1
|
Venkatesan A, Dhanabalan AK, Rajendran S, Shanmugasundharam SG, Gunasekaran K, Febin Prabhu Dass J. Structure-based pharmacophore modeling, virtual screening approaches to identifying the potent hepatitis C viral protease and polymerase novel inhibitors. J Cell Biochem 2022; 123:1366-1380. [PMID: 35726444 DOI: 10.1002/jcb.30298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 05/25/2022] [Accepted: 05/30/2022] [Indexed: 11/07/2022]
Abstract
Hepatitis C is an infectious disease that leads to acute and chronic liver illnesses. Currently, there are no effective vaccines against this deadly virus. Direct acting antiviral (DAA) drugs are given in the combination with ribavirin and pegylated interferon which lead to adverse effects. Through in silico analysis, the structure-based docking study was performed against NS3/4A protease and NS5B polymerase proteins of HCV. In the current study, multiple e-pharmacophore-based virtual screening methods such as HTVS, SP, and XP were carried out to screen natural compounds and enamine databases. Our result outcomes revealed that CID AE-848/13196185 and CID AE-848/36959205 compounds show good binding interactions with protease protein. In addition, CID 15081408 and CID 173568 show better binding interactions with the polymerase protein. Further to validate the docking results, we performed molecular dynamics simulation for the top hit compounds bound with protease and polymerase proteins to illustrate conformational differences in the stability compared with the active site of the cocrystal inhibitor. Thus, the current study emphasizes these compounds could be an effective drug to treat HCV.
Collapse
Affiliation(s)
- Arthi Venkatesan
- Department of Integrative Biology, School of Bio Sciences and Technology (SBST), VIT, Vellore, India
| | - Anantha Krishnan Dhanabalan
- Centre of Advance study in Crystallography and Biophysics & Bioinformatics Infrastructure Facility, University of Madras, Chennai, India
| | - Selvakumar Rajendran
- Centre of Advance study in Crystallography and Biophysics & Bioinformatics Infrastructure Facility, University of Madras, Chennai, India
| | | | - Krishnasamy Gunasekaran
- Centre of Advance study in Crystallography and Biophysics & Bioinformatics Infrastructure Facility, University of Madras, Chennai, India
| | - J Febin Prabhu Dass
- Department of Integrative Biology, School of Bio Sciences and Technology (SBST), VIT, Vellore, India
| |
Collapse
|
2
|
Atanasova M, Dimitrov I, Ivanov S, Georgiev B, Berkov S, Zheleva-Dimitrova D, Doytchinova I. Virtual Screening and Hit Selection of Natural Compounds as Acetylcholinesterase Inhibitors. Molecules 2022; 27:3139. [PMID: 35630613 PMCID: PMC9145144 DOI: 10.3390/molecules27103139] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 05/06/2022] [Accepted: 05/10/2022] [Indexed: 12/10/2022] Open
Abstract
Acetylcholinesterase (AChE) is one of the classical targets in the treatment of Alzheimer's disease (AD). Inhibition of AChE slows down the hydrolysis of acetycholine and increases choline levels, improving the cognitive function. The achieved success of plant-based natural drugs acting as AChE inhibitors, such as galantamine (GAL) from Galanthus genus and huperzine A from Huperzia serrate (approved drug in China), in the treatment of AD, and the fact that natural compounds (NCs) are considered as safer and less toxic compared to synthetic drugs, led us to screen the available NCs (almost 150,000) in the ZINC12 database for AChE inhibitory activity. The compounds were screened virtually by molecular docking, filtered for suitable ADME properties, and 32 ligands from 23 structural groups were selected. The stability of the complexes was estimated via 1 μs molecular dynamics simulation. Ten compounds formed stable complexes with the enzyme and had a vendor and a reasonable price per mg. They were tested for AChE inhibitory and antioxidant activity. Five compounds showed weak AChE inhibition and three of them exhibited high antioxidant activity.
Collapse
Affiliation(s)
- Mariyana Atanasova
- Chemistry Department, Faculty of Pharmacy, Medical University of Sofia, 1000 Sofia, Bulgaria; (I.D.); (S.I.); (D.Z.-D.); (I.D.)
| | - Ivan Dimitrov
- Chemistry Department, Faculty of Pharmacy, Medical University of Sofia, 1000 Sofia, Bulgaria; (I.D.); (S.I.); (D.Z.-D.); (I.D.)
| | - Stefan Ivanov
- Chemistry Department, Faculty of Pharmacy, Medical University of Sofia, 1000 Sofia, Bulgaria; (I.D.); (S.I.); (D.Z.-D.); (I.D.)
- Redesign Science, 180 Varick St, New York, NY 10014, USA
| | - Borislav Georgiev
- Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria; (B.G.); (S.B.)
| | - Strahil Berkov
- Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria; (B.G.); (S.B.)
| | - Dimitrina Zheleva-Dimitrova
- Chemistry Department, Faculty of Pharmacy, Medical University of Sofia, 1000 Sofia, Bulgaria; (I.D.); (S.I.); (D.Z.-D.); (I.D.)
| | - Irini Doytchinova
- Chemistry Department, Faculty of Pharmacy, Medical University of Sofia, 1000 Sofia, Bulgaria; (I.D.); (S.I.); (D.Z.-D.); (I.D.)
| |
Collapse
|
3
|
Yousaf R, Navid A, Azam SS. Discovery of novel Glutaminase allosteric inhibitors through drug repurposing and comparative MMGB/PBSA and molecular dynamics simulation. Comput Biol Med 2022; 146:105669. [PMID: 35654625 DOI: 10.1016/j.compbiomed.2022.105669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 05/21/2022] [Accepted: 05/23/2022] [Indexed: 11/03/2022]
Abstract
GLS1 enzymes (Glutaminase C (GAC) and kidney-type Glutaminase (KGA)) are gaining prominence as a target for tumor treatment including lung, breast, kidney, prostate, and colorectal. To date, several medicinal chemistry studies are being conducted to develop new and effective inhibitors against GLS1 enzymes. Telaglenastat, a drug that targets the allosteric site of GLS1, has undergone clinical trials for the first time for the therapy of solid tumors and hematological malignancies. A comprehensive computational investigation is performed to get insights into the inhibition mechanism of the Telaglenastat. Some novel inhibitors are also proposed against GLS1 enzymes using the drug repurposing approach using 2D-fingerprinting virtual screening method against 2.4 million compounds, application of pharmacokinetics, Molecular Docking, and Molecular Dynamic (MD) Simulations. A TIP3P water box of 10 Å was defined to solvate both enzymes to improve MD simulation reliability. The dynamics results were validated further by the MMGB/PBSA binding free energy method, RDF, and AFD analysis. Results of these computational analysis revealed a stable binding affinity of Telaglenastat, as well as an FDA approved drug Astemizole (IC50 ∼ 0.9 nM) and a novel para position oriented methoxy group containing Chembridge compound (Chem-64284604) that provides an effective inhibitory action against GAC and KGA.
Collapse
|
4
|
Nazar A, Abbas G, Azam SS. Deciphering the Inhibition Mechanism of under Trial Hsp90 Inhibitors and Their Analogues: A Comparative Molecular Dynamics Simulation. J Chem Inf Model 2020; 60:3812-3830. [PMID: 32659088 DOI: 10.1021/acs.jcim.9b01134] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Heat shock protein 90 (Hsp90) performs functions in cellular activities together with other signaling pathways. Hsp90 is evolutionarily conserved and universally articulated as a human cancer-causing agent involved in lung cancer and breast cancer followed by colon and rectum cancers. It has emerged as an effective drug candidate, and inhibition may affect several signaling pathways associated with cancer spread. Therefore, in-silico approaches, molecular docking, molecular dynamics simulation, and binding free energy calculations were applied to create insights into the inhibition mechanism against Hsp90 to identify new cancer therapeutic drugs. Top-docked Hsp90-inhibitor complexes with their analogues were selected as the best complexes based on the GOLD fitness score and orientation. The significant interaction of Hsp90 inhibitors and their analogues were observed to be bound with active site residues as well as residing within the same cavity region. System stability factors RMSD, RMSF, beta-factor, and radius of gyration were analyzed for top-docked complexes and ensure strong binding interaction between inhibitors and the Hsp90 cavity. Cavity bound inhibitors were found to retain consistent hydrogen bonding during the simulation. The radial distribution function (RDF) illustrated that interacting active site residues drive the binding and stability of the inhibitors. Similarly, the axial frequency distribution, which is an indigenously developed analytical tool, produced noteworthy knowledge of the hydrogen-bonding pattern. Results yielded new insights into the design of cancer therapeutic drugs against Hsp90. This finding suggests that under trial Hsp90 inhibitors MPC-3100 could be a potential starting point into the development of potential anticancer agents with the possibility of future directions for the improvement of early existing Hsp90 inhibitors CNF-2024 and SNX-5422 as an anticancer agent.
Collapse
Affiliation(s)
- Asma Nazar
- Computational Biology Lab, National Center for Bioinformatics (NCB), Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Ghulam Abbas
- Computational Biology Lab, National Center for Bioinformatics (NCB), Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Syed Sikander Azam
- Computational Biology Lab, National Center for Bioinformatics (NCB), Quaid-i-Azam University, Islamabad 45320, Pakistan
| |
Collapse
|
5
|
Ahmad F, Shabaz Z, Azam SS. Insight into natural inhibitors and bridging docking to dynamic simulation against sugar Isomerase (SIS) domain protein. J Mol Model 2020; 26:221. [PMID: 32748070 DOI: 10.1007/s00894-020-04475-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 07/14/2020] [Indexed: 11/28/2022]
Abstract
The pathogen Legionella longbeachae is a causative agent of legionellosis. The antibiotic resistance is the major problem of this modern world. Thus, selective pressure warrants the need for identification of newer drug target. In current study, subtractive proteomics approach screen out SIS (sugar isomerase) domain protein as an attractive receptor molecule for rational drug design. This protein is involved in lipopolysaccharide biosynthesis and catalyzes the isomerization of sedoheptulose 7-phosphate in D-glycero-D-manno-heptose 7-phosphate. Molecular docking revealed compound 1 (2-(6-(N,N-dimethyl sulfamoyl)pipridin-4-yl)pyrazin-2-yl)imidazol-3-ium-1-ide) as the potent inhibitor having GOLD fitness score of 69. The complex is affirmed by half-site effect via simulation analysis. Complex stability was investigated via several approaches that follows dynamic simulation and binding energies. Trajectory analysis revealed slight change in ring positioning of inhibitor inside the active pocket during 130 ns (nanosecond). Interestingly, it was affirmed via binding interactions' density distribution. Hence, radial distribution function (RDF) inferred that SER55 and SER83 are the major residues that take part in hydrogen bonding and complex stability. Furthermore, an indigenously developed method axial frequency distribution (AFD) has revealed that ligand moved closer to the active site with both the residues SER55 and SER83 binding to the ligand. The phenomena was observed via rotating motion with respect to receptor center cavity. Thus, inhibitor movement towards allosteric site was observed at the end of simulations. Finally, binding free energy calculations by MMPB/GBSA predicts high compound affinity for the complex. Hence, findings from the current study will aid in the novel drug discovery and future experimental studies. Graphical abstract.
Collapse
Affiliation(s)
- Faisal Ahmad
- Computational Biology Lab, National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, Pakistan
| | - Zartasha Shabaz
- Computational Biology Lab, National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, Pakistan
| | - Syed Sikander Azam
- Computational Biology Lab, National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, Pakistan.
| |
Collapse
|
6
|
Banoth S, Tangutur AD, Anthappagudem A, Ramaiah J, Bhukya B. Cloning and in vivo metabolizing activity study of CYP3A4 on amiodarone drug residues: A possible probiotic and therapeutic option. Pharmacotherapy 2020; 127:110128. [DOI: 10.1016/j.biopha.2020.110128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 03/26/2020] [Accepted: 03/27/2020] [Indexed: 10/24/2022]
|
7
|
Shahzadi Z, Abbas G, Azam SS. Relational dynamics obtained through simulation studies of thioredoxin reductase: From a multi-drug resistant Entamoeba histolytica. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.112939] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
|
8
|
Ranade SS, Ramalingam R. Hydrogen bonds in anoplin peptides aid in identification of a structurally stable therapeutic drug scaffold. J Mol Model 2020; 26:155. [PMID: 32451705 DOI: 10.1007/s00894-020-04380-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 04/07/2020] [Indexed: 12/30/2022]
Abstract
Multi-drug resistance is a major issue faced by the global pharmaceutical industry. Short antimicrobial peptides such as anoplins can be used to replace antibiotics, thus mitigating this issue. Antimicrobial activity, non-toxicity, and structural stability are essential features of a therapeutic drug. Antimicrobial activity and toxicity to human erythrocytes have been previously reported for anoplin and anoplin R5K T8W. This study attempts to identify a therapeutic peptide drug scaffold between these peptides by examining their structural stability, mainly based on the hydrogen bonds (H-bond) found in their structures. The static structure of anoplin R5K T8W displayed lower H-bond distances than anoplin, thereby exhibiting enhanced structural stability. Dynamic stability studies revealed that conformers of anoplin R5K T8W exhibited lower hydrogen bond distances (HBDs), higher H-bond occupancies, and higher radial distribution function (RDF) of H-bonds in comparison with conformers of anoplin. Furthermore, conformers of anoplin R5K T8W generated using 50-ns molecular dynamics simulation displayed lower conformational free energy than anoplin, thus establishing its higher structural stability. Overall, anoplin R5K T8W can be claimed as a promising scaffold that may be used for therapeutic purposes. In conclusion, H-bonds play a major role in structural stability and may aid in identification of a therapeutic peptide scaffold. Graphical abstract.
Collapse
Affiliation(s)
- Shruti Sunil Ranade
- Department of Biotechnology, School of Biosciences and Technology, Vellore Institute of Technology (Deemed to be University), Vellore, Tamil Nadu, 632014, India
| | - Rajasekaran Ramalingam
- Department of Biotechnology, School of Biosciences and Technology, Vellore Institute of Technology (Deemed to be University), Vellore, Tamil Nadu, 632014, India.
| |
Collapse
|
9
|
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.
Collapse
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
| |
Collapse
|
10
|
Vijayakumar S, Das P. Recent progress in drug targets and inhibitors towards combating leishmaniasis. Acta Trop 2018; 181:95-104. [PMID: 29452111 DOI: 10.1016/j.actatropica.2018.02.010] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 01/24/2018] [Accepted: 02/11/2018] [Indexed: 12/22/2022]
Abstract
Lesihmaniasis is one of the major neglected tropical disease caused by the parasite of the genus Leishmania. The disease has more than one clinical forms and the visceral form is considered fatal. With the lack of potential vaccine, chemotherapy is the major treatment source considered for the control of the disease in the infected people. Drugs including amphotericin B and miltefosine are widely used for the treatment, however, development of resistance by the parasite towards the administered drug and high-toxicity of the drug are of major concern. Hence, more attention has been shown on identifying new targets, effective inhibitors, and better drug delivery system against the disease. This review deals with recent studies on drug targets and exploring their essentiality for the survival of Leishmania. Further, new inhibitors for those targets, novel anti-leishmanial peptides and vaccines against leishmaniasis were discussed. We believe that this pool of information will ease the researchers to gain knowledge and help in choosing right targets and design of new inhibitors against Leishmaniasis.
Collapse
|
11
|
Raza S, Azam SS. AFD: an application for bi-molecular interaction using axial frequency distribution. J Mol Model 2018; 24:84. [DOI: 10.1007/s00894-018-3601-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 01/29/2018] [Indexed: 11/29/2022]
|
12
|
Roca C, Sebastián-Pérez V, Campillo NE. In silico Tools for Target Identification and Drug Molecular Docking in Leishmania. DRUG DISCOVERY FOR LEISHMANIASIS 2017. [DOI: 10.1039/9781788010177-00130] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Neglected tropical diseases represent a significant health burden in large parts of the world. Drug discovery is currently a key bottleneck in the pipeline of these diseases. In this chapter, the in silico approaches used for the processes involved in drug discovery, identification and validation of druggable Leishmania targets, and design and optimisation of new anti-leishmanial drugs are discussed. We also provide a general view of the different computational tools that can be employed in pursuit of this aim, along with the most interesting cases found in the literature.
Collapse
Affiliation(s)
- Carlos Roca
- Centro de Investigaciones Biológicas (CSIC) Ramiro de Maeztu 9 28040 Madrid Spain
| | | | - Nuria E. Campillo
- Centro de Investigaciones Biológicas (CSIC) Ramiro de Maeztu 9 28040 Madrid Spain
| |
Collapse
|
13
|
Ahmad S, Raza S, Uddin R, Azam SS. Binding mode analysis, dynamic simulation and binding free energy calculations of the MurF ligase from Acinetobacter baumannii. J Mol Graph Model 2017; 77:72-85. [DOI: 10.1016/j.jmgm.2017.07.024] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 07/20/2017] [Accepted: 07/21/2017] [Indexed: 01/16/2023]
|
14
|
Abbasi S, Raza S, Azam SS, Liedl KR, Fuchs JE. Interaction mechanisms of a melatonergic inhibitor in the melatonin synthesis pathway. J Mol Liq 2016. [DOI: 10.1016/j.molliq.2016.06.034] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
|