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Abduljalil JM, Elfiky AA, Sayed ESTA, AlKhazindar MM. In silico structural elucidation of Nipah virus L protein and targeting RNA-dependent RNA polymerase domain by nucleoside analogs. J Biomol Struct Dyn 2023; 41:8215-8229. [PMID: 36205638 DOI: 10.1080/07391102.2022.2130987] [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: 07/26/2022] [Accepted: 09/25/2022] [Indexed: 10/10/2022]
Abstract
The large (L) protein of Mononegavirales is a multi-domain protein that performs transcription and genome replication. One of the important domains in L is the RNA-dependent RNA polymerase (RdRp), a promising target for antiviral drugs. In this work, we employed rigorous computational comparative modeling to predict the structure of L protein of Nipah virus (NiV). The RdRp domain was targeted by a panel of nucleotide analogs, previously reported to inhibit different viral RNA polymerases, using molecular docking. Best binder compounds were subjected to molecular dynamics simulation to validate their binding. Molecular mechanics/generalized-born surface area (MM/GBSA) calculations estimated the binding free energy. The predicted model of NiV L has an excellent quality as judged by physics- and knowledge-based validation tests. Galidesivir, AT-9010 and Norov-29 scored the top nucleotide analogs to bind to the RdRp. Their binding free energies obtained by MM/GBSA (-31.01 ± 3.9 to -38.37 ± 4.8 kcal/mol) ranked Norov-29 as the best potential inhibitor. Purine nucleotide analogs are expected to harbor the scaffold for an effective drug against NiV. Finally, this study is expected to provide a start point for medicinal chemistry and drug discovery campaigns toward identification of effective chemotherapeutic agent(s) against NiV.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Jameel M Abduljalil
- Department of Botany and Microbiology, Faculty of Science, Cairo University, Giza, Egypt
- Department of Biological Sciences, Faculty of Applied Sciences, Thamar University, Dhamar, Yemen
| | - Abdo A Elfiky
- Department of Biophysics, Faculty of Science, Cairo University, Giza, Egypt
| | - El-Sayed T A Sayed
- Department of Botany and Microbiology, Faculty of Science, Cairo University, Giza, Egypt
| | - Maha M AlKhazindar
- Department of Botany and Microbiology, Faculty of Science, Cairo University, Giza, Egypt
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Computational identification of drug-like marine natural products as potential RNA polymerase inhibitors against Nipah virus. Comput Biol Chem 2023; 104:107850. [PMID: 36907056 DOI: 10.1016/j.compbiolchem.2023.107850] [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: 12/15/2022] [Revised: 03/05/2023] [Accepted: 03/06/2023] [Indexed: 03/09/2023]
Abstract
Nipah virus (NiV) has been an alarming threat to human populations in southern Asia for more than a decade. It is one of the most deadly viruses in the Mononegavirales order. Despite its high mortality rate and virulence, no chemotherapeutic agent or vaccine is publicly available. Hence, this work was conducted to computationally screen marine natural products database for drug-like potential inhibitors for the viral RNA-dependent RNA polymerase (RdRp). The structural model was subjected to molecular dynamics (MD) simulation to obtain the native ensemble of the protein. The CMNPDB dataset of marine natural products was filtered to retain only compounds following Lipinski's five rules. The molecules were energy minimized and docked into different conformers of the RdRp using AutoDock Vina. The best 35 molecules were rescored by GNINA, a deep learning-based docking software. The resulting nine compounds were evaluated for their pharmacokinetic profiles and medicinal chemistry properties. The best five compounds were subjected to MD simulation for 100 ns, followed by binding free energy estimation via Molecular Mechanics/ Generalized Born Surface Area (MM/GBSA) calculations. The results showed remarkable behavior of five hits as inferred by stable binding pose and orientation to block the exit channel of RNA synthesis products in the RdRp cavity. These hits are promising starting materials for in vitro validation and structural modifications to enhance the pharmacokinetic and medicinal chemistry properties for developing antiviral lead compounds.
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Exploration of natural product database for the identification of potent inhibitor against IDH2 mutational variants for glioma therapy. J Mol Model 2022; 29:6. [PMID: 36484830 DOI: 10.1007/s00894-022-05409-z] [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: 10/20/2022] [Accepted: 12/04/2022] [Indexed: 12/13/2022]
Abstract
Mutation in isocitrate dehydrogenase 2 (mIDH2) is an oncogenic driver prevalently reported in various cancer types including gliomas. To date, enasidenib is the only FDA-approved drug widely used as a mIDH2 (R140Q) inhibitor. However, dose-limiting toxicity and modest brain penetrating capability restrict its use as a plausible mIDH2 inhibitor. Furthermore, secondary site mutations (Q316E and I319M) were identified in patients with enasidenib treatments resulting in acquired therapeutic resistance. Hence, in the present investigation, we aimed to identify novel and potent drug-like compounds to overcome the existing drawbacks using an integrated in-silico strategy. A sum of 1574 natural compounds from the naturally occurring plant-based anti-cancerous compound activity target (NPACT) database was proclaimed and subjected to molecular docking. The binding affinities of the resultant natural compounds were rescored using MM-GBSA scoring functions. The resultant lead molecules were subjected to anticancer activity prediction using the machine-learning model. Furthermore, the toxicity and drug-likeliness of the lead compounds were investigated using ADMET properties. Eventually, the integrated in silico approach resulted in a lead molecule, namely squalene (NPACT00954) against mIDH2 protein. The screened compound was subjected to mutational analysis accomplishing second-site mutations. Interestingly, squalene exhibited appreciable binding affinity alongside good brain penetrating potential than enasidenib. Indeed, the reproducibility and significance of our results are examined by running 3 replicas of 100-ns simulations per system using the random initial velocities of the atoms generated by Maxwell distribution at a given temperature. Thus, we hypothesize from our results that further optimization of squalene could be beneficial for the treatment and management of glioma in the near future.
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Kuchana V, Kashetti V, Tangeda SJ, Manga V. Design, synthesis and molecular docking study of thiophenyl hydrazone derivatives as tubulin polymerization inhibitors. SYNTHETIC COMMUN 2022. [DOI: 10.1080/00397911.2022.2125324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Vinutha Kuchana
- Department of Chemistry, Sarojini Naidu Pharmacy Maha Vidyalaya, Osmania University, Hyderabad, India
- Department of Chemistry, University College of Science, Osmania University, Hyderabad, India
| | - Vaeshnavi Kashetti
- Department of Chemistry, University College of Science, Osmania University, Hyderabad, India
| | - Saritha Jyotsna Tangeda
- Department of Chemistry, Sarojini Naidu Pharmacy Maha Vidyalaya, Osmania University, Hyderabad, India
| | - Vijjulatha Manga
- Department of Chemistry, University College of Science, Osmania University, Hyderabad, India
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Raja A, Shekhar N, Singh H, Prakash A, Medhi B. In-silico discovery of dual active molecule to restore synaptic wiring against autism spectrum disorder via HDAC2 and H3R inhibition. PLoS One 2022; 17:e0268139. [PMID: 35877665 PMCID: PMC9312418 DOI: 10.1371/journal.pone.0268139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 04/22/2022] [Indexed: 11/23/2022] Open
Abstract
Metal-dependent histone deacetylases (HDACs) are essential epigenetic regulators; their molecular and pharmacological roles in medically critical diseases such as neuropsychiatric disorders, neurodegeneration, and cancer are being studied globally. HDAC2’s differential expression in the central nervous system makes it an appealing therapeutic target for chronic neurological diseases like autism spectrum disorder. In this study, we identified H3R inhibitor molecules that are computationally effective at binding to the HDAC2 metal-coordinated binding site. The study highlights the importance of pitolisant in screening the potential H3R inhibitors by using a hybrid workflow of ligand and receptor-based drug discovery. The screened lead compounds with PubChem SIDs 103179850, 103185945, and 103362074 show viable binding with HDAC2 in silico. The importance of ligand contacts with the Zn2+ ion in the HDAC2 catalytic site is also discussed and investigated for a significant role in enzyme inhibition. The proposed H3R inhibitors 103179850, 103185945, and 103362074 are estimated as dual-active molecules to block the HDAC2-mediated deacetylation of the EAAT2 gene (SLC1A2) and H3R-mediated synaptic transmission irregularity and are, therefore, open for experimental validation.
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Affiliation(s)
- Anupam Raja
- Department of Pharmacology, PGIMER, Chandigarh, India
| | | | | | - Ajay Prakash
- Department of Pharmacology, PGIMER, Chandigarh, India
| | - Bikash Medhi
- Department of Pharmacology, PGIMER, Chandigarh, India
- * E-mail:
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Zhou Y, Jiang Y, Chen SJ. RNA-ligand molecular docking: advances and challenges. WILEY INTERDISCIPLINARY REVIEWS. COMPUTATIONAL MOLECULAR SCIENCE 2022; 12:e1571. [PMID: 37293430 PMCID: PMC10250017 DOI: 10.1002/wcms.1571] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 07/20/2021] [Indexed: 12/16/2022]
Abstract
With rapid advances in computer algorithms and hardware, fast and accurate virtual screening has led to a drastic acceleration in selecting potent small molecules as drug candidates. Computational modeling of RNA-small molecule interactions has become an indispensable tool for RNA-targeted drug discovery. The current models for RNA-ligand binding have mainly focused on the docking-and-scoring method. Accurate docking and scoring should tackle four crucial problems: (1) conformational flexibility of ligand, (2) conformational flexibility of RNA, (3) efficient sampling of binding sites and binding poses, and (4) accurate scoring of different binding modes. Moreover, compared with the problem of protein-ligand docking, predicting ligand binding to RNA, a negatively charged polymer, is further complicated by additional effects such as metal ion effects. Thermodynamic models based on physics-based and knowledge-based scoring functions have shown highly encouraging success in predicting ligand binding poses and binding affinities. Recently, kinetic models for ligand binding have further suggested that including dissociation kinetics (residence time) in ligand docking would result in improved performance in estimating in vivo drug efficacy. More recently, the rise of deep-learning approaches has led to new tools for predicting RNA-small molecule binding. In this review, we present an overview of the recently developed computational methods for RNA-ligand docking and their advantages and disadvantages.
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Affiliation(s)
- Yuanzhe Zhou
- Department of Physics and Astronomy, Department of Biochemistry, Institute of Data Sciences and Informatics, University of Missouri, Columbia, MO 65211-7010, USA
| | - Yangwei Jiang
- Department of Physics and Astronomy, Department of Biochemistry, Institute of Data Sciences and Informatics, University of Missouri, Columbia, MO 65211-7010, USA
| | - Shi-Jie Chen
- Department of Physics and Astronomy, Department of Biochemistry, Institute of Data Sciences and Informatics, University of Missouri, Columbia, MO 65211-7010, USA
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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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Mabonga L, Masamba P, Kappo AP. Inhibitory potential of a benzoxazole derivative, 4FI against SNRPG∼RING finger domain protein complex as a lead compound in the discovery of anti-cancer drugs: A molecular dynamics simulation approach. INFORMATICS IN MEDICINE UNLOCKED 2022. [DOI: 10.1016/j.imu.2022.100993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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Kuchana V, Kashetti V, Peddi SKR, Sivan S, Manga V. Integrated computational approach for in silico design of new purinyl pyridine derivatives as B-Raf kinase inhibitors. J Recept Signal Transduct Res 2021; 42:439-453. [PMID: 34844526 DOI: 10.1080/10799893.2021.1999472] [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] [Indexed: 10/19/2022]
Abstract
B-Raf is one among the most frequently mutating proto-oncogene which is associated with the serine/threonine Raf kinase family involved in the RAS-RAF-MEK-ERK pathway, which is the most deregulated pathway in human cancers. Mutant B-Raf V600E got an excellent scope for investigation in cancer as a potential therapeutic target. Formerly B-RafV600E is considered the molecular target for numerous antitumor compounds like purinyl pyridine and pyrimidine derivatives. In the current research work using molecular docking approach of Schrodinger Glide 5.6 version, ligand docking, pharmacophore-based virtual screening, binding free energy calculations of a series of 2-amino purinyl pyridine and pyrimidine derivatives were modeled, their docking values were predicted, that were considered to be potent against B-Raf V600E. A five-point hypothesis accompanied by a hydrogen bond acceptor(A), two hydrogen bond donors(D), and two aromatic rings (R) was built with a justifiable R2 value of 0.91 and a Q2 value of 0.64. Then by using Asinex Elite Synergy database, virtual screening was performed, and identified several potential hits. Subsequently, the molecules which had interactions with the target B-Raf kinase were determined by subjecting the obtained hits for SP and XP docking processes. Finally, for the top leads obtained, binding free energies were accomplished. About 16 new purinyl pyridine molecules were also designed. Almost nine molecules manifested crucial ligand interactions and binding free energies. At the outset, this research paved the way for us in spotting new molecules with B-Raf inhibitory activity, which can further be explored to design molecules with enhanced pharmacokinetic profiles.
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Affiliation(s)
- Vinutha Kuchana
- Department of Chemistry, Sarojini Naidu Pharmacy Maha Vidyalaya, Osmania University, Hyderabad, India
| | - Vaeshnavi Kashetti
- Department of Chemistry, University College of Science, Osmania University, Hyderabad, India
| | - Sai Kiran Reddy Peddi
- Department of Chemistry, University College of Science, Osmania University, Hyderabad, India
| | - Sreekanth Sivan
- Department of Chemistry, Nizam College, Osmania University, Hyderabad, India
| | - Vijjulatha Manga
- Department of Chemistry, University College of Science, Osmania University, Hyderabad, India
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Bujji S, E PK, Sivan SK, Dh M, N J P S. Design, Synthesis, Anticancer Evaluation, and Molecular Docking Studies of Novel Benzoxazole Linked 1,3,4-Oxadiazoles. Anticancer Agents Med Chem 2021; 22:933-942. [PMID: 34229589 DOI: 10.2174/1871520621666210706120203] [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: 12/17/2020] [Revised: 03/18/2021] [Accepted: 04/12/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND Cancer disease is making a serious concern globally. Global cancer occurrence is steadily increasing every year. There is always a persistent need to develop new anticancer drugs with reduced side effects or act synergistically with the existing chemotherapeutics. OBJECTIVE Benzoxazoles are fused bicyclic nitrogen and oxygen-containing heterocyclic compounds and are considered biologically privileged scaffolds. We designed a synthetic route to link the benzoxazoles with oxadiazoles resulting in a better pharmacophore for anticancer activity. METHODS A series of novel amide derivatives of benzoxazole linked 1,3,4-oxadiazoles (10a-j) were synthesized and characterized by 1H NMR, 13C NMR, and mass spectroscopic techniques. The biological properties of the compounds were screened in vitro against four different tumor cell lines. RESULTS The results suggest that the compound 10b having 3,4,5-trimethoxy substitution on the phenyl ring exhibited potent anticancer activity in three cell lines (A549 = 0.13 ± 0.014 µM, MCF-7 = 0.10 ± 0.013 µM and HT-29 = 0.22 ± 0.017 µM). Notably, among the synthesized derivatives, compounds 10b, 10c, 10f, 10g, and 10i exhibited potent anticancer activity than the control IC50 in the range of 0.11 ± 0.02 to 0.93 ± 0.034 µM. Molecular docking simulation results showed compounds were stabilized by hydrogen bond and π-π interactions with the protein. CONCLUSION The molecules showed comparable binding affinities with standard Combretastatin-A4. The present research work is preliminary and needs further studies to take the synthesized compounds to the next level in the cancer research field.
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Affiliation(s)
- Sushmitha Bujji
- Department of Pharmaceutical Chemistry, University College of Technology, Osmania University, Hyderabad, Telangana-500007, India
| | - Praveen Kumar E
- Department of Chemistry, University College of Science, Osmania University, Hyderabad, Telangana-500 007, India
| | - Sree Kanth Sivan
- Department of Chemistry, Nizam College, Basheerbagh, Hyderabad, India -500001, India
| | - Manjunatha Dh
- Department of Chemistry, Davangere University, Shivagangothri, Davangere-577 002, India
| | - Subhashini N J P
- Department of Pharmacy, & Department of Chemistry, University College of Science, Osmania University, Hyderabad, Telangana-500 007, India
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Mamidala S, Aravilli RK, Ramesh G, Khajavali S, Chedupaka R, Manga V, Vedula RR. A facile one-pot, three-component synthesis of a new series of thiazolyl pyrazole carbaldehydes: In vitro anticancer evaluation, in silico ADME/T, and molecular docking studies. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130356] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Wang M, Hou S, Wei Y, Li D, Lin J. Discovery of novel dual adenosine A1/A2A receptor antagonists using deep learning, pharmacophore modeling and molecular docking. PLoS Comput Biol 2021; 17:e1008821. [PMID: 33739970 PMCID: PMC7978378 DOI: 10.1371/journal.pcbi.1008821] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 02/19/2021] [Indexed: 02/07/2023] Open
Abstract
Adenosine receptors (ARs) have been demonstrated to be potential therapeutic targets against Parkinson's disease (PD). In the present study, we describe a multistage virtual screening approach that identifies dual adenosine A1 and A2A receptor antagonists using deep learning, pharmacophore models, and molecular docking methods. Nineteen hits from the ChemDiv library containing 1,178,506 compounds were selected and further tested by in vitro assays (cAMP functional assay and radioligand binding assay); of these hits, two compounds (C8 and C9) with 1,2,4-triazole scaffolds possessing the most potent binding affinity and antagonistic activity for A1/A2A ARs at the nanomolar level (pKi of 7.16-7.49 and pIC50 of 6.31-6.78) were identified. Further molecular dynamics (MD) simulations suggested similarly strong binding interactions of the complexes between the A1/A2A ARs and two compounds (C8 and C9). Notably, the 1,2,4-triazole derivatives (compounds C8 and C9) were identified as the most potent dual A1/A2A AR antagonists in our study and could serve as a basis for further development. The effective multistage screening approach developed in this study can be utilized to identify potent ligands for other drug targets.
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Affiliation(s)
- Mukuo Wang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, China
| | - Shujing Hou
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, China
| | - Yu Wei
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, China
- * E-mail: (YW); (DL); (JL)
| | - Dongmei Li
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, China
- * E-mail: (YW); (DL); (JL)
| | - Jianping Lin
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, China
- Biodesign Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- Platform of Pharmaceutical Intelligence, Tianjin International Joint Academy of Biomedicine, Tianjin, China
- * E-mail: (YW); (DL); (JL)
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Azizian H, Forooghian S, Amanlou A, Pérez-Sánchez H, Amanlou M. Phenothiazine as novel human superoxide dismutase modulators: discovery, optimization, and biological evaluation. J Biomol Struct Dyn 2021; 40:7070-7083. [PMID: 33663349 DOI: 10.1080/07391102.2021.1893819] [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: 10/22/2022]
Abstract
Superoxide dismutases (SODs) are regarded as important antioxidants for protecting cells against damage arising from oxidative stress. Much research is focused on finding new chemicals with an ability to boost human SOD activity. In the research described herein a structure-based approach was used to identify new human Cu-Zn superoxide dismutase (SOD1) modulators based on previously reported plasmodium falciparum iron SOD inhibitors using induced fit docking and molecular dynamic (MD) protocols. The compound with the highest docking binding energy was selected for further structure simplification followed by structural similarity and MD in order to find a new activator/inhibitor scaffold of the SOD1 enzyme. According to the docking survey of the mentioned series, 1,4-bis(3-(1,4,8-trichloro-10Hphenothiazin-10-yl) propyl) piperazine (DS88) was the top scoring compound interacting with the SOD1 active site channel. Following structure simplification and similarity search, the most promising scaffold which is closely related to the phenothiazine antipsychotic class, was identified. Compared with the normal blood SOD1 activity, the percent of O2 production increased with trifluoperazine, while it decreased with the chlorpromazine. The molecular dynamic investigation shows that trifluoperazine exerts its SOD1 activating effect by stabilizing electrostatic loop while chlorpromazine employs SOD1 inhibition activity through repositioning of the electrostatic loop and increasing its distance from the catalytic metal site which diminished substrate specificity and catalytic activity of the SOD1 enzyme. The results identified the preferred region, orientation, and types of interaction for each activator or inhibitor compound.
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Affiliation(s)
- Homa Azizian
- Department of Medicinal Chemistry, School of Pharmacy, Iran University of Medical Sciences, Tehran Iran
| | - Simin Forooghian
- Faculty of Basic Science, Department of Biology, Tehran Payame Noor University, Tehran, Iran
| | - Arash Amanlou
- Faculty of Specialized Veterinary Sciences, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Horacio Pérez-Sánchez
- Structural Bioinformatics and High-Performance Computing Research Group (BIO-HPC), Computer Engineering Department, Universidad Católica de Murcia (UCAM), Murcia, Spain
| | - Massoud Amanlou
- Faculty of Pharmacy, Department of Medicinal Chemistry, Tehran University of Medical Sciences, Tehran, Iran.,Experimental Medicine Research Center, Tehran University of Medical Sciences, Tehran, Iran
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Wang X, Zhang H, Li W. DNA-binding mechanisms of human and mouse cGAS: a comparative MD and MM/GBSA study. Phys Chem Chem Phys 2020; 22:26390-26401. [PMID: 33179635 DOI: 10.1039/d0cp04162a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Cyclic GMP-AMP synthase (cGAS) can detect the presence of cytoplasmic DNA and activate the innate immune system via the cGAS-STING pathway. Although several structures of cGAS-DNA complexes were resolved recently, the molecular mechanism of cGAS in its recognition of DNA has not yet been fully understood. In order to reveal the subtle differences between human and mouse cGAS in terms of their DNA-binding mechanisms, four systems, both human and mouse cGAS in complex with two different DNA sequences of equal length, were studied by molecular dynamics simulations and molecular mechanics/generalized Born surface area analysis. Several residues, including ARG176/ARG161, ARG195/ARG180, ASN210/ASN196, LYS384/LYS372, CYM397/CYM385, LYS403/LYS391, LYS407/LYS395, and LYS411/LYS399, were identified to be the common key residues in the recognition of DNA for cGAS in both humans and mice. In addition, four residue pairs LYS173/ARG158, ASP177/LYS162, CYS199/LYS184, and GLU398/SER387 were suggested to be the major residues that make human cGAS and mouse cGAS different in terms of their binding to DNA. Besides the well-known zinc-thumb domain, two residues at the kink of the spine helix were also proposed for the first time to be the major binding motifs in cGAS-DNA interaction.
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Affiliation(s)
- Xiaowen Wang
- Institute for Advanced Study, Shenzhen University, Room 341, Administration Building, Shenzhen 518060, China.
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Synthesis, biological evaluation and molecular docking studies of novel 1,2,3-triazole tethered chalcone hybrids as potential anticancer agents. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.128356] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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In Silico Structure-Based Repositioning of Approved Drugs for Spike Glycoprotein S2 Domain Fusion Peptide of SARS-CoV-2: Rationale from Molecular Dynamics and Binding Free Energy Calculations. mSystems 2020; 5:5/5/e00382-20. [PMID: 32963099 PMCID: PMC7511214 DOI: 10.1128/msystems.00382-20] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The membrane-anchored spike (S) protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has a pivotal role in directing the fusion of the virus particle mediated by the host cell receptor angiotensin-converting enzyme 2 (ACE-2). The fusion peptide region of the S protein S2 domain provides SARS-CoV-2 with the biological machinery needed for direct fusion to the host lipid membrane. In our present study, computer-aided drug design strategies were used for the identification of FDA-approved small molecules using the optimal structure of the S2 domain, which exhibits optimal interaction ratios, structural features, and energy variables, which were evaluated based on their performances in molecular docking, molecular dynamics simulations, molecular mechanics/generalized Born model and solvent accessibility binding free energy calculations of molecular dynamics trajectories, and statistical inferences. Among the 2,625 FDA-approved small molecules, chloramphenicol succinate, imipenem, and imidurea turned out to be the molecules that bound the best at the fusion peptide hydrophobic pocket. The principal interactions of the selected molecules suggest that the potential binding site at the fusion peptide region is centralized amid the Lys790, Thr791, Lys795, Asp808, and Gln872 residues.IMPORTANCE The present study provides the structural identification of the viable binding residues of the SARS-CoV-2 S2 fusion peptide region, which holds prime importance in the virus's host cell fusion and entry mechanism. The classical molecular mechanics simulations were set on values that mimic physiological standards for a good approximation of the dynamic behavior of selected drugs in biological systems. The drug molecules screened and analyzed here have relevant antiviral properties, which are reported here and which might hint toward their utilization in the coronavirus disease 2019 (COVID-19) pandemic owing to their attributes of binding to the fusion protein binding region shown in this study.
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17
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Wang E, Liu H, Wang J, Weng G, Sun H, Wang Z, Kang Y, Hou T. Development and Evaluation of MM/GBSA Based on a Variable Dielectric GB Model for Predicting Protein–Ligand Binding Affinities. J Chem Inf Model 2020; 60:5353-5365. [DOI: 10.1021/acs.jcim.0c00024] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Ercheng Wang
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou Zhejiang 310058, China
| | - Hui Liu
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou Zhejiang 310058, China
| | - Junmei Wang
- Department of Pharmaceutical Sciences and Computational Chemical Genomics Screening Center, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Gaoqi Weng
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou Zhejiang 310058, China
| | - Huiyong Sun
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou Zhejiang 310058, China
| | - Zhe Wang
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou Zhejiang 310058, China
| | - Yu Kang
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou Zhejiang 310058, China
| | - Tingjun Hou
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou Zhejiang 310058, China
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18
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Source of oseltamivir resistance due to single E119D and double E119D/H274Y mutations in pdm09H1N1 influenza neuraminidase. J Comput Aided Mol Des 2019; 34:27-37. [PMID: 31773463 DOI: 10.1007/s10822-019-00251-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2019] [Accepted: 11/09/2019] [Indexed: 12/24/2022]
Abstract
Influenza epidemics are responsible for an average of 3-5 millions of severe cases and up to 500,000 deaths around the world. One of flu pandemic types is influenza A(H1N1)pdm09 virus (pdm09H1N1). Oseltamivir is the antiviral drug used to treat influenza targeting at neuraminidase (NA) located on the viral surface. Influenza virus undergoes high mutation rates and leads to drug resistance, and thus the development of more efficient drugs is required. In the present study, all-atom molecular dynamics simulations were applied to understand the oseltamivir resistance caused by the single E119D and double E119D/H274Y mutations on NA. The obtained results in terms of binding free energy and intermolecular interactions in the ligand-protein interface showed that the oseltamivir could not be well accommodated in the binding pocket of both NA mutants and the 150-loop moves out from oseltamivir as an "open" state. A greater number of water molecules accessible to the binding pocket could disrupt the oseltamivir binding with NA target as seen be high mobility of oseltamivir at the active site. Additionally, our finding could guide to the design and development of novel NA inhibitor drugs.
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19
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Molecular mechanisms of tetrahydropyrrolo[1,2-c]pyrimidines as HBV capsid assembly inhibitors. Arch Biochem Biophys 2019; 663:1-10. [DOI: 10.1016/j.abb.2018.12.029] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 12/20/2018] [Accepted: 12/23/2018] [Indexed: 12/22/2022]
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20
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Ramos-Guzmán CA, Zinovjev K, Tuñón I. Modeling caspase-1 inhibition: Implications for catalytic mechanism and drug design. Eur J Med Chem 2019; 169:159-167. [PMID: 30875506 DOI: 10.1016/j.ejmech.2019.02.064] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 02/21/2019] [Accepted: 02/23/2019] [Indexed: 10/27/2022]
Abstract
The metabolic product of caspase-1, IL-1β, is an important mediator in inflammation and pyroptosis cell death process. Alzheimer's disease, septic shock and rheumatoid arthritis are IL-1β mediated diseases, making the caspase-1 an interesting target of pharmacological value. Many inhibitors have been developed until now, most of them are peptidomimetic with improved potency. In the present study, all-atom molecular dynamics simulations and the MM/GBSA method were employed to reproduce and interpret the results obtained by in vitro experiments for a series of inhibitors. The analysis shows that the tautomeric state of the catalytic His237 impact significantly the performance of the prediction protocol, providing evidence for a His237 tautomeric state different to the proposed in the putative mechanism. Additionally, analysis of inhibitor-enzyme interactions indicates that the differences in the inhibitory potency of the tested ligands can be explained mainly by the interaction of the inhibitors with the S2-S4 protein region. These results provide guidelines for subsequent studies of caspase-1 catalytic reaction mechanism and for the design of novel inhibitors.
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Affiliation(s)
- Carlos A Ramos-Guzmán
- Departamento de Química Física, Universidad de Valencia, Burjassot, Valencia, 46100, Spain
| | - Kirill Zinovjev
- Departamento de Química Física, Universidad de Valencia, Burjassot, Valencia, 46100, Spain
| | - Iñaki Tuñón
- Departamento de Química Física, Universidad de Valencia, Burjassot, Valencia, 46100, Spain.
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21
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C.S. V, Tamizhselvi R, Munusami P. Exploring the drug resistance mechanism of active site, non-active site mutations and their cooperative effects in CRF01_AE HIV-1 protease: molecular dynamics simulations and free energy calculations. J Biomol Struct Dyn 2019; 37:2608-2626. [DOI: 10.1080/07391102.2018.1492459] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Vasavi C.S.
- School of Biosciences and Technology, VIT University, Vellore, India
| | | | - Punnagai Munusami
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad, India
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22
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Manjula S, Sivanandam M, Kumaradhas P. Probing the "fingers" domain binding pocket of Hepatitis C virus NS5B RdRp and D559G resistance mutation via molecular docking, molecular dynamics simulation and binding free energy calculations. J Biomol Struct Dyn 2018; 37:2440-2456. [PMID: 30047829 DOI: 10.1080/07391102.2018.1491419] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The NS5B RdRp polymerase is a prominent enzyme for the replication of Hepatitis C virus (HCV). During the HCV replication, the template RNA binding takes place in the "fingers" sub-domain of NS5B. The "fingers" domain is a new emerging allosteric site for the HCV drug development. The inhibitors of the "fingers" sub-domain adopt a new antiviral mechanism called RNA intervention. The details of essential amino acid residues, binding mode of the ligand, and the active site intermolecular interactions of RNA intervention reflect that this mechanism is ambiguous in the experimental study. To elucidate these details, we performed molecular docking analysis of the fingers domain inhibitor quercetagetin (QGN) with NS5B polymerase. The detailed analysis of QGN-NS5B intermolecular interactions was carried out and found that QGN interacts with the binding pocket amino acid residues Ala97, Ala140, Ile160, Phe162, Gly283, Gly557, and Asp559; and also forms π⋯π stacking interaction with Phe162 and hydrogen bonding interaction with Gly283. These are found to be the essential interactions for the RNA intervention mechanism. Among the strong hydrogen bonding interactions, the QGN⋯Ala140 is a newly identified important hydrogen bonding interaction by the present work and this interaction was not resolved by the previously reported crystal structure. Since D559G mutation at the fingers domain was reported for reducing the inhibition percentage of QGN to sevenfold, we carried out molecular dynamics (MD) simulation for wild and D559G mutated complexes to study the stability of protein conformation and intermolecular interactions. At the end of 50 ns MD simulation, the π⋯π stacking interaction of Phe162 with QGN found in the wild-type complex is altered into T-shaped π stacking interaction, which reduces the inhibition strength. The origin of the D559G resistance mutation was studied using combined MD simulation, binding free energy calculations and principal component analysis. The results were compared with the wild-type complex. The mutation D559G reduces the binding affinity of the QGN molecule to the fingers domain. The free energy decomposition analysis of each residue of wild-type and mutated complexes revealed that the loss of non-polar energy contribution is the origin of the resistance. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Saravanan Manjula
- a Laboratory of Biocrystallography and Computational Molecular Biology, Department of Physics , Periyar University , Salem , India
| | - Magudeeswaran Sivanandam
- a Laboratory of Biocrystallography and Computational Molecular Biology, Department of Physics , Periyar University , Salem , India
| | - Poomani Kumaradhas
- a Laboratory of Biocrystallography and Computational Molecular Biology, Department of Physics , Periyar University , Salem , India
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23
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Song LT, Tu J, Liu RR, Zhu M, Meng YJ, Zhai HL. Molecular mechanism study of several inhibitors binding to BRD9 bromodomain based on molecular simulations. J Biomol Struct Dyn 2018; 37:2970-2979. [DOI: 10.1080/07391102.2018.1502097] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Li Ting Song
- College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, P. R. China
| | - Jing Tu
- College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, P. R. China
| | - Rui Rui Liu
- College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, P. R. China
| | - Min Zhu
- College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, P. R. China
| | - Ya Jie Meng
- College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, P. R. China
| | - Hong Lin Zhai
- College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, P. R. China
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24
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Discovery and design of new PI3K inhibitors through pharmacophore-based virtual screening, molecular docking, and binding free energy analysis. Struct Chem 2018. [DOI: 10.1007/s11224-018-1154-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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25
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C.P. A, Subhramanian S, Sizochenko N, Melge AR, Leszczynski J, Mohan CG. Multiple e-Pharmacophore modeling to identify a single molecule that could target both streptomycin and paromomycin binding sites for 30S ribosomal subunit inhibition. J Biomol Struct Dyn 2018; 37:1582-1596. [DOI: 10.1080/07391102.2018.1462731] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Anju C.P.
- Centre for Nanosciences and Molecular Medicine, Amrita Institute of Medical Sciences and Research Centre, Amrita Vishwa Vidyapeetham, Kochi 682 041, Kerala, India
| | - Sunitha Subhramanian
- Centre for Nanosciences and Molecular Medicine, Amrita Institute of Medical Sciences and Research Centre, Amrita Vishwa Vidyapeetham, Kochi 682 041, Kerala, India
| | - Natalia Sizochenko
- Interdisciplinary Centre for Nanotoxicity, Department of Chemistry and Biochemistry, Jackson State University, Jackson, MS-39217, MI, USA
| | - Anu R. Melge
- Centre for Nanosciences and Molecular Medicine, Amrita Institute of Medical Sciences and Research Centre, Amrita Vishwa Vidyapeetham, Kochi 682 041, Kerala, India
| | - Jerzy Leszczynski
- Interdisciplinary Centre for Nanotoxicity, Department of Chemistry and Biochemistry, Jackson State University, Jackson, MS-39217, MI, USA
| | - C. Gopi Mohan
- Centre for Nanosciences and Molecular Medicine, Amrita Institute of Medical Sciences and Research Centre, Amrita Vishwa Vidyapeetham, Kochi 682 041, Kerala, India
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26
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Andrade-Ochoa S, García-Machorro J, Bello M, Rodríguez-Valdez L, Flores-Sandoval C, Correa-Basurto J. QSAR, DFT and molecular modeling studies of peptides from HIV-1 to describe their recognition properties by MHC-I. J Biomol Struct Dyn 2017; 36:2312-2330. [DOI: 10.1080/07391102.2017.1352538] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- S. Andrade-Ochoa
- Laboratorio de Modelado Molecular, Bioinformática y Diseño de Fármacos, de la Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón s/n, Col. Casco de Santo Tomas, Delegación Miguel Hidalgo, C.P. 11340, Ciudad de México, Mexico
- Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala S/N, Col. Santo Tomas 11340, Ciudad de México, Mexico
| | - J. García-Machorro
- Laboratorio de Medicina de Conservación, de la Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón s/n, Col. Casco de Santo Tomas, Delegación Miguel Hidalgo, C.P. 11340, Ciudad de México, Mexico
| | - Martiniano Bello
- Laboratorio de Modelado Molecular, Bioinformática y Diseño de Fármacos, de la Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón s/n, Col. Casco de Santo Tomas, Delegación Miguel Hidalgo, C.P. 11340, Ciudad de México, Mexico
| | - L.M. Rodríguez-Valdez
- Facultad de Ciencias Químicas, Universidad Autónoma de Chihuahua, Circuito Universitario s/n, C.P. 31125, Chihuahua, Chih, Mexico
| | - C.A. Flores-Sandoval
- Instituto Mexicano del Petróleo, Eje Central Lázaro Cárdenas 152, Col. San Bartolo Atepehuacan 07730, Ciudad de México, Mexico
| | - J. Correa-Basurto
- Laboratorio de Modelado Molecular, Bioinformática y Diseño de Fármacos, de la Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón s/n, Col. Casco de Santo Tomas, Delegación Miguel Hidalgo, C.P. 11340, Ciudad de México, Mexico
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27
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Itteboina R, Ballu S, Sivan SK, Manga V. Molecular modeling-driven approach for identification of Janus kinase 1 inhibitors through 3D-QSAR, docking and molecular dynamics simulations. J Recept Signal Transduct Res 2017; 37:453-469. [DOI: 10.1080/10799893.2017.1328442] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Ramesh Itteboina
- Molecular Modeling and Medicinal Chemistry Group, Department of Chemistry, University College of Science, Osmania University, Hyderabad, India
| | - Srilata Ballu
- Molecular Modeling and Medicinal Chemistry Group, Department of Chemistry, University College of Science, Osmania University, Hyderabad, India
| | - Sree Kanth Sivan
- Molecular Modeling and Medicinal Chemistry Group, Department of Chemistry, University College of Science, Osmania University, Hyderabad, India
| | - Vijjulatha Manga
- Molecular Modeling and Medicinal Chemistry Group, Department of Chemistry, University College of Science, Osmania University, Hyderabad, India
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