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Qiao F, Binkowski TA, Broughan I, Chen W, Natarajan A, Schiltz GE, Scheidt KA, Anderson WF, Bergan R. Protein Structure Inspired Discovery of a Novel Inducer of Anoikis in Human Melanoma. Cancers (Basel) 2024; 16:3177. [PMID: 39335149 PMCID: PMC11429909 DOI: 10.3390/cancers16183177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2024] [Revised: 09/11/2024] [Accepted: 09/12/2024] [Indexed: 09/30/2024] Open
Abstract
Drug discovery historically starts with an established function, either that of compounds or proteins. This can hamper discovery of novel therapeutics. As structure determines function, we hypothesized that unique 3D protein structures constitute primary data that can inform novel discovery. Using a computationally intensive physics-based analytical platform operating at supercomputing speeds, we probed a high-resolution protein X-ray crystallographic library developed by us. For each of the eight identified novel 3D structures, we analyzed binding of sixty million compounds. Top-ranking compounds were acquired and screened for efficacy against breast, prostate, colon, or lung cancer, and for toxicity on normal human bone marrow stem cells, both using eight-day colony formation assays. Effective and non-toxic compounds segregated to two pockets. One compound, Dxr2-017, exhibited selective anti-melanoma activity in the NCI-60 cell line screen. In eight-day assays, Dxr2-017 had an IC50 of 12 nM against melanoma cells, while concentrations over 2100-fold higher had minimal stem cell toxicity. Dxr2-017 induced anoikis, a unique form of programmed cell death in need of targeted therapeutics. Our findings demonstrate proof-of-concept that protein structures represent high-value primary data to support the discovery of novel acting therapeutics. This approach is widely applicable.
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Affiliation(s)
- Fangfang Qiao
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68105, USA
| | | | - Irene Broughan
- Department of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Weining Chen
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68105, USA
| | - Amarnath Natarajan
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68105, USA
| | - Gary E Schiltz
- Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
| | - Karl A Scheidt
- Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
| | - Wayne F Anderson
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, IL 60611, USA
| | - Raymond Bergan
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68105, USA
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Qiao F, Binknowski TA, Broughan I, Chen W, Natarajan A, Schiltz GE, Scheidt KA, Anderson WF, Bergan R. Protein Structure Inspired Drug Discovery. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.17.594634. [PMID: 38826221 PMCID: PMC11142055 DOI: 10.1101/2024.05.17.594634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Drug discovery starts with known function, either of a compound or a protein, in-turn prompting investigations to probe 3D structure of the compound-protein interface. As protein structure determines function, we hypothesized that unique 3D structural motifs represent primary information denoting unique function that can drive discovery of novel agents. Using a physics-based protein structure analysis platform developed by us, designed to conduct computationally intensive analysis at supercomputing speeds, we probed a high-resolution protein x-ray crystallographic library developed by us. We selected 3D structural motifs whose function was not otherwise established, that offered environments supporting binding of drug-like chemicals and were present on proteins that were not established therapeutic targets. For each of eight potential binding pockets on six different proteins we accessed a 60 million compound library and used our analysis platform to evaluate binding. Using eight-day colony formation assays acquired compounds were screened for efficacy against human breast, prostate, colon and lung cancer cells and toxicity against human bone marrow stem cells. Compounds selectively inhibiting cancer growth segregated to two pockets on separate proteins. The compound, Dxr2-017, exhibited selective activity against human melanoma cells in the NCI-60 cell line screen, had an IC50 of 19 nM against human melanoma M14 cells in our eight-day assay, while over 2100-fold higher concentrations inhibited stem cells by less than 30%. We show that Dxr2-017 induces anoikis, a unique form of programmed cell death in need of targeted therapeutics. The predicted target protein for Dxr2-017 is expressed in bacteria, not in humans. This supports our strategy of focusing on unique 3D structural motifs. It is known that functionally important 3D structures are evolutionarily conserved. Here we demonstrate proof-of-concept that protein structure represents high value primary data to support discovery of novel therapeutics. This approach is widely applicable.
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Affiliation(s)
- Fangfang Qiao
- Eppley Institute for Research in Cancer, University of Nebraska Medical Center, Omaha, NE 68105, USA
| | | | - Irene Broughan
- Department of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Weining Chen
- Eppley Institute for Research in Cancer, University of Nebraska Medical Center, Omaha, NE 68105, USA
| | - Amarnath Natarajan
- Eppley Institute for Research in Cancer, University of Nebraska Medical Center, Omaha, NE 68105, USA
| | - Gary E. Schiltz
- Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
| | - Karl A. Scheidt
- Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
| | - Wayne F. Anderson
- Department of Biochemistry and Molecular Genetics, Northwestern University, Chicago, IL 60611, USA
| | - Raymond Bergan
- Eppley Institute for Research in Cancer, University of Nebraska Medical Center, Omaha, NE 68105, USA
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Mydin RBSMN, Mahboob A, Sreekantan S, Saharudin KA, Qazem EQ, Hazan R, Wajidi MFF. Mechano-cytoskeleton remodeling mechanism and molecular docking studies on nanosurface technology: Titania nanotube arrays. Biotechnol Appl Biochem 2022. [PMID: 36567620 DOI: 10.1002/bab.2421] [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: 03/13/2022] [Accepted: 06/26/2022] [Indexed: 12/27/2022]
Abstract
In biomedical implant technology, nanosurface such as titania nanotube arrays (TNA) could provide better cellular adaptation, especially for long-term tissue acceptance response. Mechanotransduction activities of TNA nanosurface could involve the cytoskeleton remodeling mechanism. However, there is no clear insight into TNA mechano-cytoskeleton remodeling activities, especially computational approaches. Epithelial cells have played critical interface between biomedical implant surface and tissue acceptance, particularly for long-term interaction. Therefore, this study investigates genomic responses that are responsible for cell-TNA mechano-stimulus using epithelial cells model. Findings suggested that cell-TNA interaction may improve structural and extracellular matrix (ECM) support on the cells as an adaptive response toward the nanosurface topography. More specifically, the surface topography of the TNA might improve the cell polarity and adhesion properties via the interaction of the plasma membrane and intracellular matrix responses. TNA nanosurface might engross the cytoskeleton remodeling activities for multidirectional cell movement and cellular protrusions on TNA nanosurface. These observations are supported by the molecular docking profiles that determine proteins' in silico binding mechanism on TNA. This active cell-surface revamping would allow cells to adapt to develop a protective barrier toward TNA nanosurface, thus enhancing biocompatibility properties distinctly for long-term interaction. The findings from this study will be beneficial toward nano-molecular knowledge of designing functional nanosurface technology for advanced medical implant applications.
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Affiliation(s)
- Rabiatul Basria S M N Mydin
- Department of Biomedical Science, Advanced Medical and Dental Institute, Universiti Sains Malaysia, Pulau Pinang, Malaysia
| | - Alam Mahboob
- Division of Chemistry & Biotechnology, Dongguk University, Gyeongju, Republic of Korea
| | - Srimala Sreekantan
- School of Materials and Mineral Resources Engineering, Universiti Sains Malaysia, Pulau Pinang, Malaysia
| | - Khairul Arifah Saharudin
- School of Materials and Mineral Resources Engineering, Universiti Sains Malaysia, Pulau Pinang, Malaysia.,Qdos Interconnect Sdn Bhd, Pulau Pinang, Malaysia
| | - Ekhlas Qaid Qazem
- Materials Technology Group, Industrial Technology Division, Nuclear Malaysia Agency, Kajang, Selangor, Malaysia
| | - Roshasnorlyza Hazan
- Department of Medical Laboratory, College of Medicine and Health Sciences, Hodeidah University, Hodeidah, Yemen
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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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Smyk JM, Majewska A. Favipiravir in the Battle with Respiratory Viruses. Mini Rev Med Chem 2022; 22:2224-2236. [DOI: 10.2174/1389557522666220218122744] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 10/12/2021] [Accepted: 01/13/2022] [Indexed: 11/22/2022]
Abstract
Abstract:
Among antiviral drugs, the vast majority targets only one or two related viruses. The conventional model, one virus - one drug, significantly limits therapeutic options. Therefore, in the strategy of controlling viral infections, there is a necessity to develop compounds with pleiotropic effects. Favipiravir (FPV) emerged as a strong candidate to become such a drug. The aim of the study is to present up-to-date information on the role of favipiravir in the treatment of viral respiratory infections. The anti-influenza activity of favipiravir has been confirmed in cell culture experiments, animal models and clinical trials. Thoroughly different - from the previously registered drugs - mechanism of action suggests that FVP can be used as a countermeasure for the novel or re-emerging influenza virus infections.
In recent months, favipiravir has been broadly investigated due to its potential efficacy in the treatment of Covid-19. Based on preclinical and clinical studies and a recently published meta-analysis it seems that favipiravir may be a promising antiviral drug in the treatment of patients with Covid-19.
FPV is also effective against other RNA respiratory viruses and may be a candidate for the treatment of serious infections caused by human rhinovirus, respiratory syncytial virus, metapneumovirus, parainfluenza viruses and hantavirus pulmonary syndrome.
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Affiliation(s)
- Julia M. Smyk
- Department of Medical Microbiology, Medical University of Warsaw, Chalubinskiego 5 Str., 02-004 Warsaw, Poland
| | - Anna Majewska
- Department of Medical Microbiology, Medical University of Warsaw, Chalubinskiego 5 Str., 02-004 Warsaw, Poland
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Validation of reference genes for expression analysis in a murine trauma model combining traumatic brain injury and femoral fracture. Sci Rep 2020; 10:15057. [PMID: 32929099 PMCID: PMC7490670 DOI: 10.1038/s41598-020-71895-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 08/17/2020] [Indexed: 02/06/2023] Open
Abstract
Systemic and local posttraumatic responses are often monitored on mRNA expression level using quantitative real-time PCR (qRT-PCR), which requires normalisation to adjust for confounding sources of variability. Normalisation requests reference (housekeeping) genes stable throughout time and divergent experimental conditions in the tissue of interest, which are crucial for a reliable and reproducible gene expression analysis. Although previous animal studies analysed reference genes following isolated trauma, this multiple-trauma gene expression analysis provides a notable study analysing reference genes in primarily affected (i.e. bone/fracture callus and hypothalamus) and secondarily affected organs (i.e. white adipose tissue, liver, muscle and spleen), following experimental long bone fracture and traumatic brain injury. We considered tissue-specific and commonly used top-ranked reference candidates from different functional groups that were evaluated applying the established expression stability analysis tools NormFinder, GeNorm, BestKeeper and RefFinder. In conclusion, reference gene expression in primary organs is highly time point as well as tissue-specific, and therefore requires careful evaluation for qRT-PCR analysis. Furthermore, the general application of Ppia, particularly in combination with a second reference gene, is strongly recommended for the analysis of systemic effects in the case of indirect trauma affecting secondary organs through local and systemic pathophysiological responses.
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Leite ACL, Espíndola JWP, de Oliveira Cardoso MV, de Oliveira Filho GB. Privileged Structures in the Design of Potential Drug Candidates for Neglected Diseases. Curr Med Chem 2019; 26:4323-4354. [DOI: 10.2174/0929867324666171023163752] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 09/15/2017] [Accepted: 09/19/2017] [Indexed: 11/22/2022]
Abstract
Background:
Privileged motifs are recurring in a wide range of biologically
active compounds that reach different pharmaceutical targets and pathways and could represent
a suitable start point to access potential candidates in the neglected diseases field.
The current therapies to treat these diseases are based in drugs that lack of the desired effectiveness,
affordable methods of synthesis and allow a way to emergence of resistant
strains. Due the lack of financial return, only few pharmaceutical companies have been
investing in research for new therapeutics for neglected diseases (ND).
Methods:
Based on the literature search from 2002 to 2016, we discuss how six privileged
motifs, focusing phthalimide, isatin, indole, thiosemicarbazone, thiazole, and thiazolidinone
are particularly recurrent in compounds active against some of neglected diseases.
Results:
It was observed that attention was paid particularly for Chagas disease, malaria,
tuberculosis, schistosomiasis, leishmaniasis, dengue, African sleeping sickness (Human
African Trypanosomiasis - HAT) and toxoplasmosis. It was possible to verify that, among
the ND, antitrypanosomal and antiplasmodial activities were between the most searched.
Besides, thiosemicarbazone moiety seems to be the most versatile and frequently explored
scaffold. As well, phthalimide, isatin, thiazole, and thiazolidone nucleus have been also
explored in the ND field.
Conclusion:
Some described compounds, appear to be promising drug candidates, while
others could represent a valuable inspiration in the research for new lead compounds.
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Affiliation(s)
- Ana Cristina Lima Leite
- Departamento de Ciencias Farmaceuticas, Centro de Ciencias da Saude, Universidade Federal de Pernambuco, 50740-520, Recife, PE, Brazil
| | - José Wanderlan Pontes Espíndola
- Departamento de Ciencias Farmaceuticas, Centro de Ciencias da Saude, Universidade Federal de Pernambuco, 50740-520, Recife, PE, Brazil
| | | | - Gevanio Bezerra de Oliveira Filho
- Departamento de Ciencias Farmaceuticas, Centro de Ciencias da Saude, Universidade Federal de Pernambuco, 50740-520, Recife, PE, Brazil
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Kumar M, Topno RK, Dikhit MR, Bhawana, Sahoo GC, Madhukar M, Pandey K, Das P. Molecular docking studies of chloroquine and its derivatives against P23 pro-zbd domain of chikungunya virus: Implication in designing of novel therapeutic strategies. J Cell Biochem 2019; 120:18298-18308. [PMID: 31310373 DOI: 10.1002/jcb.29139] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 02/25/2019] [Accepted: 02/28/2019] [Indexed: 01/26/2023]
Abstract
The arthropod-transmitted chikungunya virus has emerged as an epidemic menace that causes debilitating polyarthritis. With this life-threatening impact on humans, the possible treatment requires to cure the viral infectivity. But, devoid of any vaccine against the chikungunya virus (CHIKV), there is a need to develop a novel chemotherapeutic strategy to treat this noxious infection. CHIKV carries highly compact P23pro-zbd structure that possesses potential RNA-binding surface domains which extremely influences the use of RNA template during genome replication at the time of infection and pathogenesis. Therefore, computational approaches were used to explore the novel small molecule inhibitors targeting P23pro-zbd domain. The tertiary structure was modeled and optimized using in silico approaches. The results obtained from PROCHECK (93.1% residues in favored regions), ERRAT (87.480 overall model quality) and ProSA (Z-score: -11.72) revealed the reliability of the proposed model. Interestingly, a previously reported inhibitor, chloroquine possesses good binding affinities with the target domain. In-depth analysis revealed that chloroquine derivatives such as didesethyl chloroquine hydroxyacetamide, cletoquine, hydroxychloroquine exhibited a better binding affinity. Notably, MD simulation analysis exhibited that Thr1312, Ala1355, Ala1356, Asn1357, Asp1364, Val1366, Cys1367, Ala1401, Gly1403, Ser1443, Tyr1444, Gly1445, Asn1459, and Thr1463 residues are the key amino acid responsible for stable ligand-protein interaction. The results obtained from this study provide new insights and advances the understanding to develop a new approach to consider effective and novel drug against chikungunya. However, a detailed in vivo study is required to explore its drug likeliness against this life-threatening disease.
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Affiliation(s)
- Maneesh Kumar
- Department of Virology, ICMR-Rajendra Memorial Research Institute of Medical Sciences, Agamkuan, Patna, India
| | - Roshan Kamal Topno
- Department of Epidemiology, ICMR-Rajendra Memorial Research Institute of Medical Sciences, Agamkuan, Patna, India
| | - Manas Ranjan Dikhit
- Department of Bioinformatics, ICMR-Rajendra Memorial Research Institute of Medical Sciences, Agamkuan, Patna, India
| | - Bhawana
- Department of Virology, ICMR-Rajendra Memorial Research Institute of Medical Sciences, Agamkuan, Patna, India
| | - Ganesh Chandra Sahoo
- Department of Bioinformatics, ICMR-Rajendra Memorial Research Institute of Medical Sciences, Agamkuan, Patna, India
| | - Major Madhukar
- Department of Clinical Medicine, ICMR-Rajendra Memorial Research Institute of Medical Sciences, Agamkuan, Patna, India
| | - Krishna Pandey
- Department of Clinical Medicine, ICMR-Rajendra Memorial Research Institute of Medical Sciences, Agamkuan, Patna, India
| | - Pradeep Das
- Department of Molecular Biology, ICMR-Rajendra Memorial Research Institute of Medical Sciences, Agamkuan, Patna, India
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Computational elucidation of novel antagonists and binding insights by structural and functional analyses of serine hydroxymethyltransferase and interaction with inhibitors. GENE REPORTS 2018. [DOI: 10.1016/j.genrep.2017.10.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Ansari MY, Dikhit MR, Sahoo GC, Ali V, Das P. Recent advancement and treatment of leishmaniasis based on pharmacoinformatics approach: Current and future outlook. GENE REPORTS 2017. [DOI: 10.1016/j.genrep.2017.09.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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12
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Patel RD, Kumar SP, Patel CN, Shankar SS, Pandya HA, Solanki HA. Parallel screening of drug-like natural compounds using Caco-2 cell permeability QSAR model with applicability domain, lipophilic ligand efficiency index and shape property: A case study of HIV-1 reverse transcriptase inhibitors. J Mol Struct 2017. [DOI: 10.1016/j.molstruc.2017.05.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Ansari MY, Ahsan MJ, Yasmin S, Sahoo GC, Saini V, Das P. In silico identification of novel antagonists and binding insights by structural and functional analyses of guanylate kinase of Leishmania donovani and interaction with inhibitors. GENE REPORTS 2017. [DOI: 10.1016/j.genrep.2017.07.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Ghosh AK, Saini S, Das S, Mandal A, Sardar AH, Ansari MY, Abhishek K, Kumar A, Singh R, Verma S, Equbal A, Ali V, Das P. Glucose-6-phosphate dehydrogenase and Trypanothione reductase interaction protects Leishmania donovani from metalloid mediated oxidative stress. Free Radic Biol Med 2017; 106:10-23. [PMID: 28179112 DOI: 10.1016/j.freeradbiomed.2017.02.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Revised: 02/02/2017] [Accepted: 02/04/2017] [Indexed: 10/20/2022]
Abstract
Exploration of metabolons as viable drug target is rare in kinetoplastid biology. Here we present a novel protein-protein interaction among Glucose-6-phosphate dehydrogenase (LdG6PDH) and Trypanothione reductase (LdTryR) of Leishmania donovani displaying interconnection between central glucose metabolism and thiol metabolism of this parasite. Digitonin fractionation patterns observed through immunoblotting indicated localisation of both LdG6PDH and LdTryR in cytosol. In-silico and in-vitro interaction observed by size exclusion chromatography, co-purification, pull-down assay and spectrofluorimetric analysis revealed LdG6PDH and LdTryR physically interact with each other in a NADPH dependent manner. Coupled enzymatic assay displayed that NADPH generation was severely impaired by addition of SbIII, AsIII and TeIV extraneously, which hint towards metalloid driven structural changes of the interacting proteins. Co-purification patterns and pull-down assays also depicted that metalloids (SbIII, AsIII and TeIV) hinder the in-vitro interaction of these two enzymes. Surprisingly, metalloids at sub-lethal concentrations induced the in-vivo interaction of LdG6PDH and LdTryR, as analyzed by pull-down assays and fluorescence microscopy signifying protection against metalloid mediated ROS. Inhibition of LdTryR by thioridazine in LdG6PDH-/- parasites resulted in metalloid induced apoptotic death of the parasites due to abrupt fall in reduced thiol content, disrupted NADPH/NADP+ homeostasis and lethal oxidative stress. Interestingly, clinical isolates of L.donovani resistant to SAG exhibited enhanced interaction between LdG6PDH and LdTryR and showed cross resistivity towards AsIII and TeIV. Thus, our findings propose the metabolon of LdG6PDH and LdTryR as an alternate therapeutic target and provide mechanistic insight about metalloid resistance in Visceral Leishmaniasis.
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Affiliation(s)
- Ayan Kumar Ghosh
- Division of Molecular Biology, Bioinformatics and Molecular Biochemistry & Cell Biology, Rajendra Memorial Research Institute of Medical Sciences (I.C.M.R.), Agamkuan, Patna 800007, Bihar, India
| | - Savita Saini
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research (NIPER), Export Promotion Industrial Park, Hajipur, Vaishali 844101, Bihar, India
| | - Sushmita Das
- Department of Microbiology, All India Institute of Medical Sciences, Phulwarisharif, Patna 801505, Bihar, India
| | - Abhishek Mandal
- Division of Molecular Biology, Bioinformatics and Molecular Biochemistry & Cell Biology, Rajendra Memorial Research Institute of Medical Sciences (I.C.M.R.), Agamkuan, Patna 800007, Bihar, India
| | - Abul Hasan Sardar
- Division of Molecular Biology, Bioinformatics and Molecular Biochemistry & Cell Biology, Rajendra Memorial Research Institute of Medical Sciences (I.C.M.R.), Agamkuan, Patna 800007, Bihar, India
| | - Md Yousuf Ansari
- Division of Molecular Biology, Bioinformatics and Molecular Biochemistry & Cell Biology, Rajendra Memorial Research Institute of Medical Sciences (I.C.M.R.), Agamkuan, Patna 800007, Bihar, India
| | - Kumar Abhishek
- Division of Molecular Biology, Bioinformatics and Molecular Biochemistry & Cell Biology, Rajendra Memorial Research Institute of Medical Sciences (I.C.M.R.), Agamkuan, Patna 800007, Bihar, India
| | - Ajay Kumar
- Division of Molecular Biology, Bioinformatics and Molecular Biochemistry & Cell Biology, Rajendra Memorial Research Institute of Medical Sciences (I.C.M.R.), Agamkuan, Patna 800007, Bihar, India
| | - Ruby Singh
- Division of Molecular Biology, Bioinformatics and Molecular Biochemistry & Cell Biology, Rajendra Memorial Research Institute of Medical Sciences (I.C.M.R.), Agamkuan, Patna 800007, Bihar, India
| | - Sudha Verma
- Division of Molecular Biology, Bioinformatics and Molecular Biochemistry & Cell Biology, Rajendra Memorial Research Institute of Medical Sciences (I.C.M.R.), Agamkuan, Patna 800007, Bihar, India
| | - Asif Equbal
- Division of Molecular Biology, Bioinformatics and Molecular Biochemistry & Cell Biology, Rajendra Memorial Research Institute of Medical Sciences (I.C.M.R.), Agamkuan, Patna 800007, Bihar, India
| | - Vahab Ali
- Division of Molecular Biology, Bioinformatics and Molecular Biochemistry & Cell Biology, Rajendra Memorial Research Institute of Medical Sciences (I.C.M.R.), Agamkuan, Patna 800007, Bihar, India
| | - Pradeep Das
- Division of Molecular Biology, Bioinformatics and Molecular Biochemistry & Cell Biology, Rajendra Memorial Research Institute of Medical Sciences (I.C.M.R.), Agamkuan, Patna 800007, Bihar, India.
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Shityakov S, Salmas RE, Durdagi S, Roewer N, Förster C, Broscheit J. Solubility profiles, hydration and desolvation of curcumin complexed with γ-cyclodextrin and hydroxypropyl-γ-cyclodextrin. J Mol Struct 2017. [DOI: 10.1016/j.molstruc.2016.12.028] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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16
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Sasikala D, Jeyakanthan J, Srinivasan P. Structure-based virtual screening and biological evaluation of LuxT inhibitors for targeting quorum sensing through an in vitro biofilm formation. J Mol Struct 2017. [DOI: 10.1016/j.molstruc.2016.07.118] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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Computational prediction and analysis of potential antigenic CTL epitopes in Zika virus: A first step towards vaccine development. INFECTION GENETICS AND EVOLUTION 2016; 45:187-197. [DOI: 10.1016/j.meegid.2016.08.037] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 08/27/2016] [Accepted: 08/29/2016] [Indexed: 02/03/2023]
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Up-regulation of cytosolic tryparedoxin in Amp B resistant isolates of Leishmania donovani and its interaction with cytosolic tryparedoxin peroxidase. Biochimie 2016; 121:312-25. [DOI: 10.1016/j.biochi.2015.12.017] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 12/26/2015] [Indexed: 11/18/2022]
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Ansari MY, Equbal A, Dikhit MR, Mansuri R, Rana S, Ali V, Sahoo GC, Das P. Establishment of correlation between in-silico and in-vitro test analysis against Leishmania HGPRT to inhibitors. Int J Biol Macromol 2015; 83:78-96. [PMID: 26616453 DOI: 10.1016/j.ijbiomac.2015.11.051] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Revised: 11/13/2015] [Accepted: 11/18/2015] [Indexed: 10/22/2022]
Abstract
Hypoxanthine Phosphoribosyltransferase (HGPRT; EC 2.4.2.8) is a central enzyme in the purine recycling pathway of all protozoan parasites. Protozoan parasites cannot synthesize purine bases (DNA/RNA) which is essential for survival as lack of de-novo pathway. Thus its good target for drug design and discovery as inhibition leads to cessation of replication. PRTase (transferase enzyme) has common PRTase type I folding pattern domain for its activities. Genomic studies revealed the sequence pattern and identified highly conserved residues that catalyzed the reaction in protozoan parasites. A recombinant protein has 24 kDa molecular mass (rLdHGPRT) was cloned, expressed and purified for testing of guanosine monophosphate (GMP) analogous compounds in-vitro by spectroscopically to the rLdHGPRT, lysates protein and MTT assay on Leishmania donovani. The predicted inhibitors of different libraries were screen into FlexX. The reported inhibitors were tested in-vitro. The 2'-deoxyguanosine 5'-diphosphate (DGD) (IC50 value 12.5 μM) is two times more effective when compared to guanosine-5'-diphosphate sodium (GD). Interestingly, LdHGPRT complex has shown stable after 24 ns in molecular dynamics simulation with interacting amino acids are Glu125, Ile127, Lys87 and Val186. QSAR studies revealed the correlation between predicted and experimental values has shown R2 0.998. Concludes that inversely proportional to their docked score with activities.
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Affiliation(s)
- Md Yousuf Ansari
- Pharmacoinformatics Department, National Institute of Pharmaceutical Education and Research (NIPER), Hajipur 844102, India; BioMedical Informatics Division, Rajendra Memorial Research Institute of Medical Sciences, Agam Kuan, Patna 800007, India
| | - Asif Equbal
- Biochemistry Department, Rajendra Memorial Research Institute of Medical Sciences, Agam Kuan, Patna 800007, India
| | - Manas Ranjan Dikhit
- BioMedical Informatics Division, Rajendra Memorial Research Institute of Medical Sciences, Agam Kuan, Patna 800007, India
| | - Rani Mansuri
- Pharmacoinformatics Department, National Institute of Pharmaceutical Education and Research (NIPER), Hajipur 844102, India; BioMedical Informatics Division, Rajendra Memorial Research Institute of Medical Sciences, Agam Kuan, Patna 800007, India
| | - Sindhuprava Rana
- BioMedical Informatics Division, Rajendra Memorial Research Institute of Medical Sciences, Agam Kuan, Patna 800007, India
| | - Vahab Ali
- Biochemistry Department, Rajendra Memorial Research Institute of Medical Sciences, Agam Kuan, Patna 800007, India
| | - Ganesh Chandra Sahoo
- BioMedical Informatics Division, Rajendra Memorial Research Institute of Medical Sciences, Agam Kuan, Patna 800007, India.
| | - Pradeep Das
- Pharmacoinformatics Department, National Institute of Pharmaceutical Education and Research (NIPER), Hajipur 844102, India; BioMedical Informatics Division, Rajendra Memorial Research Institute of Medical Sciences, Agam Kuan, Patna 800007, India
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A comprehensive review on bioactive fused heterocycles as purine-utilizing enzymes inhibitors. Med Chem Res 2014. [DOI: 10.1007/s00044-014-1295-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Kim BJ, Hong SH, Shin KC, Jo YS, Oh DK. Characterization of a F280N variant of l-arabinose isomerase from Geobacillus thermodenitrificans identified as a d-galactose isomerase. Appl Microbiol Biotechnol 2014; 98:9271-81. [DOI: 10.1007/s00253-014-5827-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Revised: 05/07/2014] [Accepted: 05/13/2014] [Indexed: 10/25/2022]
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Zhou ZL, Liu HL, Wu JW, Tsao CW, Chen WH, Liu KT, Ho Y. Combining Structure-Based Pharmacophore andIn SilicoApproaches to Discover Novel Selective Serotonin Reuptake Inhibitors. Chem Biol Drug Des 2013; 82:705-17. [DOI: 10.1111/cbdd.12192] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2013] [Revised: 06/20/2013] [Accepted: 07/09/2013] [Indexed: 01/04/2023]
Affiliation(s)
- Zheng-Li Zhou
- Institute of Biochemical and Biomedical Engineering; National Taipei University of Technology; 1 Sec. 3 ZhongXiao E. Road Taipei 10608 Taiwan
| | - Hsuan-Liang Liu
- Institute of Biochemical and Biomedical Engineering; National Taipei University of Technology; 1 Sec. 3 ZhongXiao E. Road Taipei 10608 Taiwan
- Department of Chemical Engineering and Biotechnology; National Taipei University of Technology; 1 Sec. 3 ZhongXiao E. Road Taipei 10608 Taiwan
| | - Josephine W. Wu
- Department of Optometry; Central Taiwan University of Science and Technology; 666 Buzih Road Taichung 40601 Taiwan
| | - Cheng-Wen Tsao
- Department of Applied Cosmetology; Taoyuan Innovation Institute of Technology; 414 Sec. 3, Jhongshan E. Road Jhongli City Taoyuan County 32091 Taiwan
| | - Wei-Hsi Chen
- Chemistry Division; Institute of Nuclear Energy Research; 1000 Wunhua Road Longtan Township Taoyuan County 32546 Taiwan
| | - Kung-Tien Liu
- Everlight Chemical Industrial Corporation; 6th Fl, 77, Tun Hua South Road, Sec.2 Taipei 106 Taiwan
| | - Yih Ho
- School of Pharmacy; Taipei Medical University; 250 Wu-Hsing Street Taipei 110 Taiwan
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Sahoo GC, Yousuf Ansari M, Dikhit MR, Kannan M, Rana S, Das P. Structure prediction of gBP21 protein ofL. donovaniand its molecular interaction. J Biomol Struct Dyn 2013; 32:709-29. [DOI: 10.1080/07391102.2013.789400] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Rana S, Dikhit MR, Rani M, Moharana KC, Sahoo GC, Das P. CPDB: cysteine protease annotation database in Leishmania species. Integr Biol (Camb) 2013; 4:1351-7. [PMID: 23001143 DOI: 10.1039/c2ib20131c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
UNLABELLED There has been a revival of interest in Cysteine protease for Visceral Leishmaniasis (VL) attributed to massive outbreaks of leishmaniasis in the tropical region. The cysteine protease database (CPDB) was designed to find data related to cysteine protease (CP) of different species of Leishmania and Trypanosoma brucei in a single platform. This has reflected in substantial increase in the submission of Leishmania genome sequences to NCBI (National Center for Biotechnology Information) database. The CPDB database aims to provide a summary of data analysis, such as physiochemical and molecular properties, proteolytic cleavage sites, classification into functional families using SVMProt and other ExPASy tools. The main aim of this database is to provide different protein inhibitors of cysteine protease groups that were collected from literature and make available their 3-D structures through JMol with JAVA platform. These CP inhibitors are freely downloadable and also have added links for functional analyses of other proteins, which is helpful for users. All this information in CPDB, a single platform, will prove to be of great help for researchers who are involved in drug discovery and analysis of other physiochemical and molecular properties of the protein. AVAILABILITY the database is available for free at.
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Affiliation(s)
- Sindhuprava Rana
- Biomedical Informatics Division, Rajendra Memorial Research Institute of Medical Sciences, Agam Kuan, Patna, India800007.
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Sahoo GC, Dikhit MR, Rani M, Ansari MY, Jha C, Rana S, Das P. Analysis of sequence, structure of GAPDH of Leishmania donovani and its interactions. J Biomol Struct Dyn 2012; 31:258-75. [PMID: 22830998 DOI: 10.1080/07391102.2012.698189] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Drug resistance acquired by Leishmania donovani (Ldv) is a major problem in the treatment and control of visceral leishmaniasis (VL). Glyceraldehyde-3-phosphate dehydrogenase (GAPDH), a major glycolytic enzyme has been targeted as is found in other protozoan which cause diseases like sleeping sickness. GAPDH gene of Ldv (AG83 strain) was amplified, sequenced, and modeled on the basis of crystal structure of Leishmania mexicana. The model of the Ldv GAPDH exhibited NAD-binding domain with Rossmann folding. Virtual screening of different experimentally proved compounds with the crystal and the modeled structures of GAPDH of Leishmania strains revealed diverse binding affinities of different compounds. Comparison of binding affinities (based on different programs) of compounds revealed that discovery studio v2.5 (Ligandfit) was able to predict the most hit compounds, the best hit compounds against GAPDH of Leishmania strains are hydrazine, vetrazine, and benzyl carbazate. It is predicted that patients suffering from both VL and cardiac disorders (atrial fibrillation) may benefit if they are treated with warfarin in conjunction with first-line antileishmanial therapies such as miltefosine and AmBisome.
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Affiliation(s)
- Ganesh Chandra Sahoo
- BioMedical Informatics Center, Rajendra Memorial Research Institute of Medical Sciences, Agam Kuan, 800007 Patna, India.
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