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Challapa-Mamani MR, Tomás-Alvarado E, Espinoza-Baigorria A, León-Figueroa DA, Sah R, Rodriguez-Morales AJ, Barboza JJ. Molecular Docking and Molecular Dynamics Simulations in Related to Leishmania donovani: An Update and Literature Review. Trop Med Infect Dis 2023; 8:457. [PMID: 37888585 PMCID: PMC10610989 DOI: 10.3390/tropicalmed8100457] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 09/19/2023] [Accepted: 09/20/2023] [Indexed: 10/28/2023] Open
Abstract
Leishmaniasis, a disease caused by Leishmania parasites and transmitted via sandflies, presents in two main forms: cutaneous and visceral, the latter being more severe. With 0.7 to 1 million new cases each year, primarily in Brazil, diagnosing remains challenging due to diverse disease manifestations. Traditionally, the identification of Leishmania species is inferred from clinical and epidemiological data. Advances in disease management depend on technological progress and the improvement of parasite identification programs. Current treatments, despite the high incidence, show limited efficacy due to factors like cost, toxicity, and lengthy regimens causing poor adherence and resistance development. Diagnostic techniques have improved but a significant gap remains between scientific progress and application in endemic areas. Complete genomic sequence knowledge of Leishmania allows for the identification of therapeutic targets. With the aid of computational tools, testing, searching, and detecting affinity in molecular docking are optimized, and strategies that assess advantages among different options are developed. The review focuses on the use of molecular docking and molecular dynamics (MD) simulation for drug development. It also discusses the limitations and advancements of current treatments, emphasizing the importance of new techniques in improving disease management.
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Affiliation(s)
- Mabel R. Challapa-Mamani
- Escuela de Medicina, Universidad Cesar Vallejo, Trujillo 13007, Peru;
- Sociedad Científica de Estudiantes de Medicina de la Universidad César Vallejo, Trujillo 13007, Peru
| | - Eduardo Tomás-Alvarado
- Hospital General Regional 17, Instituto Mexicano del Seguro Social, Cancún 75533, Mexico;
| | | | | | - Ranjit Sah
- Department of Clinical Microbiology, Institute of Medicine, Tribhuvan University Teaching Hospital, Kathmandu 44600, Nepal;
- Department of Microbiology, Dr. D. Y. Patil Medical College, Hospital and Research Centre, Dr. D. Y. Patil Vidyapeeth, Pune 411018, Maharashtra, India
| | - Alfonso J. Rodriguez-Morales
- Faculty of Health Sciences, Universidad Científica del Sur, Lima 150152, Peru;
- Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Beirut 350000, Lebanon
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Singh R, Kashif M, Srivastava P, Manna PP. Recent Advances in Chemotherapeutics for Leishmaniasis: Importance of the Cellular Biochemistry of the Parasite and Its Molecular Interaction with the Host. Pathogens 2023; 12:pathogens12050706. [PMID: 37242374 DOI: 10.3390/pathogens12050706] [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: 12/20/2022] [Revised: 05/08/2023] [Accepted: 05/09/2023] [Indexed: 05/28/2023] Open
Abstract
Leishmaniasis, a category 1 neglected protozoan disease caused by a kinetoplastid pathogen called Leishmania, is transmitted through dipteran insect vectors (phlebotomine, sand flies) in three main clinical forms: fatal visceral leishmaniasis, self-healing cutaneous leishmaniasis, and mucocutaneous leishmaniasis. Generic pentavalent antimonials have long been the drug of choice against leishmaniasis; however, their success is plagued with limitations such as drug resistance and severe side effects, which makes them redundant as frontline therapy for endemic visceral leishmaniasis. Alternative therapeutic regimens based on amphotericin B, miltefosine, and paromomycin have also been approved. Due to the unavailability of human vaccines, first-line chemotherapies such as pentavalent antimonials, pentamidine, and amphotericin B are the only options to treat infected individuals. The higher toxicity, adverse effects, and perceived cost of these pharmaceutics, coupled with the emergence of parasite resistance and disease relapse, makes it urgent to identify new, rationalized drug targets for the improvement in disease management and palliative care for patients. This has become an emergent need and more relevant due to the lack of information on validated molecular resistance markers for the monitoring and surveillance of changes in drug sensitivity and resistance. The present study reviewed the recent advances in chemotherapeutic regimens by targeting novel drugs using several strategies including bioinformatics to gain new insight into leishmaniasis. Leishmania has unique enzymes and biochemical pathways that are distinct from those of its mammalian hosts. In light of the limited number of available antileishmanial drugs, the identification of novel drug targets and studying the molecular and cellular aspects of these drugs in the parasite and its host is critical to design specific inhibitors targeting and controlling the parasite. The biochemical characterization of unique Leishmania-specific enzymes can be used as tools to read through possible drug targets. In this review, we discuss relevant metabolic pathways and novel drugs that are unique, essential, and linked to the survival of the parasite based on bioinformatics and cellular and biochemical analyses.
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Affiliation(s)
- Ranjeet Singh
- Immunobiology Laboratory, Department of Zoology, Institute of Science, Banaras Hindu University, Varanasi 221005, India
| | - Mohammad Kashif
- Immunobiology Laboratory, Department of Zoology, Institute of Science, Banaras Hindu University, Varanasi 221005, India
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Prateek Srivastava
- Immunobiology Laboratory, Department of Zoology, Institute of Science, Banaras Hindu University, Varanasi 221005, India
- Department of Clinical Biochemistry and Pharmacology, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Partha Pratim Manna
- Immunobiology Laboratory, Department of Zoology, Institute of Science, Banaras Hindu University, Varanasi 221005, India
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Abirami M, Karan Kumar B, Dey S, Johri S, Reguera RM, Balaña-Fouce R, Gowri Chandra Sekhar KV, Sankaranarayanan M. Molecular-level strategic goals and repressors in Leishmaniasis - Integrated data to accelerate target-based heterocyclic scaffolds. Eur J Med Chem 2023; 257:115471. [PMID: 37257213 DOI: 10.1016/j.ejmech.2023.115471] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 05/05/2023] [Accepted: 05/06/2023] [Indexed: 06/02/2023]
Abstract
Leishmaniasis is a complex of neglected tropical diseases caused by various species of leishmanial parasites that primarily affect the world's poorest people. A limited number of standard medications are available for this disease that has been used for several decades, these drugs have many drawbacks such as resistance, higher cost, and patient compliance, making it difficult to reach the poor. The search for novel chemical entities to treat leishmaniasis has led to target-based scaffold research. Among several identified potential molecular targets, enzymes involved in the purine salvage pathway include polyamine biosynthetic process, such as arginase, ornithine decarboxylase, S-adenosylmethionine decarboxylase, spermidine synthase, trypanothione reductase as well as enzymes in the DNA cell cycle, such as DNA topoisomerases I and II plays vital role in the life cycle survival of leishmanial parasite. This review mainly focuses on various heterocyclic scaffolds, and their specific inhibitory targets against leishmaniasis, particularly those from the polyamine biosynthesis pathway and DNA topoisomerases with estimated activity studies of various heterocyclic analogs in terms of their IC50 or EC50 value, reported molecular docking analysis from available published literatures.
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Affiliation(s)
- M Abirami
- Medicinal Chemistry Research Laboratory, Department of Pharmacy, Birla Institute of Technology and Science Pilani, Pilani Campus, Pilani, 333031, India
| | - Banoth Karan Kumar
- Medicinal Chemistry Research Laboratory, Department of Pharmacy, Birla Institute of Technology and Science Pilani, Pilani Campus, Pilani, 333031, India; Department of Pharmacy, Koneru Lakshmaiah Education Foundation, Vaddeswaram, AP, India
| | - Sanchita Dey
- Medicinal Chemistry Research Laboratory, Department of Pharmacy, Birla Institute of Technology and Science Pilani, Pilani Campus, Pilani, 333031, India
| | - Samridhi Johri
- Medicinal Chemistry Research Laboratory, Department of Pharmacy, Birla Institute of Technology and Science Pilani, Pilani Campus, Pilani, 333031, India
| | - Rosa M Reguera
- Department of Biomedical Sciences, University of León, 24071, León, Spain
| | | | - Kondapalli Venkata Gowri Chandra Sekhar
- Department of Chemistry, Birla Institute of Technology and Science, Pilani, Hyderabad Campus, Jawahar Nagar, Kapra Mandal, Hyderabad, 500078, Telangana, India
| | - Murugesan Sankaranarayanan
- Medicinal Chemistry Research Laboratory, Department of Pharmacy, Birla Institute of Technology and Science Pilani, Pilani Campus, Pilani, 333031, India.
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Targeting trypanosomes: how chemogenomics and artificial intelligence can guide drug discovery. Biochem Soc Trans 2023; 51:195-206. [PMID: 36606702 DOI: 10.1042/bst20220618] [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: 10/20/2022] [Revised: 12/01/2022] [Accepted: 12/05/2022] [Indexed: 01/07/2023]
Abstract
Trypanosomatids are protozoan parasites that cause human and animal neglected diseases. Despite global efforts, effective treatments are still much needed. Phenotypic screens have provided several chemical leads for drug discovery, but the mechanism of action for many of these chemicals is currently unknown. Recently, chemogenomic screens assessing the susceptibility or resistance of parasites carrying genome-wide modifications started to define the mechanism of action of drugs at large scale. In this review, we discuss how genomics is being used for drug discovery in trypanosomatids, how integration of chemical and genomics data from these and other organisms has guided prioritisations of candidate therapeutic targets and additional chemical starting points, and how these data can fuel the expansion of drug discovery pipelines into the era of artificial intelligence.
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Singh S, Prajapati VK. Exploring actinomycetes natural products to identify potential multi-target inhibitors against Leishmania donovani. 3 Biotech 2022; 12:235. [PMID: 35999912 PMCID: PMC9392678 DOI: 10.1007/s13205-022-03304-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 08/09/2022] [Indexed: 12/16/2022] Open
Abstract
Visceral leishmaniasis (VL) is a neglected tropical disease that mainly affects the poor population of the Indian, African, and South American subcontinent. The increasing resistance to antimonial and miltefosine and frequent toxicity of amphotericin B drives an urgent need to develop an anti-leishmanial drug with excellent efficacy and safety profile. In this study, three sequential docking protocols (HTVS, SP, and XP) were performed to screen the secondary metabolites (n = 6519) from the actinomycetes source against five key proteins involved in the metabolic pathway of Leishmania donovani. Those proteins were adenine phosphoribosyltransferase (PDB ID: 1QB7), trypanothione reductase (PDB ID: 2JK6), N-myristoyl transferase (PDB ID: 2WUU), pteridine reductase (PDB ID: 2XOX), and MAP kinase (PDB ID: 4QNY). Although the binding energy of top ligands was predicted using the MM-GBSA module of the Schrödinger suite. SP and XP docking mode resulted in 55 multi-targeted ligands against L donovani. MM-GBSA analysis selected the top 18 ligands with good-binding affinity and the binding-free energy for four proteins, as mentioned earlier, when compared with the miltefosine, paromomycin, and a reference ligand selected for each target. Finally, molecular dynamics simulation, post-MD-binding-free energy (MM-PBSA), and principal component analysis (PCA) proposed three best ligands (Adenosine pentaphosphate, Atetra P, and GDP-4-keto-6-deoxymannose) qualifying the above screening parameters and confirmed as a potential drug candidate to fight against Leishmania donovani parasites.
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Affiliation(s)
- Satyendra Singh
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, NH-8, Bandarsindri, Kishangarh, Ajmer, Rajasthan 305817 India
| | - Vijay Kumar Prajapati
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, NH-8, Bandarsindri, Kishangarh, Ajmer, Rajasthan 305817 India
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Prasanna P, Joshi T, Pant M, Pundir H, Chandra S. Evaluation of the inhibitory potential of Valproic acid against histone deacetylase of Leishmania donovani and computational studies of Valproic acid derivatives. J Biomol Struct Dyn 2022:1-18. [PMID: 35706132 DOI: 10.1080/07391102.2022.2087103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Valproic acid (VA) is a proven inhibitor of human histone deacetylases (HDACs). The homogenous HDAC has been associated with all major human parasitic pathogens and hence, it has been considered an attractive drug target for anti-leishmanial therapy. To assist in drug design endeavors for HDACs, an in-vitro study has been presented to investigate the VA inhibition on Leishmania donovani HDAC (LdHDAC). The regression analysis of VA by 24 hrs viability assay confirmed its activity against LdHDAC. Moreover, the toxicity of VA is also well documented. Thus, the in-silico experiments were also conducted to screen the non-toxic VA derivatives as anti-leishmanial drug candidates having potential as inhibitors of LdHDAC. For in-silico study, the 3D structure of target LdHDAC was developed by homology modeling. Based on their in-silico activity, we shortlisted 13 VA derivatives having maximum affinity for LdHDAC and identified four potential derivatives that can specifically bind to this protein. After that, these ligands were subjected to molecular dynamics simulation. These derivatives may be effective against L. donovani promastigotes since they followed Lipinski's RO5 and were non-toxic. Thus, screened derivatives can be considered as lead ligands for targeting LdHDAC and may be used as possible drug candidates to treat leishmaniasis and overcome the limitation of anti-leishmanial drugs. This is the first report of antileishmanial potential of VA and its derivatives targeting LdHDAC. Hence, the current investigation presents a search for novel target specific drugs to aid the anti-leishmanial drug development. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Pragya Prasanna
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research (NIPER), Hajipur, Vaishali, India
| | - Tanuja Joshi
- Computational Biology & Biotechnology Laboratory, Department of Botany, Soban Singh Jeena University, Almora, Uttarakhand, India
| | - Manish Pant
- Department of Post-Harvest Process and Food Engineering, Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, Uttarakhand, India
| | - Hemlata Pundir
- Computational Biology & Biotechnology Laboratory, Department of Botany, Soban Singh Jeena University, Almora, Uttarakhand, India
| | - Subhash Chandra
- Computational Biology & Biotechnology Laboratory, Department of Botany, Soban Singh Jeena University, Almora, Uttarakhand, India
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In Silico Antiprotozoal Evaluation of 1,4-Naphthoquinone Derivatives against Chagas and Leishmaniasis Diseases Using QSAR, Molecular Docking, and ADME Approaches. Pharmaceuticals (Basel) 2022; 15:ph15060687. [PMID: 35745607 PMCID: PMC9228275 DOI: 10.3390/ph15060687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 05/24/2022] [Accepted: 05/27/2022] [Indexed: 12/04/2022] Open
Abstract
Chagas and leishmaniasis are two neglected diseases considered as public health problems worldwide, for which there is no effective, low-cost, and low-toxicity treatment for the host. Naphthoquinones are ligands with redox properties involved in oxidative biological processes with a wide variety of activities, including antiparasitic. In this work, in silico methods of quantitative structure–activity relationship (QSAR), molecular docking, and calculation of ADME (absorption, distribution, metabolism, and excretion) properties were used to evaluate naphthoquinone derivatives with unknown antiprotozoal activity. QSAR models were developed for predicting antiparasitic activity against Trypanosoma cruzi, Leishmania amazonensis, and Leishmania infatum, as well as the QSAR model for toxicity activity. Most of the evaluated ligands presented high antiparasitic activity. According to the docking results, the family of triazole derivatives presented the best affinity with the different macromolecular targets. The ADME results showed that most of the evaluated compounds present adequate conditions to be administered orally. Naphthoquinone derivatives show good biological activity results, depending on the substituents attached to the quinone ring, and perhaps the potential to be converted into drugs or starting molecules.
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Yadav M, Abdalla M, Madhavi M, Chopra I, Bhrdwaj A, Soni L, Shaheen U, Prajapati L, Sharma M, Sikarwar MS, Albogami S, Hussain T, Nayarisseri A, Singh SK. Structure-Based Virtual Screening, Molecular Docking, Molecular Dynamics Simulation and Pharmacokinetic modelling of Cyclooxygenase-2 (COX-2) inhibitor for the clinical treatment of Colorectal Cancer. MOLECULAR SIMULATION 2022. [DOI: 10.1080/08927022.2022.2068799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Manasi Yadav
- In silico Research Laboratory, Eminent Biosciences, Indore, Madhya Pradesh, India
| | - Mohnad Abdalla
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Pharmaceutics, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong Province, PR People’s Republic of China
| | - Maddala Madhavi
- Department of Zoology, Osmania University, Hyderabad, Telangana State, India
| | - Ishita Chopra
- In silico Research Laboratory, Eminent Biosciences, Indore, Madhya Pradesh, India
- Bioinformatics Research Laboratory, LeGene Biosciences Pvt Ltd, Indore, Madhya Pradesh, India
| | - Anushka Bhrdwaj
- In silico Research Laboratory, Eminent Biosciences, Indore, Madhya Pradesh, India
- Computer Aided Drug Designing and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu, India
| | - Lovely Soni
- In silico Research Laboratory, Eminent Biosciences, Indore, Madhya Pradesh, India
| | - Uzma Shaheen
- In silico Research Laboratory, Eminent Biosciences, Indore, Madhya Pradesh, India
| | - Leena Prajapati
- In silico Research Laboratory, Eminent Biosciences, Indore, Madhya Pradesh, India
| | - Megha Sharma
- In silico Research Laboratory, Eminent Biosciences, Indore, Madhya Pradesh, India
| | | | - Sarah Albogami
- Department of Biotechnology, College of Science, Taif University, Taif, Saudi Arabia
| | - Tajamul Hussain
- Research Chair for Biomedical Applications of Nanomaterials, Biochemistry Department, College of Science, King Saud University, Riyadh, Saudi Arabia
- Center of Excellence in Biotechnology Research, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Anuraj Nayarisseri
- In silico Research Laboratory, Eminent Biosciences, Indore, Madhya Pradesh, India
- Bioinformatics Research Laboratory, LeGene Biosciences Pvt Ltd, Indore, Madhya Pradesh, India
- Research Chair for Biomedical Applications of Nanomaterials, Biochemistry Department, College of Science, King Saud University, Riyadh, Saudi Arabia
- Computer Aided Drug Designing and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu, India
| | - Sanjeev Kumar Singh
- Computer Aided Drug Designing and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu, India
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Ali A, Ali A, Warsi MH, Rahman MA, Ahsan MJ, Azam F. An Insight into the Structural Requirements and Pharmacophore Identification of Carbonic Anhydrase Inhibitors to Combat Oxidative Stress at High Altitudes: An In-Silico Approach. Curr Issues Mol Biol 2022; 44:1027-1045. [PMID: 35723291 PMCID: PMC8947748 DOI: 10.3390/cimb44030068] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 02/15/2022] [Accepted: 02/16/2022] [Indexed: 01/18/2023] Open
Abstract
Carbonic anhydrases (CA) inhibitory action could be linked to the treatment of a number of ailments, including cancer, osteoporosis, glaucoma, and several neurological problems. For the development of effective CA inhibitors, a variety of heterocyclic rings have been investigated. Furthermore, at high altitudes, oxygen pressure drops, resulting in the formation of reactive oxygen and nitrogen species, and CA inhibitors having role in combating this oxidative stress. Acetazolamide contains thiadiazole ring, which has aroused researchers’ interest because of its CA inhibitory action. In the present study, we used a number of drug design tools, such as pharmacophore modeling, 3D QSAR, docking, and virtual screening on twenty-seven 1,3,4-thiadiazole derivatives that have been described as potential CA inhibitors in the literature. An atom-based 3D-QSAR analysis was carried out to determine the contribution of individual atoms to model generation, while a pharmacophore mapping investigation was carried out to find the common unique pharmacophoric properties required for biological activity. The coefficient of determination for both the training and test sets were statistically significant in the generated model. The best QSAR model was chosen based on the values of R2 (0.8757) and Q2 (0.7888). A molecular docking study was also conducted against the most potent analogue 4m, which has the highest SP docking score (−5.217) (PDB ID: 6g3v). The virtual screening revealed a number of promising compounds. The screened compound ZINC77699643 interacted with the amino acid residues, Pro201 and Thr199, in the virtual screening study (PDB ID: 6g3v). These interactions demonstrated the significance of the CA inhibitory activity of the compound. Furthermore, ADME study revealed useful information regarding compound’s drug-like properties. Therefore, the findings of the present investigation could aid in the development of more potent CA inhibitors, which could benefit the treatment of oxidative stress at high altitudes.
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Affiliation(s)
- Amena Ali
- High Altitude Research Center, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
- Department of Pharmaceutical Chemistry, College of Pharmacy, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
- Correspondence:
| | - Abuzer Ali
- Department of Pharmacognosy, College of Pharmacy, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia;
| | - Musarrat Husain Warsi
- Department of Pharmaceutics and Industrial Pharmacy, College of Pharmacy, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia; (M.H.W.); (M.A.R.)
| | - Mohammad Akhlaquer Rahman
- Department of Pharmaceutics and Industrial Pharmacy, College of Pharmacy, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia; (M.H.W.); (M.A.R.)
| | - Mohamed Jawed Ahsan
- Department of Pharmaceutical Chemistry, Maharishi Arvind College of Pharmacy, Ambabari Circle, Jaipur 302 039, Rajasthan, India;
| | - Faizul Azam
- Department of Pharmaceutical Chemistry & Pharmacognosy, Unaizah College of Pharmacy, Qassim University, P.O. Box 5888, Unaizah 51911, Saudi Arabia;
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Almeida FS, Sousa GLS, Rocha JC, Ribeiro FF, de Oliveira MR, de Lima Grisi TCS, Araújo DAM, de C Nobre MS, Castro RN, Amaral IPG, Keesen TSL, de Moura RO. In vitro anti-Leishmania activity and molecular docking of spiro-acridine compounds as potential multitarget agents against Leishmania infantum. Bioorg Med Chem Lett 2021; 49:128289. [PMID: 34311084 DOI: 10.1016/j.bmcl.2021.128289] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 07/13/2021] [Accepted: 07/20/2021] [Indexed: 11/28/2022]
Abstract
Leishmaniasis is an infectious disease with several limitations regarding treatment schemes. This work reports the anti-Leishmania activity of spiroacridine compounds against the promastigote (IC50 = 1.1 to 6.0 µg / mL) and amastigote forms of the best compounds (EC50 = 4.9 and 0.9 µg / mL) inLeishmania (L.) infantumand proposes an in-silico study with possible selective therapeutic targets for L. infantum. The substituted dimethyl-amine compound (AMTAC 11) showed the best leishmanicidal activity in vitro, and was found to interact with TryRandLdTopoI. comparisons with standard inhibitors were performed, and its main interactions were elucidated. Based on the biological assessment and the structure-activity relationship study, the spiroacridine compounds appear to be promisinganti-leishmaniachemotherapeutic agents to be explored.
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Affiliation(s)
- Fernanda S Almeida
- Programa de Doutorado em Biotecnologia, Rede Nordeste de Biotecnologia, Universidade Federal da Paraíba, João Pessoa, PB 58051-900, Brazil; Laboratório de Imunologia das Doenças Infeciosas, Universidade Federal da Paraíba, João Pessoa, PB 58051-900, Brazil
| | - Gleyton L S Sousa
- Programa de Doutorado em Química, Universidade Federal Rural do Rio de Janeiro, Seropédica, RJ 23897-000, Brazil
| | - Juliana C Rocha
- Laboratório de Imunologia das Doenças Infeciosas, Universidade Federal da Paraíba, João Pessoa, PB 58051-900, Brazil
| | - Frederico F Ribeiro
- Centro de Ciências Exatas e da Natureza, Universidade Federal da Paraíba, João Pessoa, PB 58059-900, Brazil
| | - Márcia Rosa de Oliveira
- Departamento de Biologia Molecular, Centro de Ciências Exatas e da Natureza, Universidade Federal da Paraíba, Joao Pessoa, Paraíba CEP 58059-900, Brazil
| | | | - Demetrius A M Araújo
- Departamento de Biologia Celular e Molecular, Universidade Federal da Paraíba, João Pessoa, PB 58059-900, Brazil
| | - Michelangela S de C Nobre
- Programa de Doutorado em Ciências Farmacêuticas, Universidade Federal de Pernambuco, Recife, PE 50670-901, Brazil
| | - Rosane N Castro
- Programa de Doutorado em Química, Universidade Federal Rural do Rio de Janeiro, Seropédica, RJ 23897-000, Brazil
| | - Ian P G Amaral
- Departamento de Biologia Celular e Molecular, Universidade Federal da Paraíba, João Pessoa, PB 58059-900, Brazil
| | - Tatjana S L Keesen
- Departamento de Biologia Celular e Molecular, Universidade Federal da Paraíba, João Pessoa, PB 58059-900, Brazil; Laboratório de Imunologia das Doenças Infeciosas, Universidade Federal da Paraíba, João Pessoa, PB 58051-900, Brazil
| | - Ricardo Olímpio de Moura
- Centro de Ciências Biológicas e da Saúde, Universidade Estadual da Paraíba, Campina Grande, PB 58429-500, Brazil.
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Tevyashova AN, Chudinov MV. Progress in the medicinal chemistry of organoboron compounds. RUSSIAN CHEMICAL REVIEWS 2021. [DOI: 10.1070/rcr4977] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The review aims to draw attention to the latest advances in the organoboron chemistry and therapeutic use of organoboron compounds. The synthetic strategies towards boron-containing compounds with proven in vitro and/or in vivo biological activities, including derivatives of boronic acids, benzoxaboroles, benzoxaborines and benzodiazaborines, are summarized. Approaches to the synthesis of hybrid structures containing an organoboron moiety as one of the pharmacophores are considered, and the effect of this modification on the pharmacological activity of the initial molecules is analyzed. On the basis of analysis of the published data, the most promising areas of research in the field of organoboron compounds are identified, including the latest methods of synthesis, modification and design of effective therapeutic agents.
The bibliography includes 246 references.
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Tomiotto-Pellissier F, Alves DR, Morais SMD, Bortoleti BTDS, Gonçalves MD, Silva TF, Tavares ER, Yamauchi LM, Costa IN, Marinho ES, Marinho MM, Conchon-Costa I, Miranda-Sapla MM, Pavanelli WR. Caryocar coriaceum Wittm. fruit extracts as Leishmania inhibitors: in-vitro and in-silico approaches. J Biomol Struct Dyn 2021; 40:8040-8055. [PMID: 33769210 DOI: 10.1080/07391102.2021.1905557] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Leishmaniasis is a group of neglected diseases caused by parasites of the Leishmania genus. The treatment of Leishmaniasis represents a great challenge, because the available drugs present high toxicity and none of them is fully effective. Caryocar is a botanical genus rich in phenolic compounds, which leaves extracts have already been described by its antileishmanial action. Thus, we investigated the effect of pulp and peel extracts of the Caryocar coriaceum fruit on promastigote and amastigote forms of Leishmania amazonensis. Both extracts had antipromastigote effect after 24, 48, and 72 h, and this effect was by apoptosis-like process induction, with reactive oxygen species (ROS) production, damage to the mitochondria and plasma membrane, and phosphatidylserine exposure. Knowing that the fruit extracts did not alter the viability of macrophages, we observed that the treatment reduced the infection of these cells. Thereafter, in the in vitro infection context, the extracts showed antioxidant proprieties, by reducing NO, ROS, and MDA levels. Besides, both peel and pulp extracts up-regulated Nrf2/HO-1/Ferritin expression and increase the total iron-bound in infected macrophages, which culminates in a depletion of available iron for L. amazonensis replication. In silico, the molecular modeling experiments showed that the three flavonoids presented in the C. coriaceum extracts can act as synergistic inhibitors of Leishmania proteins, and compete for the active site. Also, there is a preference for rutin at the active site due to its greater interaction binding strength.
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Affiliation(s)
- Fernanda Tomiotto-Pellissier
- Biosciences and Biotechnology Graduate Program, Carlos Chagas Institute (ICC), Fiocruz, Curitiba, Paraná, Brazil.,Department of Pathology Science, Center of Biological Sciences, State University of Londrina, Londrina, Paraná, Brazil
| | - Daniela Ribeiro Alves
- Department of Natural Sciences, Ceará State University, Fortaleza, Ceará, Brazil.,Theoretical and Electrochemical Chemistry Group, Faculty of Philosophy Dom Aureliano Matos, State University of Ceará, Limoeiro do Norte, Ceará, Brazil
| | | | - Bruna Taciane da Silva Bortoleti
- Biosciences and Biotechnology Graduate Program, Carlos Chagas Institute (ICC), Fiocruz, Curitiba, Paraná, Brazil.,Department of Pathology Science, Center of Biological Sciences, State University of Londrina, Londrina, Paraná, Brazil
| | - Manoela Daiele Gonçalves
- Department of Chemistry, Center of Exact Sciences, State University of Londrina, Londrina, Paraná, Brazil
| | - Taylon Felipe Silva
- Department of Pathology Science, Center of Biological Sciences, State University of Londrina, Londrina, Paraná, Brazil
| | - Eliandro Reis Tavares
- Department of Microbiology, Center of Biological Sciences, State University of Londrina, Londrina, Paraná, Brazil
| | - Lucy Megumi Yamauchi
- Department of Microbiology, Center of Biological Sciences, State University of Londrina, Londrina, Paraná, Brazil
| | - Idessania Nazareth Costa
- Department of Pathology Science, Center of Biological Sciences, State University of Londrina, Londrina, Paraná, Brazil
| | - Emmanuel Silva Marinho
- Theoretical and Electrochemical Chemistry Group, Faculty of Philosophy Dom Aureliano Matos, State University of Ceará, Limoeiro do Norte, Ceará, Brazil
| | - Marcia Machado Marinho
- Iguatu Faculty of Education, Science and Letters, State University of Ceará, Iguatu, Ceará, Brazil
| | - Ivete Conchon-Costa
- Department of Pathology Science, Center of Biological Sciences, State University of Londrina, Londrina, Paraná, Brazil
| | | | - Wander Rogério Pavanelli
- Biosciences and Biotechnology Graduate Program, Carlos Chagas Institute (ICC), Fiocruz, Curitiba, Paraná, Brazil.,Department of Pathology Science, Center of Biological Sciences, State University of Londrina, Londrina, Paraná, Brazil
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13
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Boniface PK, Sano CM, Elizabeth FI. Unveiling the Targets Involved in the Quest of Antileishmanial Leads Using In silico Methods. Curr Drug Targets 2021; 21:681-712. [PMID: 32003668 DOI: 10.2174/1389450121666200128112948] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 01/08/2020] [Accepted: 01/09/2020] [Indexed: 02/01/2023]
Abstract
BACKGROUND Leishmaniasis is a neglected tropical disease associated with several clinical manifestations, including cutaneous, mucocutaneous, and visceral forms. As currently available drugs have some limitations (toxicity, resistance, among others), the target-based identification has been an important approach to develop new leads against leishmaniasis. The present study aims to identify targets involved in the pharmacological action of potent antileishmanial compounds. METHODS The literature information regarding molecular interactions of antileishmanial compounds studied over the past half-decade is discussed. The information was obtained from databases such as Wiley, SciFinder, Science Direct, National Library of Medicine, American Chemical Society, Scientific Electronic Library Online, Scopus, Springer, Google Scholar, Web of Science, etc. Results: Numerous in vitro antileishmanial compounds showed affinity and selective interactions with enzymes such as arginase, pteridine reductase 1, trypanothione reductase, pyruvate kinase, among others, which are crucial for the survival and virulence of the Leishmania parasite. CONCLUSION The in-silico activity of small molecules (enzymes, proteins, among others) might be used as pharmacological tools to develop candidate compounds for the treatment of leishmaniasis. As some pharmacologically active compounds may act on more than one target, additional studies of the mechanism (s) of action of potent antileishmanial compounds might help to better understand their pharmacological action. Also, the optimization of promising antileishmanial compounds might improve their biological activity.
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Affiliation(s)
- Pone K Boniface
- Department of Pharmacy, Faculty of Pharmaceutical Sciences, University of Sao Paulo, Sao Paulo, Brazil
| | - Cinthya M Sano
- Department of Pharmacy, Faculty of Pharmaceutical Sciences, University of Sao Paulo, Sao Paulo, Brazil
| | - Ferreira I Elizabeth
- Department of Pharmacy, Faculty of Pharmaceutical Sciences, University of Sao Paulo, Sao Paulo, Brazil
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14
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Salari-Jazi A, Mahnam K, Sadeghi P, Damavandi MS, Faghri J. Discovery of potential inhibitors against New Delhi metallo-β-lactamase-1 from natural compounds: in silico-based methods. Sci Rep 2021; 11:2390. [PMID: 33504907 PMCID: PMC7841178 DOI: 10.1038/s41598-021-82009-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 01/13/2021] [Indexed: 11/16/2022] Open
Abstract
New Delhi metallo-β-lactamase variants and different types of metallo-β-lactamases have attracted enormous consideration for hydrolyzing almost all β-lactam antibiotics, which leads to multi drug resistance bacteria. Metallo-β-lactamases genes have disseminated in hospitals and all parts of the world and became a public health concern. There is no inhibitor for New Delhi metallo-β-lactamase-1 and other metallo-β-lactamases classes, so metallo-β-lactamases inhibitor drugs became an urgent need. In this study, multi-steps virtual screening was done over the NPASS database with 35,032 natural compounds. At first Captopril was extracted from 4EXS PDB code and use as a template for the first structural screening and 500 compounds obtained as hit compounds by molecular docking. Then the best ligand, i.e. NPC120633 was used as templet and 800 similar compounds were obtained. As a final point, ten compounds i.e. NPC171932, NPC100251, NPC18185, NPC98583, NPC112380, NPC471403, NPC471404, NPC472454, NPC473010 and NPC300657 had proper docking scores, and a 50 ns molecular dynamics simulation was performed for calculation binding free energy of each compound with New Delhi metallo-β-lactamase. Protein sequence alignment, 3D conformational alignment, pharmacophore modeling on all New Delhi metallo-β-lactamase variants and all types of metallo-β-lactamases were done. Quantum chemical perspective based on the fragment molecular orbital (FMO) method was performed to discover conserved and crucial residues in the catalytic activity of metallo-β-lactamases. These residues had similar 3D coordinates of spatial location in the 3D conformational alignment. So it is posibble that all types of metallo-β-lactamases can inhibit by these ten compounds. Therefore, these compounds were proper to mostly inhibit all metallo-β-lactamases in experimental studies.
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Affiliation(s)
- Azhar Salari-Jazi
- Department of Microbiology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Karim Mahnam
- Biology Department, Faculty of Sciences, Shehrekord University, Shahrekord, Iran
| | - Parisa Sadeghi
- Department of Microbiology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mohamad Sadegh Damavandi
- Department of Microbiology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Jamshid Faghri
- Department of Microbiology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran.
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15
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Yagiz G, Noma SAA, Altundas A, Al-Khafaji K, Taskin-Tok T, Ates B. Synthesis, inhibition properties against xanthine oxidase and molecular docking studies of dimethyl N-benzyl-1H-1,2,3-triazole-4,5-dicarboxylate and (N-benzyl-1H-1,2,3-triazole-4,5-diyl)dimethanol derivatives. Bioorg Chem 2021; 108:104654. [PMID: 33493930 DOI: 10.1016/j.bioorg.2021.104654] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 12/30/2020] [Accepted: 01/08/2021] [Indexed: 11/17/2022]
Abstract
This study focused on synthesis various dimethyl N-benzyl-1H-1,2,3-triazole-4,5-dicarboxylate and (N-benzyl-1H-1,2,3-triazole-4,5-diyl)dimethanol derivatives under the conditions of green chemistry without the use of solvent and catalysts. Their inhibition properties were also investigated on xanthine oxidase (XO) activity. All dimethanol and dicarboxylate derivatives exhibited significant inhibition activities with IC50 values ranging from 0.71 to 2.25 μM. Especially, (1-(3-bromobenzyl)-1H-1,2,3-triazole-4,5-diyl)dimethanol (5c) and dimethyl 1-(4-chlorobenzyl)-1H-1,2,3-triazole-4,5-dicarboxylate (6 g) compounds were found to be the most promising derivatives on the XO enzyme inhibition with IC50 values 0.71 and 0.73 μM, respectively. Moreover, the double docking procedure was to evaluate compound modes of inhibition and their interactions with the protein (XO) at atomic level. Surprisingly, the docking results showed a good correlation with IC50 [correlation coefficient (R2 = 0.7455)]. Also, the docking results exhibited that the 5c, 6f and 6 g have lowest docking scores -4.790, -4.755, and -4.730, respectively. These data were in agreement with the IC50 values. These results give promising beginning stages to assist in the improvement of novel and powerful inhibitor against XO.
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Affiliation(s)
- Güler Yagiz
- Department of Chemistry, Faculty of Science, Gazi University, 06500 Ankara, Turkey
| | - Samir Abbas Ali Noma
- Department of Chemistry, Faculty of Science and Arts, Inonu University, 44280 Malatya, Turkey
| | - Aliye Altundas
- Department of Chemistry, Faculty of Science, Gazi University, 06500 Ankara, Turkey
| | - Khattab Al-Khafaji
- Department of Chemistry, Faculty of Arts and Sciences, Gaziantep University, 27310 Gaziantep, Turkey
| | - Tugba Taskin-Tok
- Department of Chemistry, Faculty of Arts and Sciences, Gaziantep University, 27310 Gaziantep, Turkey; Department of Bioinformatics and Computational Biology, Institute of Health Sciences, Gaziantep University, 27310 Gaziantep, Turkey
| | - Burhan Ates
- Department of Chemistry, Faculty of Science and Arts, Inonu University, 44280 Malatya, Turkey.
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16
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Al-Khafaji K, Taskin Tok T. Amygdalin as multi-target anticancer drug against targets of cell division cycle: double docking and molecular dynamics simulation. J Biomol Struct Dyn 2020; 39:1965-1974. [DOI: 10.1080/07391102.2020.1742792] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Khattab Al-Khafaji
- Faculty of Arts and Sciences, Department of Chemistry, Gaziantep University, Gaziantep, Turkey
| | - Tugba Taskin Tok
- Faculty of Arts and Sciences, Department of Chemistry, Gaziantep University, Gaziantep, Turkey
- Institute of Health Sciences, Department of Bioinformatics and Computational Biology, Gaziantep University, Gaziantep, Turkey
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17
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Scotti MT, Monteiro AFM, de Oliveira Viana J, Bezerra Mendonça Junior FJ, Ishiki HM, Tchouboun EN, De Araújo RSA, Scotti L. Recent Theoretical Studies Concerning Important Tropical Infections. Curr Med Chem 2020; 27:795-834. [DOI: 10.2174/0929867326666190711121418] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 07/20/2018] [Accepted: 04/12/2019] [Indexed: 01/02/2023]
Abstract
Neglected Tropical Diseases (NTDs) form a group of diseases that are strongly associated
with poverty, flourish in impoverished environments, and thrive best in tropical areas,
where they tend to present overlap. They comprise several diseases, and the symptoms
vary dramatically from disease to disease, often causing from extreme pain, and untold misery
that anchors populations to poverty, permanent disability, and death. They affect more than 1
billion people worldwide; mostly in poor populations living in tropical and subtropical climates.
In this review, several complementary in silico approaches are presented; including
identification of new therapeutic targets, novel mechanisms of activity, high-throughput
screening of small-molecule libraries, as well as in silico quantitative structure-activity relationship
and recent molecular docking studies. Current and active research against Sleeping
Sickness, American trypanosomiasis, Leishmaniasis and Schistosomiasis infections will hopefully
lead to safer, more effective, less costly and more widely available treatments against
these parasitic forms of Neglected Tropical Diseases (NTDs) in the near future.
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Affiliation(s)
- Marcus Tullius Scotti
- Postgraduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba, Joao Pessoa - PB, Brazil
| | - Alex France Messias Monteiro
- Postgraduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba, Joao Pessoa - PB, Brazil
| | - Jéssika de Oliveira Viana
- Postgraduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba, Joao Pessoa - PB, Brazil
| | | | - Hamilton M. Ishiki
- University of Western Sao Paulo (Unoeste), Presidente Prudente, SP, Brazil
| | | | - Rodrigo Santos A. De Araújo
- Laboratory of Synthesis and Drug Delivery, Department of Biological Science, State University of Paraiba, Joao Pessoa, PB, Brazil
| | - Luciana Scotti
- Postgraduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba, Joao Pessoa - PB, Brazil
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18
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Halder AK, Dias Soeiro Cordeiro MN. Advanced in Silico Methods for the Development of Anti- Leishmaniasis and Anti-Trypanosomiasis Agents. Curr Med Chem 2020; 27:697-718. [DOI: 10.2174/0929867325666181031093702] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 07/24/2018] [Accepted: 09/19/2018] [Indexed: 11/22/2022]
Abstract
Leishmaniasis and trypanosomiasis occur primarily in undeveloped countries and account
for millions of deaths and disability-adjusted life years. Limited therapeutic options, high toxicity of
chemotherapeutic drugs and the emergence of drug resistance associated with these diseases demand
urgent development of novel therapeutic agents for the treatment of these dreadful diseases. In the last
decades, different in silico methods have been successfully implemented for supporting the lengthy and
expensive drug discovery process. In the current review, we discuss recent advances pertaining to in
silico analyses towards lead identification, lead modification and target identification of antileishmaniasis
and anti-trypanosomiasis agents. We describe recent applications of some important in
silico approaches, such as 2D-QSAR, 3D-QSAR, pharmacophore mapping, molecular docking, and so
forth, with the aim of understanding the utility of these techniques for the design of novel therapeutic
anti-parasitic agents. This review focuses on: (a) advanced computational drug design options; (b) diverse
methodologies - e.g.: use of machine learning tools, software solutions, and web-platforms; (c)
recent applications and advances in the last five years; (d) experimental validations of in silico predictions;
(e) virtual screening tools; and (f) rationale or justification for the selection of these in silico
methods.
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Affiliation(s)
- Amit Kumar Halder
- LAQV@ REQUIMTE/Department of Chemistry and Biochemistry, University of Porto, Porto 4169-007, Portugal
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19
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Al-Khafaji K, Taskin Tok T. Understanding the mechanism of amygdalin's multifunctional anti-cancer action using computational approach. J Biomol Struct Dyn 2020; 39:1600-1610. [PMID: 32107968 DOI: 10.1080/07391102.2020.1736159] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Amygdalin possesses anticancer properties and induces apoptosis. Based on experimental studies the presence of amygdalin with cancer cells led to activate the caspase-3 and BAX and inhibits Bcl-2 and Poly (ADP-ribose) polymerase-1 (PARP-1) but without deep information on action mode of these activities. Herein, we leaped forward to examine the molecular dynamics of the bound amygdalin and free ligand proteins, to identify precise action (conformation changes in targeted proteins) of amygdalin through using double docking and molecular dynamics (MD) simulations for 50 ns time scale. The MD simulations revealed that the binding of amygdalin led to disrupting the interaction between the Bcl-2/BAX complex. We furthermore conducted MD simulation for Bcl-2/amygdalin to investigate the stability of the complex which is responsible for inhibition of Bcl-2. It has been obtained a stable Bcl-2/amygdalin complex during the 50 ns. The results give a detail explanation of how amygdalin activates BAX and inhibits Bcl-2. For caspase-3, the matter is different, we found that amygdalin led to disrupting the interaction of caspase-3's two chains for intervals during 50 ns and then bind together repeatedly. The mechanism of caspase-3's activation through switching by disrupt the interacts for periodic intervals manner. For PARP-1, the dynamics simulations results indicated amygdalin interacts with PARP-1's binding site and forms stable interaction during simulation to render it inactive. Hence, amygdalin revealed a supernatural behavior through the MD simulations: it revealed a further clarification of the mystery amygdalin's experimental action which can act as a multifunctional drug in the cancer therapeutics.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Khattab Al-Khafaji
- Faculty of Arts and Sciences, Department of Chemistry, Gaziantep University, Gaziantep, Turkey
| | - Tugba Taskin Tok
- Faculty of Arts and Sciences, Department of Chemistry, Gaziantep University, Gaziantep, Turkey.,Institute of Health Sciences, Department of Bioinformatics and Computational Biology, Gaziantep University, Gaziantep, Turkey
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20
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Çınaroğlu SS, Timuçin E. Comprehensive evaluation of the MM-GBSA method on bromodomain-inhibitor sets. Brief Bioinform 2019; 21:2112-2125. [DOI: 10.1093/bib/bbz143] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 10/01/2019] [Accepted: 10/17/2019] [Indexed: 12/11/2022] Open
Abstract
Abstract
MM-PB/GBSA methods represent a higher-level scoring theory than docking. This study reports an extensive testing of different MM-GBSA scoring schemes on two bromodomain (BRD) datasets. The first set is composed of 24 BRPF1 complexes, and the second one is a nonredundant set constructed from the PDBbind and composed of 28 diverse BRD complexes. A variety of MM-GBSA schemes were analyzed to evaluate the performance of four protocols with different numbers of minimization and MD steps, 10 different force fields and three different water models. Results showed that neither additional MD steps nor unfixing the receptor atoms improved scoring or ranking power. On the contrary, our results underscore the advantage of fixing receptor atoms or limiting the number of MD steps not only for a reduction in the computational costs but also for boosting the prediction accuracy. Among Amber force fields tested, ff14SB and its derivatives rather than ff94 or polarized force fields provided the most accurate scoring and ranking results. The TIP3P water model yielded the highest scoring and ranking power compared to the others. Posing power was further evaluated for the BRPF1 set. A slightly better posing power for the protocol which uses both minimization and MD steps with a fixed receptor than the one which uses only minimization with a fully flexible receptor-ligand system was observed. Overall, this study provides insights into the usage of the MM-GBSA methods for screening of BRD inhibitors, substantiating the benefits of shorter protocols and latest force fields and maintaining the crystal waters for accuracy.
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Affiliation(s)
| | - Emel Timuçin
- Department of Biostatistics and Medical Informatics, School of Medicine, Acıbadem Mehmet Ali Aydınlar University, İstanbul, 34752, Turkey
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21
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Cheng G, Mei XB, Yan YY, Chen J, Zhang B, Li J, Dong XW, Lin NM, Zhou YB. Identification of new NIK inhibitors by discriminatory analysis-based molecular docking and biological evaluation. Arch Pharm (Weinheim) 2019; 352:e1800374. [PMID: 31116887 DOI: 10.1002/ardp.201800374] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 04/05/2019] [Accepted: 04/07/2019] [Indexed: 12/13/2022]
Abstract
NF-κB inducing kinase (NIK) is a key regulator in the noncanonical nuclear factor κB cells (NF-κB) signaling pathway. Dysregulation of NIK is often related with autoimmune disorders and malignancies. However, the number of reported NIK inhibitors is scarce. Discriminatory analysis-based molecular docking was used to examine the accuracy of the binding conformation and to estimate the binding affinity, leading to the identification of several new NIK inhibitors with moderate IC50 (ranging from 48.9 to 103.4 μM). Among them, compound 5, the most potent one (IC50 48.9 ± 6.9 μM), also showed moderate antiproliferation activity against cancer SW1990 cells, with an IC50 value of 20.1 ± 6.0 μM. Further dynamic simulations were performed to provide more in-depth details on the binding conformation of compound 5 and the NIK protein, providing some structural clues for further optimization of compound 5 as a novel NIK inhibitor.
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Affiliation(s)
- Gang Cheng
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
- College of Pharmaceutical Science, Zhejiang Chinese Medical University, Hangzhou, People's Republic of China
| | - Xiao-Bing Mei
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
| | - You-You Yan
- Translational Medicine Research Center, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, People's Republic of China
| | - Jing Chen
- College of Pharmaceutical Science, Zhejiang Chinese Medical University, Hangzhou, People's Republic of China
| | - Bo Zhang
- Translational Medicine Research Center, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, People's Republic of China
| | - Jia Li
- State Key Laboratory of Drug Research, National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Xiao-Wu Dong
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
| | - Neng-Ming Lin
- Translational Medicine Research Center, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, People's Republic of China
| | - Yu-Bo Zhou
- State Key Laboratory of Drug Research, National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
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22
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Pandey RK, Prajapati VK. Exploring sand fly salivary proteins to design multiepitope subunit vaccine to fight against visceral leishmaniasis. J Cell Biochem 2019; 120:1141-1155. [PMID: 29377223 DOI: 10.1002/jcb.26719] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 01/24/2018] [Indexed: 01/24/2023]
Abstract
Visceral leishmaniasis (VL) is caused by the parasites of Leishmania donovani complex, leads to the death of 20 000 to 40 000 people from 56 affected countries, worldwide. Till date, there is not a single available vaccine candidate to prevent the VL infection, and treatment only relies upon expensive and toxic chemotherapeutic options. Consequently, immunoinformatics approach was applied to design a multiepitope-based subunit vaccine to enhance the humoral as well as cell-mediated immunity. Constructed vaccine candidate was further subjected to evaluation on allergenicity and antigenicity and physiochemical parameters. Later on, disulfide engineering was performed to increase the stability of vaccine construct. Also, molecular docking and molecular dynamics simulation study were performed to check the binding affinity and stability of toll-like receptor-4 to vaccine construct complex. Finally, codon optimization and in silico cloning were performed to ensure the expression of proposed vaccine construct in a microbial expression system.
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Affiliation(s)
- Rajan Kumar Pandey
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Ajmer, India
| | - Vijay Kumar Prajapati
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Ajmer, India
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23
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Pandey RK, Ojha R, Chatterjee N, Upadhyay N, Mishra A, Prajapati VK. Combinatorial screening algorithm to engineer multiepitope subunit vaccine targeting human T-lymphotropic virus-1 infection. J Cell Physiol 2018; 234:8717-8726. [PMID: 30370533 DOI: 10.1002/jcp.27531] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 09/10/2018] [Indexed: 12/17/2022]
Abstract
Human T-lymphotropic virus (HTLV), the first human retrovirus has been discovered which is known to cause the age-old assassinating disease HTLV-1 associated myelopathy. Cancer caused by this virus is adult T cell leukemia/lymphoma which targets 10-20 million throughout the world. The effect of this virus extends to the fact that it causes chronic disease to the spinal cord resulting in loss of sensation and further causes blood cancer. So, to overcome the complications, we designed a subunit vaccine by the assimilation of B-cell, cytotoxic T-lymphocyte , and helper T-lymphocyte epitopes. The epitopes were joined together along with adjuvant and linkers and a vaccine was fabricated which was further subjected to 3D modeling. The physiochemical properties, allergenicity, and antigenicity were evaluated. Molecular docking and dynamics were performed with the obtained 3D model against toll like receptor (TLR-3) immune receptor. Lastly, in silico cloning was performed to ensure the expression of the designed vaccine in pET28a(+) expression vector. The future prospects of the study entailed the in vitro and in vivo experimental analysis for evaluating the immune response of the designed vaccine construct.
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Affiliation(s)
- Rajan K Pandey
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Ajmer, Rajasthan, India
| | - Rupal Ojha
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Ajmer, Rajasthan, India
| | - Nina Chatterjee
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Ajmer, Rajasthan, India
| | - Nitesh Upadhyay
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Ajmer, Rajasthan, India
| | - Amit Mishra
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Jodhpur, Rajasthan, India
| | - Vijay K Prajapati
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Ajmer, Rajasthan, India
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Pandey RK, Dahiya S, Mahita J, Sowdhamini R, Prajapati VK. Vaccination and immunization strategies to design Aedes aegypti salivary protein based subunit vaccine tackling Flavivirus infection. Int J Biol Macromol 2018; 122:1203-1211. [PMID: 30219509 DOI: 10.1016/j.ijbiomac.2018.09.071] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2018] [Revised: 09/04/2018] [Accepted: 09/12/2018] [Indexed: 10/28/2022]
Abstract
Flavivirus causes arthropod-borne severe diseases that sometimes lead to the death. The Flavivirus species including Dengue virus, Zika virus and yellow fever virus are transmitted by the bite of Aedes mosquitoes. All these viral species target the people living in their respective endemic zone causing a high mortality rate. Recent studies show that immune factors present in the Ae. aegypti saliva is the hidden culprit promoting blood meal collection, suppressing host immune molecules and promoting disease establishment. This study was designed to develop a subunit vaccine using Aedes mosquito salivary proteins targeting the aforementioned Flaviviruses. Subunit vaccine was designed very precisely by combining the immunogenic B-cell epitope with CTL and HTL epitopes and also suitable adjuvant and linkers. Immunogenicity, allergenicity and physiochemical characterization were also performed for scientific validation. Molecular docking and molecular dynamics simulations studies were carried out to confirm the stable affinity between the vaccine protein (3D) and TLR3 receptor. At last, in silico cloning was executed to get the subunit vaccine restriction clone into pET28a vectro to express it in microbial expression system. Additionally, this study warrants the experimental evaluation for the validation purposes.
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Affiliation(s)
- Rajan Kumar Pandey
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Bandarsindri, Kishangarh (305817), Ajmer, Rajasthan, India
| | - Surbhi Dahiya
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Bandarsindri, Kishangarh (305817), Ajmer, Rajasthan, India
| | - Jarjapu Mahita
- National Centre for Biological Sciences (NCBS), Tata Institute of Fundamental Research (TIFR), Bangalore, India
| | - Ramanathan Sowdhamini
- National Centre for Biological Sciences (NCBS), Tata Institute of Fundamental Research (TIFR), Bangalore, India
| | - Vijay Kumar Prajapati
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Bandarsindri, Kishangarh (305817), Ajmer, Rajasthan, India.
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25
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Chemical system biology based molecular interactions to identify inhibitors against Q151M mutant of HIV-1 reverse transcriptase. INFECTION GENETICS AND EVOLUTION 2018; 63:5-12. [DOI: 10.1016/j.meegid.2018.05.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 05/02/2018] [Accepted: 05/08/2018] [Indexed: 11/17/2022]
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26
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Kumar Pandey R, Ojha R, Mishra A, Kumar Prajapati V. Designing B- and T-cell multi-epitope based subunit vaccine using immunoinformatics approach to control Zika virus infection. J Cell Biochem 2018; 119:7631-7642. [PMID: 29900580 DOI: 10.1002/jcb.27110] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 05/04/2018] [Indexed: 12/25/2022]
Abstract
The Zika virus is a rapidly spreading Aedes mosquito-borne sickness, which creates an unanticipated linkage birth deformity and neurological turmoil. This study represents the use of the combinatorial immunoinformatics approach to develop a multiepitope subunit vaccine using the structural and nonstructural proteins of the Zika virus. The designed subunit vaccine consists of cytotoxic T-lymphocyte and helper T-lymphocyte epitopes accompanied by suitable adjuvant and linkers. The presence of humoral immune response specific B-cell epitopes was also confirmed by B-cell epitope mapping among vaccine protein. Further, the vaccine protein was characterized for its allergenicity, antigenicity, and physiochemical parameters and found to be safe and immunogenic. Molecular docking and molecular dynamics studies of the vaccine protein with the toll-like receptor-3 were performed to ensure the binding affinity and stability of their complex. Finally, in silico cloning was performed for the effective expression of vaccine construct in the microbial system (Escherichia coli K12 strain). Aforementioned approaches result in the multiepitope subunit vaccine which may have the ability to induce cellular as well as humoral immune response. Moreover, this study needs the experimental validation to prove the immunogenic and protective behavior of the developed subunit vaccine.
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Affiliation(s)
- Rajan Kumar Pandey
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Ajmer, Rajasthan, India
| | - Rupal Ojha
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Ajmer, Rajasthan, India
| | - Amit Mishra
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Jodhpur, India
| | - Vijay Kumar Prajapati
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Ajmer, Rajasthan, India
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27
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Pandey RK, Ojha R, Aathmanathan VS, Krishnan M, Prajapati VK. Immunoinformatics approaches to design a novel multi-epitope subunit vaccine against HIV infection. Vaccine 2018; 36:2262-2272. [PMID: 29571972 DOI: 10.1016/j.vaccine.2018.03.042] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 02/19/2018] [Accepted: 03/15/2018] [Indexed: 01/05/2023]
Abstract
The end goal of HIV vaccine designing requires novel strategies to elicit a strong humoral and cell-mediated immune response. The emergence of drug resistance and the requirement of next line treatment necessitate the finding of the potential and immunogenic vaccine candidate. This study employed a novel immunoinformatics approach to design multi-epitope subunit vaccine against HIV infection. Here, we designed the subunit vaccine by the combination of CTL, HTL and BCL epitopes along with suitable adjuvant and linkers. Physiochemical characterization of subunit vaccine was assessed to ensure its thermostability, theoretical PI, and amphipathic behavior. In further assessment, subunit vaccine was found to be immunogenic with the capability to generate humoral and cell-mediated immune response. Further, homology modeling and refinement was performed and the refined modeled structure was used for molecular docking with the immune receptor (TLR-3) present on lymphocyte cells. Consequently, molecular dynamics simulation ensured the molecular interaction between TLR-3 and subunit vaccine candidate. Disulfide engineering was performed by placing the cysteine residues in the region of high mobility to enhance the vaccine stability. At last, in silico cloning was performed to warrant the translational efficiency and microbial expression of the designed vaccine.
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Affiliation(s)
- Rajan Kumar Pandey
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Bandarsindri, Kishangarh, Ajmer 305817, Rajasthan, India
| | - Rupal Ojha
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Bandarsindri, Kishangarh, Ajmer 305817, Rajasthan, India
| | | | - Muthukalingan Krishnan
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Bandarsindri, Kishangarh, Ajmer 305817, Rajasthan, India; Department of Environmental Biotechnology, Bharathidasan University, Tiruchirappalli 620 024, Tamil Nadu, India
| | - Vijay Kumar Prajapati
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Bandarsindri, Kishangarh, Ajmer 305817, Rajasthan, India.
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28
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Excavating chikungunya genome to design B and T cell multi-epitope subunit vaccine using comprehensive immunoinformatics approach to control chikungunya infection. INFECTION GENETICS AND EVOLUTION 2018. [PMID: 29535024 DOI: 10.1016/j.meegid.2018.03.007] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Chikungunya infection has been a cause of countless deaths worldwide. Due to lack of permanent treatment and prevention of this disease, the mortality rate remains very high. Therefore, we followed an immunoinformatics approach for the development of multi-epitope subunit vaccine which is able to elucidate humoral, cell-mediated and innate immune responses inside the host body. Both structural and non-structural proteins of chikungunya virus were utilized for prediction of B-cell and T-cell binding epitopes along with interferon-γ (IFN-γ) inducing epitopes. The vaccine construct is composed of β-defensin as an adjuvant at the N-terminal followed by Cytotoxic T-Lymphocytes (CTL) and Helper T-Lymphocyte (HTL) epitopes. The same vaccine construct was also utilized for the prediction of B-cell binding epitopes and IFN-γ inducing epitopes. This was followed by the 3D model generation, refinement and validation of the vaccine construct. Later on, the interaction of modeled vaccine with the innate immune receptor (TLR-3) was explored by performing molecular docking and molecular dynamics simulation studies. Also to check the efficiency of expression of this vaccine construct in an expression vector, in silico cloning was performed at the final stage of vaccine development. Further, designed multi-epitope subunit vaccine necessitates experimental and clinical investigation to develop as an immunogenic vaccine candidate.
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29
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Zhang N, Zoltner M, Leung KF, Scullion P, Hutchinson S, del Pino RC, Vincent IM, Zhang YK, Freund YR, Alley MRK, Jacobs RT, Read KD, Barrett MP, Horn D, Field MC. Host-parasite co-metabolic activation of antitrypanosomal aminomethyl-benzoxaboroles. PLoS Pathog 2018; 14:e1006850. [PMID: 29425238 PMCID: PMC5823473 DOI: 10.1371/journal.ppat.1006850] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 02/22/2018] [Accepted: 01/03/2018] [Indexed: 12/22/2022] Open
Abstract
Recent development of benzoxaborole-based chemistry gave rise to a collection of compounds with great potential in targeting diverse infectious diseases, including human African Trypanosomiasis (HAT), a devastating neglected tropical disease. However, further medicinal development is largely restricted by a lack of insight into mechanism of action (MoA) in pathogenic kinetoplastids. We adopted a multidisciplinary approach, combining a high-throughput forward genetic screen with functional group focused chemical biological, structural biology and biochemical analyses, to tackle the complex MoAs of benzoxaboroles in Trypanosoma brucei. We describe an oxidative enzymatic pathway composed of host semicarbazide-sensitive amine oxidase and a trypanosomal aldehyde dehydrogenase TbALDH3. Two sequential reactions through this pathway serve as the key underlying mechanism for activating a series of 4-aminomethylphenoxy-benzoxaboroles as potent trypanocides; the methylamine parental compounds as pro-drugs are transformed first into intermediate aldehyde metabolites, and further into the carboxylate metabolites as effective forms. Moreover, comparative biochemical and crystallographic analyses elucidated the catalytic specificity of TbALDH3 towards the benzaldehyde benzoxaborole metabolites as xenogeneic substrates. Overall, this work proposes a novel drug activation mechanism dependent on both host and parasite metabolism of primary amine containing molecules, which contributes a new perspective to our understanding of the benzoxaborole MoA, and could be further exploited to improve the therapeutic index of antimicrobial compounds. Human African Trypanomiasis (HAT) is among a list of Neglected Tropical Diseases (NTDs) that impose devastating burdens on both public health and economy of some of the most unprivileged societies across the world. To secure the long-term global control of the disease, it is critical to understand the mechanisms underlying the interactions of drugs and drug candidates with the causative agents as well as resistance potentially arising from use of the compounds. We demonstrated here a metabolic enzymatic cascade dependent on a host-pathogen interaction that determines potency against T. brucei of a series of benzoxaborole compounds. More importantly, this pathway represents a metabolic interaction network between host and pathogen, illuminating an important perspective on understanding mechanism of action.
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Affiliation(s)
- Ning Zhang
- Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Martin Zoltner
- Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Ka-Fai Leung
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Paul Scullion
- Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Sebastian Hutchinson
- Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Ricardo C. del Pino
- Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Isabel M. Vincent
- Wellcome Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Yong-Kang Zhang
- Anacor Pharmaceuticals, Inc., Palo Alto, California, United States of America
| | - Yvonne R. Freund
- Anacor Pharmaceuticals, Inc., Palo Alto, California, United States of America
| | - Michael R. K. Alley
- Anacor Pharmaceuticals, Inc., Palo Alto, California, United States of America
| | - Robert T. Jacobs
- Anacor Pharmaceuticals, Inc., Palo Alto, California, United States of America
| | - Kevin D. Read
- Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Michael P. Barrett
- Wellcome Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - David Horn
- Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Mark C. Field
- Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dundee, United Kingdom
- * E-mail:
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30
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Novel Immunoinformatics Approaches to Design Multi-epitope Subunit Vaccine for Malaria by Investigating Anopheles Salivary Protein. Sci Rep 2018; 8:1125. [PMID: 29348555 PMCID: PMC5773588 DOI: 10.1038/s41598-018-19456-1] [Citation(s) in RCA: 147] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 01/02/2018] [Indexed: 12/19/2022] Open
Abstract
Malaria fever has been pervasive for quite a while in tropical developing regions causing high morbidity and mortality. The causal organism is a protozoan parasite of genus Plasmodium which spreads to the human host by the bite of hitherto infected female Anopheles mosquito. In the course of biting, a salivary protein of Anopheles helps in blood feeding behavior and having the ability to elicit the host immune response. This study represents a series of immunoinformatics approaches to design multi-epitope subunit vaccine using Anopheles mosquito salivary proteins. Designed subunit vaccine was evaluated for its immunogenicity, allergenicity and physiochemical parameters. To enhance the stability of vaccine protein, disulfide engineering was performed in a region of high mobility. Codon adaptation and in silico cloning was also performed to ensure the higher expression of designed subunit vaccine in E. coli K12 expression system. Finally, molecular docking and simulation study was performed for the vaccine protein and TLR-4 receptor, to determine the binding free energy and complex stability. Moreover, the designed subunit vaccine was found to induce anti-salivary immunity which may have the ability to prevent the entry of Plasmodium sporozoites into the human host.
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31
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Pandey RK, Prajapati VK. Molecular and immunological toxic effects of nanoparticles. Int J Biol Macromol 2017; 107:1278-1293. [PMID: 29017884 DOI: 10.1016/j.ijbiomac.2017.09.110] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 09/21/2017] [Accepted: 09/27/2017] [Indexed: 02/07/2023]
Abstract
Nanoparticles have emerged as a boon for the public health applications such as drug delivery, diagnostic, and imaging. Biodegradable and non-bio degradable nanoparticles have been used at a large scale level to increase the efficiency of the biomedical process at the cellular, animal and human level. Exponential use of nanoparticles reinforces the adverse immunological changes at the human health level. Physical and chemical properties of nanoparticles often lead to a variety of immunotoxic effects such as activation of stress-related genes, membrane disruption, and release of pro-inflammatory cytokines. Delivered nanoparticles in animal or human interact with various components of the immune system such as lymphocytes, macrophages, neutrophils etc. Nanoparticles delivered above the threshold level damages the cellular physiology by the generation of reactive oxygen and nitrogen species. This review article represents the potential of nanoparticles in the field of nanomedicine and provides the critical evidence which leads to develop immunotoxicity in living cells and organisms by altering immunological responses.
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Affiliation(s)
- Rajan Kumar Pandey
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Kishangarh, 305817, Ajmer, Rajasthan, India
| | - Vijay Kumar Prajapati
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Kishangarh, 305817, Ajmer, Rajasthan, India.
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32
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Jain V, Jain K. Molecular targets and pathways for the treatment of visceral leishmaniasis. Drug Discov Today 2017; 23:161-170. [PMID: 28919438 DOI: 10.1016/j.drudis.2017.09.006] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 06/28/2017] [Accepted: 09/06/2017] [Indexed: 12/25/2022]
Abstract
Visceral leishmaniasis (VL) represents the most severe form of the tropical disease, leishmaniasis. Treatment of VL is complicated because of the few clinically approved antileishmanial drugs available; emerging resistance to first-line drugs; need for a temperature-controlled 'cold' supply chain; serious toxicity concerns over drugs such as amphotericin B; high cost of medication; and unavailability of clinically approved antileishmanial vaccines. Attacking potential molecular targets, specific to the parasite, is a vital step in the treatment of this and other infectious diseases. As we discuss here, comprehensive investigation of these targets could provide a promising strategy for the treatment of visceral leishmaniasis.
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Affiliation(s)
- Vineet Jain
- Department of Pharmaceutics, National Institute of Pharmaceutical Education and Research (NIPER), Raebareli, India
| | - Keerti Jain
- Department of Pharmaceutics, National Institute of Pharmaceutical Education and Research (NIPER), Raebareli, India.
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33
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Ali M, Pandey RK, Khatoon N, Narula A, Mishra A, Prajapati VK. Exploring dengue genome to construct a multi-epitope based subunit vaccine by utilizing immunoinformatics approach to battle against dengue infection. Sci Rep 2017; 7:9232. [PMID: 28835708 PMCID: PMC5569093 DOI: 10.1038/s41598-017-09199-w] [Citation(s) in RCA: 218] [Impact Index Per Article: 31.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 07/24/2017] [Indexed: 11/24/2022] Open
Abstract
Dengue is considered as a major health issue which causes a number of deaths worldwide each year; tropical countries are majorly affected by dengue outbreaks. It is considered as life threatening issue because, since many decades not a single effective approach for treatment and prevention of dengue has been developed. Therefore, to find new preventive measure, we used immunoinformatics approaches to develop a multi-epitope based subunit vaccine for dengue which can generate various immune responses inside the host. Different B-cell, TC cell, and TH cell binding epitopes were predicted for structural and non-structural proteins of dengue virus. Final vaccine constructs consisting of TC and TH cell epitopes and an adjuvant (β-defensin) at N-terminal of the construct. Presence of B-cell and IFN-γ inducing epitopes confirms the humoral and cell mediated immune response developed by designed vaccine. Designed vaccine was not found allergic and was potentially antigenic in nature. Modeling of tertiary structure and the refined model was used for molecular docking with TLR-3 (immune receptor). Molecular docking and dynamics simulation confirms the microscopic interactions between ligand and receptor. In silico cloning approach was used to ensure the expression and translation efficiency of vaccine within an expression vector.
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MESH Headings
- Amino Acid Sequence
- Antigens, Viral/chemistry
- Antigens, Viral/immunology
- Computational Biology/methods
- Dengue/immunology
- Dengue/prevention & control
- Dengue Vaccines/immunology
- Dengue Virus/genetics
- Dengue Virus/immunology
- Epitope Mapping
- Epitopes/chemistry
- Epitopes/immunology
- Epitopes, B-Lymphocyte/chemistry
- Epitopes, B-Lymphocyte/immunology
- Epitopes, T-Lymphocyte/chemistry
- Epitopes, T-Lymphocyte/immunology
- Genome, Viral
- Humans
- Interferon-gamma/chemistry
- Interferon-gamma/metabolism
- Ligands
- Models, Molecular
- Protein Conformation
- Structure-Activity Relationship
- T-Lymphocytes, Cytotoxic/immunology
- Vaccines, Subunit/immunology
- Viral Proteins/chemistry
- Viral Proteins/immunology
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Affiliation(s)
- Mudassar Ali
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Bandarsindri, Kishangarh, Ajmer, 305817, Rajasthan, India
| | - Rajan Kumar Pandey
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Bandarsindri, Kishangarh, Ajmer, 305817, Rajasthan, India
| | - Nazia Khatoon
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Bandarsindri, Kishangarh, Ajmer, 305817, Rajasthan, India
| | - Aruna Narula
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Bandarsindri, Kishangarh, Ajmer, 305817, Rajasthan, India
| | - Amit Mishra
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Jodhpur, India
| | - Vijay Kumar Prajapati
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Bandarsindri, Kishangarh, Ajmer, 305817, Rajasthan, India.
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34
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Khatoon N, Pandey RK, Prajapati VK. Exploring Leishmania secretory proteins to design B and T cell multi-epitope subunit vaccine using immunoinformatics approach. Sci Rep 2017; 7:8285. [PMID: 28811600 PMCID: PMC5557753 DOI: 10.1038/s41598-017-08842-w] [Citation(s) in RCA: 216] [Impact Index Per Article: 30.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 07/13/2017] [Indexed: 12/20/2022] Open
Abstract
Visceral leishmaniasis (VL) is a fatal form of leishmaniasis which affects 70 countries, worldwide. Increasing drug resistance, HIV co-infection, and poor health system require operative vaccination strategy to control the VL transmission dynamics. Therefore, a holistic approach is needed to generate T and B memory cells to mediate long-term immunity against VL infection. Consequently, immunoinformatics approach was applied to design Leishmania secretory protein based multi-epitope subunit vaccine construct consisting of B and T cell epitopes. Further, the physiochemical characterization was performed to check the aliphatic index, theoretical PI, molecular weight, and thermostable nature of vaccine construct. The allergenicity and antigenicity were also predicted to ensure the safety and immunogenic behavior of final vaccine construct. Moreover, homology modeling, followed by molecular docking and molecular dynamics simulation study was also performed to evaluate the binding affinity and stability of receptor (TLR-4) and ligand (vaccine protein) complex. This study warrants the experimental validation to ensure the immunogenicity and safety profile of presented vaccine construct which may be further helpful to control VL infection.
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MESH Headings
- Amino Acid Sequence
- Antigens, Protozoan/chemistry
- Antigens, Protozoan/genetics
- Antigens, Protozoan/immunology
- Codon
- Computational Biology
- Epitopes, B-Lymphocyte/chemistry
- Epitopes, B-Lymphocyte/genetics
- Epitopes, B-Lymphocyte/immunology
- Epitopes, T-Lymphocyte/chemistry
- Epitopes, T-Lymphocyte/genetics
- Epitopes, T-Lymphocyte/immunology
- Humans
- Immunogenicity, Vaccine
- Leishmania/immunology
- Leishmaniasis/immunology
- Leishmaniasis/metabolism
- Leishmaniasis/prevention & control
- Leishmaniasis Vaccines/chemistry
- Leishmaniasis Vaccines/immunology
- Models, Molecular
- Protein Binding
- Protein Conformation
- Quantitative Structure-Activity Relationship
- T-Lymphocytes/immunology
- Toll-Like Receptor 4/chemistry
- Toll-Like Receptor 4/metabolism
- Vaccines, Subunit/chemistry
- Vaccines, Subunit/genetics
- Vaccines, Subunit/immunology
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Affiliation(s)
- Nazia Khatoon
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, NH-8, Bandarsindri, Kishangarh, 305817, Ajmer, Rajasthan, India
| | - Rajan Kumar Pandey
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, NH-8, Bandarsindri, Kishangarh, 305817, Ajmer, Rajasthan, India
| | - Vijay Kumar Prajapati
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, NH-8, Bandarsindri, Kishangarh, 305817, Ajmer, Rajasthan, India.
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35
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Implementing WebGL and HTML5 in Macromolecular Visualization and Modern Computer-Aided Drug Design. Trends Biotechnol 2017; 35:559-571. [DOI: 10.1016/j.tibtech.2017.03.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 03/16/2017] [Accepted: 03/17/2017] [Indexed: 11/21/2022]
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36
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Ying H, Xie J, Liu X, Yao T, Dong X, Hu C. Discriminatory analysis based molecular docking study for in silico identification of epigallocatechin-3-gallate (EGCG) derivatives as B-RafV600E inhibitors. RSC Adv 2017. [DOI: 10.1039/c7ra04788f] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Virtual screening and biological testing were utilized to identify novel B-RafV600E inhibitors.
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Affiliation(s)
- Huazhou Ying
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research
- College of Pharmaceutical Sciences
- Zhejiang University
- Hangzhou
- P. R. China
| | - Jiangfeng Xie
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research
- College of Pharmaceutical Sciences
- Zhejiang University
- Hangzhou
- P. R. China
| | - Xingguo Liu
- School of Chemical Engineering and Light Industry
- Guangdong University of Technology
- Guangzhou
- P. R. China
| | - Tingting Yao
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research
- College of Pharmaceutical Sciences
- Zhejiang University
- Hangzhou
- P. R. China
| | - Xiaowu Dong
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research
- College of Pharmaceutical Sciences
- Zhejiang University
- Hangzhou
- P. R. China
| | - Chunqi Hu
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research
- College of Pharmaceutical Sciences
- Zhejiang University
- Hangzhou
- P. R. China
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