribeirao Preto - University of Sao Paulo, Sao Paulo, Brazil
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Ribeiro CV, Rocha BFB, Moreira DDS, Peruhype-Magalhães V, Murta SMF. Mannosyltransferase (GPI-14) overexpression protects promastigote and amastigote forms of Leishmania braziliensis against trivalent antimony. Parasit Vectors 2019; 12:60. [PMID: 30683152 PMCID: PMC6346506 DOI: 10.1186/s13071-019-3305-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 01/08/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Glycosylphosphatidylinositol is a surface molecule important for host-parasite interactions. Mannosyltransferase (GPI-14) is an essential enzyme for adding mannose on the glycosylphosphatidyl group. This study attempted to overexpress the GPI-14 gene in Leishmania braziliensis to investigate its role in the antimony-resistance phenotype of this parasite. RESULTS GPI-14 mRNA levels determined by quantitative real-time PCR (qRT-PCR) showed an increased expression in clones transfected with GPI-14 compared to its respective wild-type line. In order to investigate the expression profile of the surface carbohydrates of these clones, the intensity of the fluorescence emitted by the parasites after concanavalin-A (a lectin that binds to the terminal regions of α-D-mannosyl and α-D-glucosyl residues) treatment was analyzed. The results showed that the clones transfected with GPI-14 express 2.8-fold more mannose and glucose residues than those of the wild-type parental line, indicating effective GPI-14 overexpression. Antimony susceptibility tests using promastigotes showed that clones overexpressing the GPI-14 enzyme are 2.4- and 10.5-fold more resistant to potassium antimonyl tartrate (SbIII) than the parental non-transfected line. Infection analysis using THP-1 macrophages showed that amastigotes from both GPI-14 overexpressing clones were 3-fold more resistant to SbIII than the wild-type line. CONCLUSIONS Our results suggest the involvement of the GPI-14 enzyme in the SbIII-resistance phenotype of L. braziliensis.
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Affiliation(s)
- Christiana Vargas Ribeiro
- Instituto René Rachou IRR, Fundação Oswaldo Cruz - FIOCRUZ/Minas, Avenida Augusto de Lima, Belo Horizonte, MG, 1715, Brazil
| | - Bruna Fonte Boa Rocha
- Instituto René Rachou IRR, Fundação Oswaldo Cruz - FIOCRUZ/Minas, Avenida Augusto de Lima, Belo Horizonte, MG, 1715, Brazil
| | - Douglas de Souza Moreira
- Instituto René Rachou IRR, Fundação Oswaldo Cruz - FIOCRUZ/Minas, Avenida Augusto de Lima, Belo Horizonte, MG, 1715, Brazil
| | - Vanessa Peruhype-Magalhães
- Instituto René Rachou IRR, Fundação Oswaldo Cruz - FIOCRUZ/Minas, Avenida Augusto de Lima, Belo Horizonte, MG, 1715, Brazil
| | - Silvane Maria Fonseca Murta
- Instituto René Rachou IRR, Fundação Oswaldo Cruz - FIOCRUZ/Minas, Avenida Augusto de Lima, Belo Horizonte, MG, 1715, Brazil.
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Abdizadeh T, Kalani MR, Abnous K, Tayarani-Najaran Z, Khashyarmanesh BZ, Abdizadeh R, Ghodsi R, Hadizadeh F. Design, synthesis and biological evaluation of novel coumarin-based benzamides as potent histone deacetylase inhibitors and anticancer agents. Eur J Med Chem 2017; 132:42-62. [PMID: 28340413 DOI: 10.1016/j.ejmech.2017.03.024] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2017] [Revised: 03/06/2017] [Accepted: 03/14/2017] [Indexed: 01/26/2023]
Abstract
Histone deacetylases (HDACs) are attractive therapeutic targets for the treatment of cancer and other diseases. It has four classes (I-IV), among them especially class I isozyme are involved in promoting tumor cells proliferation, angiogenesis, differentiation, invasion and metastasis and also viable targets for cancer therapeutics. A novel series of coumarin-based benzamides was designed and synthesized as HDAC inhibitors. The cytotoxic activity of the synthesized compounds (8a-u) was evaluated against six human cancer cell lines including HCT116, A2780, MCF7, PC3, HL60 and A549 and a single normal cell line (Huvec). We evaluated their inhibitory activities against pan HDAC and HDAC1 isoform. Four compounds (8f, 8q, 8r and 8u) showed significant cytotoxicity with IC50 in the range of 0.53-57.59 μM on cancer cells and potent pan-HDAC inhibitory activity (consists of HDAC isoenzymes) (IC50 = 0.80-14.81 μM) and HDAC1 inhibitory activity (IC50 = 0.47-0.87 μM and also, had no effect on Huvec (human normal cell line) viability (IC50 > 100 μM). Among them, 8u displayed a higher potency for HDAC1 inhibition with IC50 value of 0.47 ± 0.02 μM near equal to the reference drug Entinostat (IC50 = 0.41 ± 0.06 μM). Molecular docking studies and Molecular dynamics simulation of compound 8a displayed possible mode of interaction between this compound and HDAC1enzyme.
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Affiliation(s)
- Tooba Abdizadeh
- Biotechnology Research Center, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohammad Reza Kalani
- School of Cell and Molecular Biology, University of Illinois at Urbana-Champaign, Urbana, United States; Department of Molecular Medicine, Golestan University of Medical Sciences, Golestan, Iran
| | - Khalil Abnous
- Pharmaceutical Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Zahra Tayarani-Najaran
- Department of Pharmacodynamics and Toxicology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Bibi Zahra Khashyarmanesh
- Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Rahman Abdizadeh
- Department of Medical Parasitology and Mycology, Faculty of Medicine, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Razieh Ghodsi
- Biotechnology Research Center, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Farzin Hadizadeh
- Biotechnology Research Center, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran.
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Singh SL, Rai RC, Sah SK, Komath SS. The catalytic subunit of the first mannosyltransferase in the GPI biosynthetic pathway affects growth, cell wall integrity and hyphal morphogenesis in Candida albicans. Yeast 2016; 33:365-83. [PMID: 27337589 DOI: 10.1002/yea.3179] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Revised: 06/04/2016] [Accepted: 06/05/2016] [Indexed: 01/13/2023] Open
Abstract
CaGpi14 is the catalytic subunit of the first mannosyltransferase that is involved in the glycosylphosphatidylinositol (GPI) biosynthetic pathway in Candida albicans. We show that CaGPI14 is able to rescue a conditionally lethal gpi14 mutant of Saccharomyces cerevisiae, unlike its mammalian homologue. The depletion of this enzyme in C. albicans leads to severe growth defects, besides causing deficiencies in GPI anchor levels. In addition, CaGpi14 depletion results in cell wall defects and upregulation of the cell wall integrity response pathway. This in turn appears to trigger the osmotic-stress dependent activation of the HOG1 pathway and an upregulation of HOG1 as well as its downstream target, SKO1, a known suppressor of expression of hyphae-specific genes. Consistent with this, mutants of CaGPI14 are unable to undergo hyphal transformations in different hyphae-inducing media, under conditions that produce abundant hyphae in the wild-type cells. Hyphal defects in the CaGPI14 mutants could not be attributed either to reduced protein kinase C activation or to defective Ras signalling in these cells but appeared to be driven by perturbations in the HOG1 pathway. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Sneh Lata Singh
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Ramesh Chandra Rai
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | | | - Sneha Sudha Komath
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
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The effect of glycosylation on the transferrin structure: A molecular dynamic simulation analysis. J Theor Biol 2016; 404:73-81. [PMID: 27235585 DOI: 10.1016/j.jtbi.2016.05.024] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 05/10/2016] [Accepted: 05/18/2016] [Indexed: 11/20/2022]
Abstract
Transferrins have been defined by the highly cooperative binding of iron and a carbonate anion to form a Fe-CO3-Tf ternary complex. As such, the layout of the binding site residues affects transferrin function significantly; In contrast to N-lobe, C-lobe binding site of the transferrin structure has been less characterized and little research which surveyed the interaction of carbonate with transferrin in the C-lobe binding site has been found. In the present work, molecular dynamic simulation was employed to gain access into the molecular level understanding of carbonate binding site and their interactions in each lobe. Residues responsible for carbonate binding of transferrin structure were pointed out. In addition, native human transferrin is a glycoprotein that two N-linked complex glycan chains located in the C-lobe. Usually, in the molecular dynamic simulation for simplifying, glycan is removed from the protein structure. Here, we explore the effect of glycosylation on the transferrin structure. Glycosylation appears to have an effect on the layout of the binding site residue and transferrin structure. On the other hand, sometimes the entire transferrin formed by separated lobes that it allows the results to be interpreted in a straightforward manner rather than more parameters required for full length protein. But, it should be noted that there are differences between the separated lobe and full length transferrin, hence, a comparative analysis by the molecular dynamic simulation was performed to investigate such structural variations. Results revealed that separation in C-lobe caused a significant structural variation in comparison to N-lobe. Consequently, the separated lobes and the full length one are different, showing the importance of the interlobe communication and the impact of the lobes on each other in the transferrin structure.
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Ling B, Yan X, Sun M, Bi S. Theoretical investigations on the interactions of glucokinase regulatory protein with fructose phosphates. Comput Biol Chem 2015; 60:21-31. [PMID: 26629747 DOI: 10.1016/j.compbiolchem.2015.07.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Revised: 07/16/2015] [Accepted: 07/25/2015] [Indexed: 10/23/2022]
Abstract
Glucokinase (GK) plays a critical role in maintaining glucose homeostasis in the human liver and pancreas. In the liver, the activity of GK is modulated by the glucokinase regulatory protein (GKRP) which functions as a competitive inhibitor of glucose to bind to GK. Moreover, the inhibitory intensity of GKRP-GK is suppressed by fructose 1-phosphate (F1P), and reinforced by fructose 6-phosphate (F6P). Here, we employed a series of computational techniques to explore the interactions of fructose phosphates with GKRP. Calculation results reveal that F1P and F6P can bind to the same active site of GKRP with different binding modes, and electrostatic interaction provides a major driving force for the ligand binding. The presence of fructose phosphate severely influences the motions of protein and the conformational space, and the structural change of sugar phosphate influences its interactions with GKRP, leading to a large conformational rearrangement of loop2 in the SIS2 domain. In particular, the binding of F6P to GKRP facilitates the protruding loop2 contacting with GK to form the stable GK-GKRP complex. The conserved residues 179-184 of GKRP play a major role in the binding of phosphate group and maintaining the stability of GKRP. These results may provide deep insight into the regulatory mechanism of GKRP to the activity of GK.
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Affiliation(s)
- Baoping Ling
- School of Chemistry and Chemical Engineering, Qufu Normal University, Qufu, Shandong Province 273165, China.
| | - Xueyuan Yan
- School of Chemistry and Chemical Engineering, Qufu Normal University, Qufu, Shandong Province 273165, China
| | - Min Sun
- School of Chemistry and Chemical Engineering, Qufu Normal University, Qufu, Shandong Province 273165, China
| | - Siwei Bi
- School of Chemistry and Chemical Engineering, Qufu Normal University, Qufu, Shandong Province 273165, China.
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Kotowski N, Jardim R, Dávila AMR. Improved orthologous databases to ease protozoan targets inference. Parasit Vectors 2015; 8:494. [PMID: 26416523 PMCID: PMC4587786 DOI: 10.1186/s13071-015-1090-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 09/11/2015] [Indexed: 11/10/2022] Open
Abstract
Background Homology inference helps on identifying similarities, as well as differences among organisms, which provides a better insight on how closely related one might be to another. In addition, comparative genomics pipelines are widely adopted tools designed using different bioinformatics applications and algorithms. In this article, we propose a methodology to build improved orthologous databases with the potential to aid on protozoan target identification, one of the many tasks which benefit from comparative genomics tools. Methods Our analyses are based on OrthoSearch, a comparative genomics pipeline originally designed to infer orthologs through protein-profile comparison, supported by an HMM, reciprocal best hits based approach. Our methodology allows OrthoSearch to confront two orthologous databases and to generate an improved new one. Such can be later used to infer potential protozoan targets through a similarity analysis against the human genome. Results The protein sequences of Cryptosporidium hominis, Entamoeba histolytica and Leishmania infantum genomes were comparatively analyzed against three orthologous databases: (i) EggNOG KOG, (ii) ProtozoaDB and (iii) Kegg Orthology (KO). That allowed us to create two new orthologous databases, “KO + EggNOG KOG” and “KO + EggNOG KOG + ProtozoaDB”, with 16,938 and 27,701 orthologous groups, respectively. Such new orthologous databases were used for a regular OrthoSearch run. By confronting “KO + EggNOG KOG” and “KO + EggNOG KOG + ProtozoaDB” databases and protozoan species we were able to detect the following total of orthologous groups and coverage (relation between the inferred orthologous groups and the species total number of proteins): Cryptosporidium hominis: 1,821 (11 %) and 3,254 (12 %); Entamoeba histolytica: 2,245 (13 %) and 5,305 (19 %); Leishmania infantum: 2,702 (16 %) and 4,760 (17 %). Using our HMM-based methodology and the largest created orthologous database, it was possible to infer 13 orthologous groups which represent potential protozoan targets; these were found because of our distant homology approach. We also provide the number of species-specific, pair-to-pair and core groups from such analyses, depicted in Venn diagrams. Conclusions The orthologous databases generated by our HMM-based methodology provide a broader dataset, with larger amounts of orthologous groups when compared to the original databases used as input. Those may be used for several homology inference analyses, annotation tasks and protozoan targets identification. Electronic supplementary material The online version of this article (doi:10.1186/s13071-015-1090-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nelson Kotowski
- Computational and Systems Biology Laboratory, Oswaldo Cruz Institute, FIOCRUZ, Avenida Brasil, 4365, 21040-360, Rio de Janeiro, RJ, Brazil.
| | - Rodrigo Jardim
- Computational and Systems Biology Laboratory, Oswaldo Cruz Institute, FIOCRUZ, Avenida Brasil, 4365, 21040-360, Rio de Janeiro, RJ, Brazil.
| | - Alberto M R Dávila
- Computational and Systems Biology Laboratory, Oswaldo Cruz Institute, FIOCRUZ, Avenida Brasil, 4365, 21040-360, Rio de Janeiro, RJ, Brazil.
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