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Pandey V, Adhikrao PA, Motiram GM, Yadav N, Jagtap U, Kumar G, Paul A. Biaryl carboxamide-based peptidomimetics analogs as potential pancreatic lipase inhibitors for treating obesity. Arch Pharm (Weinheim) 2024; 357:e2300503. [PMID: 38251950 DOI: 10.1002/ardp.202300503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 12/30/2023] [Accepted: 01/02/2024] [Indexed: 01/23/2024]
Abstract
A series of 1,1'-biphenyl-3-carboxamide and furan-phenyl-carboxamide analogs were synthesized using an optimized scheme and confirmed by 1H and 13C nuclear magnetic resonance and high-resolution mass spectrometry techniques. The synthesized peptidomimetics analogs were screened in vitro to understand the inhibitory potential of pancreatic lipase (PL). Analogs were assessed for the PL inhibitory activity based on interactions, geometric complementarity, and docking score. Among the synthesized analogs, 9, 29, and 24 were found to have the most potent PL inhibitory activity with IC50 values of 3.87, 4.95, and 5.34 µM, respectively, compared to that of the standard drug, that is, orlistat, which inhibits PL with an IC50 value of 0.99 µM. The most potent analog, 9, exhibited a competitive-type inhibition with an inhibition constant (Ki) of 2.72 µM. In silico molecular docking of analog 9 with the PL (PDB ID:1LPB) showed a docking score of -11.00 kcal/mol. Analog 9 formed crucial hydrogen bond interaction with Ser152, His263, π-cation interaction with Asp79, Arg256, and π-π stacking with Phe77, Tyr114 at the protein's active site. The molecular dynamic simulation confirmed that analog 9 forms stable interactions with PL at the end of 200 ns with root mean square deviation values of 2.5 and 6 Å. No toxicity was observed for analog 9 (concentration range of 1-20 µM) when tested by MTT assay in RAW 264.7 cells.
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Affiliation(s)
- Vikash Pandey
- Department of Natural Products, Chemical Sciences, National Institute of Pharmaceutical Education and Research, Hyderabad, Telangana, India
| | - Patil A Adhikrao
- Department of Natural Products, Chemical Sciences, National Institute of Pharmaceutical Education and Research, Hyderabad, Telangana, India
| | - Gudle M Motiram
- Department of Natural Products, Chemical Sciences, National Institute of Pharmaceutical Education and Research, Hyderabad, Telangana, India
| | - Nisha Yadav
- Laboratory of Natural Product Chemistry, Department of Pharmacy, Birla Institute of Technology and Science, Pilani (Pilani Campus), Pilani, Rajasthan, India
| | - Utkarsh Jagtap
- Laboratory of Natural Product Chemistry, Department of Pharmacy, Birla Institute of Technology and Science, Pilani (Pilani Campus), Pilani, Rajasthan, India
| | - Gautam Kumar
- Department of Natural Products, Chemical Sciences, National Institute of Pharmaceutical Education and Research, Hyderabad, Telangana, India
| | - Atish Paul
- Laboratory of Natural Product Chemistry, Department of Pharmacy, Birla Institute of Technology and Science, Pilani (Pilani Campus), Pilani, Rajasthan, India
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Kottekad S, Roy S, Dandamudi U. A computational study to probe the binding aspects of potent polyphenolic inhibitors of pancreatic lipase. J Biomol Struct Dyn 2024; 42:3472-3491. [PMID: 37199285 DOI: 10.1080/07391102.2023.2212795] [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: 10/19/2022] [Accepted: 05/07/2023] [Indexed: 05/19/2023]
Abstract
Pancreatic lipase (PL) is a keen target for anti-obesity therapy that reduces dietary fat absorption. Here, we investigated the binding patterns of 220 PL inhibitors having experimental IC50 values, using molecular docking and binding energy calculations. Screening of these compounds illustrated most of them bound at the catalytic site (S1-S2 channel) and a few compounds are at the non-catalytic site (S2-S3 channel/S1-S3 channel) of PL. This binding pattern could be due to structural uniqueness or bias in conformational search. A strong correlation of pIC50 values with SP/XP docking scores, binding energies (ΔGMMGBSA) assured the binding poses are more true positives. Further, understanding of each class and subclasses of polyphenols indicated tannins preferred non-catalytic site wherein binding energies are underestimated due to huge desolvation energy. In contrast, most of the flavonoids and furan-flavonoids have good binding energies due to strong interactions with catalytic residues. While scoring functions limited the understanding of sub-classes of flavonoids. Hence, focused on 55 potent PL inhibitors of IC50 < 5 µM for better in vivo efficacy. The prediction of bioactivity, drug-likeness properties, led to 14 bioactive compounds. The low root mean square deviation (0.1-0.2 nm) of these potent flavonoids and non-flavonoid/non-polyphenols PL-inhibitor complexes during 100 ns molecular dynamics runs (MD) as well as binding energies obtained from both MD and well-tempered metadynamics, support strong binding to catalytic site. Based on the bioactivity, ADMET properties, and binding affinity data of MD and wt-metaD of potent PL-inhibitors suggests Epiafzelechin 3-O-gallate, Sanggenon C, and Sanggenofuran A shall be promising inhibitors at in vivo conditions.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sanjay Kottekad
- Department of Food Safety and Analytical Quality Control Laboratory, Central Food Technological Research Institute, Council of Scientific and Industrial Research, Mysuru, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Sudip Roy
- Prescience Insilico Private Limited, Bangalore, India
| | - Usharani Dandamudi
- Department of Food Safety and Analytical Quality Control Laboratory, Central Food Technological Research Institute, Council of Scientific and Industrial Research, Mysuru, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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Mohan A, Krishnamoorthy S, Sabanayagam R, Schwenk G, Feng E, Ji HF, Muthusami S. Pharmacophore based virtual screening for identification of effective inhibitors to combat HPV 16 E6 driven cervical cancer. Eur J Pharmacol 2023; 957:175961. [PMID: 37549730 DOI: 10.1016/j.ejphar.2023.175961] [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: 02/07/2023] [Revised: 08/02/2023] [Accepted: 08/02/2023] [Indexed: 08/09/2023]
Abstract
Targeting HPV16 E6 has emerged as an effective drug target for the treatment/management of cervical cancer. We utilized pharmacophore-based virtual screening, molecular docking, absorption, distribution, metabolism and excretion (ADME) prediction, and molecular dynamics simulation approach for identifying potential inhibitors of HPV16 E6. Initially, we generated a ligand-based pharmacophore model based on the features of four known HPV16 E6 inhibitors (CA24, CA25, CA26, and CA27) via the PHASE module implanted in the Schrödinger suite. We constructed four-point pharmacophore features viz., three hydrogen bond acceptors (A) and one aromatic ring (R). The common pharmacophore feature further employed as a query for virtual screening against the ASINEX database via Schrödinger suite. The pharmacophore-based virtual screening filtered out top 2000 hits, based on the fitness score. We then applied the high throughput virtual screening (HTVS), standard precision (SP) and extra precision (XP). 1000 compounds were obtained from HTVS docking. Based on the glide score, they were further filtered to 500 hits by employing docking in standard precision mode. Finally, the best four hits and a negative molecule were identified using docking in XP mode. The four lead compounds and a negative molecule were then further subjected to ADME profile prediction by engaging Qikprop module. The ADME properties of the four lead molecules indicate good pharmacokinetic (PK) properties rather than the negative molecule. The binding stability of the HPV16 E6-hit complexes were investigated at a different time scale (100 ns) by using the desmond package and the results were examined using Root Mean Square Deviation (RMSD) and Root Mean Square Fluctuation (RMSF) and it revealed the stability of the protein-ligand complex throughout the simulation. Key residues, CYS 51 and GLN 107, also play a crucial role in enhancing the stability of the protein-ligand complex during the simulation. Furthermore, the binding free energy of the HPV16 E6-leads complexes was analyzed by prime which revealed that the ΔGbind coulomb and ΔGbind vdW interactions are crucially contributes to the binding affinity. In order to validate the computational findings, the efficacy of benzoimidazole and benzotriazole were ascertained for regulating ME180 cervical cancer cell survival, migration and ability to release MMP-2.
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Affiliation(s)
- Anbuselvam Mohan
- Department of Biochemistry, Karpagam Academy of Higher Education, Coimbatore, 641 021, Tamil Nadu, India; Department of Biotechnology, Selvamm Arts and Science College (Autonomous), Namakkal, 637003, Tamil Nadu, India
| | - Sneha Krishnamoorthy
- Department of Biochemistry, Karpagam Academy of Higher Education, Coimbatore, 641 021, Tamil Nadu, India
| | - Rajalakshmi Sabanayagam
- Department of Biochemistry, Karpagam Academy of Higher Education, Coimbatore, 641 021, Tamil Nadu, India
| | - Gregory Schwenk
- Department of Chemistry, Drexel University, Philadelphia, PA, 19104, USA
| | - Eric Feng
- Department of Chemistry, Drexel University, Philadelphia, PA, 19104, USA
| | - Hai-Feng Ji
- Department of Chemistry, Drexel University, Philadelphia, PA, 19104, USA
| | - Sridhar Muthusami
- Department of Biochemistry, Karpagam Academy of Higher Education, Coimbatore, 641 021, Tamil Nadu, India; Centre for Cancer Research, Karpagam Academy of Higher Education, Coimbatore, Tamil Nadu, India.
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Cao L, Wang Y, Chen X, Deng F, Li Z, Wang M, Zhang Y, Su R, Kim CK. Discovery of novel glucosinolates inhibiting advanced glycation end products: Virtual screening and molecular dynamic simulation. Proteins 2023; 91:1351-1360. [PMID: 37163477 DOI: 10.1002/prot.26506] [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: 11/01/2022] [Revised: 02/07/2023] [Accepted: 04/19/2023] [Indexed: 05/12/2023]
Abstract
Protein glycation can result in the formation of advanced glycation end products (AGEs), which pose a potential health risk due to their association with diabetic complications. Natural products are a source of drugs discovery and the search for potential natural inhibitors of AGEs is of great significance. Glucosinolates (GSLs) mainly from cruciferous plants have potential antioxidant, anti-inflammatory, and anti-glycation activities. In this study, the inhibitory activity of GSLs on bovine serum albumin (BSA) along with its mechanism was investigated by virtual screening and various computational simulation techniques. Virtual screening revealed that 174 GSLs were screened using Maestro based on the glide score and 89% of the compounds were found to have potential anti-glycation ability with the docking scores less than -5 kcal/mol. Molecular docking showed that the top 10 GSLs were bound to the IIA structural domain of BSA. Among them, glucohesperin (1) and 2-hydroxyethyl glucosinolate (2) had the lowest docking scores of -9.428 and -9.333 kcal/mol, respectively, reflecting their good binding affinity. Molecular dynamics simulations of 1 (ΔG = -43.46 kcal/mol) and 2 (ΔG = -43.71 kcal/mol) revealed that the complexes of these two compounds with proteins had good stability. Further binding site analysis suggested that the mechanism of inhibition of protein glycation by these two active ingredients might be through competitive hydrogen bonding to maintain the structural integrity of the protein, thus inhibiting glycation reaction. Moreover, the ADMET values and CYP450 metabolism prediction data were within the recommended values. Therefore, it can be concluded that 1 and 2 may act as potential anti-glycation agents.
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Affiliation(s)
- Lan Cao
- School of Chemistry and Chemical Engineering, North University of China, Taiyuan, China
| | - Yueyang Wang
- School of Chemistry and Chemical Engineering, North University of China, Taiyuan, China
| | - Xin'an Chen
- School of Chemistry and Chemical Engineering, North University of China, Taiyuan, China
| | - Fanyu Deng
- School of Chemistry and Chemical Engineering, North University of China, Taiyuan, China
| | - Zongchang Li
- School of Chemistry and Chemical Engineering, North University of China, Taiyuan, China
| | - Maosheng Wang
- School of Environment and Safety Engineering, North University of China, Taiyuan, China
| | - Yiqing Zhang
- School of Chemistry and Chemical Engineering, North University of China, Taiyuan, China
| | - Rui Su
- School of Chemistry and Chemical Engineering, North University of China, Taiyuan, China
| | - Chan Kyung Kim
- Department of Chemistry and Chemical Engineering, Inha University, Incheon, Republic of Korea
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Rajagopal K, Kalusalingam A, Bharathidasan AR, Sivaprakash A, Shanmugam K, Sundaramoorthy M, Byran G. In Silico Drug Design of Anti-Breast Cancer Agents. Molecules 2023; 28:molecules28104175. [PMID: 37241915 DOI: 10.3390/molecules28104175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 04/18/2023] [Accepted: 05/12/2023] [Indexed: 05/28/2023] Open
Abstract
Cancer is a condition marked by abnormal cell proliferation that has the potential to invade or indicate other health issues. Human beings are affected by more than 100 different types of cancer. Some cancer promotes rapid cell proliferation, whereas others cause cells to divide and develop more slowly. Some cancers, such as leukemia, produce visible tumors, while others, such as breast cancer, do not. In this work, in silico investigations were carried out to investigate the binding mechanisms of four major analogs, which are marine sesquiterpene, sesquiterpene lactone, heteroaromatic chalcones, and benzothiophene against the target estrogen receptor-α for targeting breast cancer using Schrödinger suite 2021-4. The Glide module handled the molecular docking experiments, the QikProp module handled the ADMET screening, and the Prime MM-GB/SA module determined the binding energy of the ligands. The benzothiophene analog BT_ER_15f (G-score -15.922 Kcal/mol) showed the best binding activity against the target protein estrogen receptor-α when compared with the standard drug tamoxifen which has a docking score of -13.560 Kcal/mol. TRP383 (tryptophan) has the highest interaction time with the ligand, and hence it could act for a long time. Based on in silico investigations, the benzothiophene analog BT_ER_15f significantly binds with the active site of the target protein estrogen receptor-α. Similar to the outcomes of molecular docking, the target and ligand complex interaction motif established a high affinity of lead candidates in a dynamic system. This study shows that estrogen receptor-α targets inhibitors with better potential and low toxicity when compared to the existing market drugs, which can be made from a benzothiophene derivative. It may result in considerable activity and be applied to more research on breast cancer.
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Affiliation(s)
- Kalirajan Rajagopal
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, JSS Academy of Higher Education & Research, The Nilgiris, Ooty 643001, Tamilnadu, India
| | - Anandarajagopal Kalusalingam
- Centre of Excellence for Pharmaceutical Sciences, School of Pharmacy, KPJ Healthcare University College, Nilai 71800, Negeri Sembilan, Malaysia
| | - Anubhav Raj Bharathidasan
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, JSS Academy of Higher Education & Research, The Nilgiris, Ooty 643001, Tamilnadu, India
| | - Aadarsh Sivaprakash
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, JSS Academy of Higher Education & Research, The Nilgiris, Ooty 643001, Tamilnadu, India
| | - Krutheesh Shanmugam
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, JSS Academy of Higher Education & Research, The Nilgiris, Ooty 643001, Tamilnadu, India
| | - Monall Sundaramoorthy
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, JSS Academy of Higher Education & Research, The Nilgiris, Ooty 643001, Tamilnadu, India
| | - Gowramma Byran
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, JSS Academy of Higher Education & Research, The Nilgiris, Ooty 643001, Tamilnadu, India
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6
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Vidhya R, Anbumani VI, Dinakara Rao A, Anuradha CV. Identification of novel human neutrophil elastase inhibitors from dietary phytochemicals using in silico and in vitro studies. J Biomol Struct Dyn 2022; 40:3451-3461. [DOI: 10.1080/07391102.2020.1847685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Ramachandran Vidhya
- Department of Biochemistry and Biotechnology, Annamalai University, Annamalai Nagar, Tamil Nadu, India
| | | | - Ampasala Dinakara Rao
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry, India
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7
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Mohan A, Rendine N, Mohammed MKS, Jeeva A, Ji HF, Talluri VR. Structure-based virtual screening, in silico docking, ADME properties prediction and molecular dynamics studies for the identification of potential inhibitors against SARS-CoV-2 M pro. Mol Divers 2021; 26:1645-1661. [PMID: 34480682 PMCID: PMC8417657 DOI: 10.1007/s11030-021-10298-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 08/02/2021] [Indexed: 11/30/2022]
Abstract
COVID-19 is a viral pandemic caused by SARS-CoV-2. Due to its highly contagious nature, millions of people are getting affected worldwide knocking down the delicate global socio-economic equilibrium. According to the World Health Organization, COVID-19 has affected over 186 million people with a mortality of around 4 million as of July 09, 2021. Currently, there are few therapeutic options available for COVID-19 control. The rapid mutations in SARS-CoV-2 genome and development of new virulent strains with increased infection and mortality among COVID-19 patients, there is a great need to discover more potential drugs for SARS-CoV-2 on a priority basis. One of the key viral enzymes responsible for the replication and maturation of SARS-CoV-2 is Mpro protein. In the current study, structure-based virtual screening was used to identify four potential ligands against SARS-CoV-2 Mpro from a set of 8,722 ASINEX library compounds. These four compounds were evaluated using ADME filter to check their ADME profile and druggability, and all the four compounds were found to be within the current pharmacological acceptable range. They were individually docked to SARS-CoV-2 Mpro protein to assess their molecular interactions. Further, molecular dynamics (MD) simulations was carried out on protein–ligand complex using Desmond at 100 ns to explore their binding conformational stability. Based on RMSD, RMSF and hydrogen bond interactions, it was found that the stability of protein–ligand complex was maintained throughout the entire 100 ns simulations for all the four compounds. Some of the key ligand amino acid residues participated in stabilizing the protein–ligand interactions includes GLN 189, SER 10, GLU 166, ASN 142 with PHE 66 and TRP 132 of SARS-CoV-2 Mpro. Further optimization of these compounds could lead to promising drug candidates for SARS-CoV-2 Mpro target.
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Affiliation(s)
- Anbuselvam Mohan
- Department of Biotechnology, Selvamm Arts and Science College (Autonomous), Namakkal, Tamil Nadu, 637 003, India
| | - Nicole Rendine
- Department of Chemistry, Drexel University, Philadelphia, PA, 19104, USA
| | | | - Anbuselvam Jeeva
- Department of Animal Science, Bharathidasan University, Tiruchirappalli, Tamil Nadu, 620 024, India
| | - Hai-Feng Ji
- Department of Chemistry, Drexel University, Philadelphia, PA, 19104, USA
| | - Venkateswara Rao Talluri
- Prof.TNA Innovation Centre, Varsha Bioscience and Technology India Private Limited, Jiblakpally, Yadadri District, Hyderabad, Telangana, 508 284, India.
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Panwar U, Singh SK. In silico virtual screening of potent inhibitor to hamper the interaction between HIV-1 integrase and LEDGF/p75 interaction using E-pharmacophore modeling, molecular docking, and dynamics simulations. Comput Biol Chem 2021; 93:107509. [PMID: 34153658 DOI: 10.1016/j.compbiolchem.2021.107509] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 05/11/2021] [Indexed: 02/07/2023]
Abstract
The rapid increase of HIV-1 infection throughout the globe has a high demand for a superior drug with lesser side effects. LEDGF/p75, the human Lens Epithelium-Derived Growth Factor is identified as a promising cellular cofactor with integrase in facilitating the viral replication in an early stage by acting as a tethering factor in the pre-integration to the chromatin. Therefore, the present study was designed to identify a potent inhibitor by applying an E-pharmacophore based virtual screening, molecular docking, and dynamics simulation approaches. Finally, ZINC22077550 and ZINC32124441 were best identified potent molecules with the efficient binding affinity, strong hydrogen bonding, and acceptable pharmacological properties to hamper the interaction between integrase and LEDGF/p75. Further, the DFT and MDS studies were also analyzed, and shown a favorable energetic state and dynamic stability then reference compound. In conclusion, we suggest that these findings could be novel therapeutics in the future and may increase the lifespan of individuals suffering from viral infection.
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Affiliation(s)
- Umesh Panwar
- Computer Aided Drug Design and Molecular Modelling Lab, Department of Bioinformatics, Alagappa University, Karaikudi, 630 004, Tamil Nadu, India
| | - Sanjeev Kumar Singh
- Computer Aided Drug Design and Molecular Modelling Lab, Department of Bioinformatics, Alagappa University, Karaikudi, 630 004, Tamil Nadu, India.
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Chandra I, Prabhu SV, Nayak C, Singh SK. E-pharmacophore based screening to identify potential HIV-1 gp120 and CD4 interaction blockers for wild and mutant types. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2021; 32:353-377. [PMID: 33832362 DOI: 10.1080/1062936x.2021.1901310] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 03/07/2021] [Indexed: 06/12/2023]
Abstract
HIV-1 gp120 provides a multistage viral entry process through the conserved CD4 binding site. Hunting of potential blockers can diminish the interaction of gp120 with the CD4 host receptor leading to the suppression of HIV-1 infection. Structure-based pharmacophore virtual screening followed by binding free energy calculation, molecular dynamics (MD) simulation and density functional theory (DFT) calculation is applied to discriminate the potential blockers from six small molecule databases. Five compounds from six databases exhibited vital interactions with key residues ASP368, GLU370, ASN425, MET426, TRP427 and GLY473 of gp120, involved in the binding with CD4, host receptor. Most importantly, compound NCI-254200 displayed strong communication with key residues of wild type and drug resistance single mutant gp120 (M426L and W427V) even in the dynamic condition, evidenced from MD simulation. This investigation provided a potential compound NCI-254200 which may show inhibitory activity against HIV-1 gp120 variant interactions with CD4 host cell receptors.
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Affiliation(s)
- I Chandra
- Computer Aided Drug Design and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi, India
| | - S V Prabhu
- Computer Aided Drug Design and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi, India
| | - C Nayak
- Computer Aided Drug Design and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi, India
| | - S K Singh
- Computer Aided Drug Design and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi, India
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Kumar A, Chauhan S. Pancreatic lipase inhibitors: The road voyaged and successes. Life Sci 2021; 271:119115. [PMID: 33515565 DOI: 10.1016/j.lfs.2021.119115] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 01/20/2021] [Accepted: 01/21/2021] [Indexed: 01/26/2023]
Abstract
Human pancreatic lipase (triacylglycerol acyl hydrolase EC3.1.1.3) is the most widely studied member of the human lipase superfamily related to carboxyl esterase. It is secreted from the acinar cell of pancreas and has strong preference for triacylglycerides over cholesterol esters, phospholipids, and galactolipids. Apart from the hydrolysis of triacylglycerides, pancreatic lipase may cause the hydrolysis of retinyl esters in vivo. So, it is very much evidenced that pancreatic lipase with its cofactor colipase has prominent role in efficient digestion of dietary fat. Hence, the modulation of human pancreatic lipase may represent a new insight in the discovery of a number of therapeutics that can inhibit the absorption of fat in body and can be used in obesity and other related metabolic disorders. Even, the only Food and drug administration (FDA) approved antiobesity drug, orlistat, is also an inhibitor of pancreatic lipase. This review summarizes studies about structure, mechanistic approach of pancreatic lipase enzyme while emphasizing on the various synthetic pancreatic lipase inhibitors with their structure activity relationship (SAR).
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Affiliation(s)
- Ashwani Kumar
- Department of Pharmaceutical Sciences, Guru Jambheshwar University of Science and Technology, Hisar, India
| | - Shilpi Chauhan
- Lloyd Institute of Management and Technology (Pharm.), U.P., India.
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11
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George G, Auti PS, Paul AT. Design, synthesis, in silico molecular modelling studies and biological evaluation of novel indole-thiazolidinedione hybrid analogues as potential pancreatic lipase inhibitors. NEW J CHEM 2021. [DOI: 10.1039/d0nj05649a] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
A series of thiazolidinedione-indole hybrids are designed and synthesized as a potential inhibitor for pancreatic lipase (PL).
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Affiliation(s)
- Ginson George
- Laboratory of Natural Product Chemistry
- Department of Pharmacy
- Birla Institute of Technology and Science
- Pilani (BITS Pilani)
- Pilani - 333 031
| | - Prashant S. Auti
- Laboratory of Natural Product Chemistry
- Department of Pharmacy
- Birla Institute of Technology and Science
- Pilani (BITS Pilani)
- Pilani - 333 031
| | - Atish T. Paul
- Laboratory of Natural Product Chemistry
- Department of Pharmacy
- Birla Institute of Technology and Science
- Pilani (BITS Pilani)
- Pilani - 333 031
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12
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Design, synthesis and biological evaluation of novel chalcone-like compounds as potent and reversible pancreatic lipase inhibitors. Bioorg Med Chem 2021; 29:115853. [DOI: 10.1016/j.bmc.2020.115853] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 10/15/2020] [Accepted: 11/01/2020] [Indexed: 01/19/2023]
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13
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Khatua B, El-Kurdi B, Patel K, Rood C, Noel P, Crowell M, Yaron JR, Kostenko S, Guerra A, Faigel DO, Lowe M, Singh VP. Adipose saturation reduces lipotoxic systemic inflammation and explains the obesity paradox. SCIENCE ADVANCES 2021; 7:7/5/eabd6449. [PMID: 33514548 PMCID: PMC7846167 DOI: 10.1126/sciadv.abd6449] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 12/11/2020] [Indexed: 05/10/2023]
Abstract
Obesity sometimes seems protective in disease. This obesity paradox is predominantly described in reports from the Western Hemisphere during acute illnesses. Since adipose triglyceride composition corresponds to long-term dietary patterns, we performed a meta-analysis modeling the effect of obesity on severity of acute pancreatitis, in the context of dietary patterns of the countries from which the studies originated. Increased severity was noted in leaner populations with a higher proportion of unsaturated fat intake. In mice, greater hydrolysis of unsaturated visceral triglyceride caused worse organ failure during pancreatitis, even when the mice were leaner than those having saturated triglyceride. Saturation interfered with triglyceride's interaction and lipolysis by pancreatic triglyceride lipase, which mediates organ failure. Unsaturation increased fatty acid monomers in vivo and aqueous media, resulting in greater lipotoxic cellular responses and organ failure. Therefore, visceral triglyceride saturation reduces the ensuing lipotoxicity despite higher adiposity, thus explaining the obesity paradox.
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Affiliation(s)
| | - Bara El-Kurdi
- Department of Medicine, Mayo Clinic, Scottsdale, AZ, USA
| | - Krutika Patel
- Department of Medicine, Mayo Clinic, Scottsdale, AZ, USA
| | | | - Pawan Noel
- Department of Medicine, Mayo Clinic, Scottsdale, AZ, USA
| | | | - Jordan R Yaron
- Department of Medicine, Mayo Clinic, Scottsdale, AZ, USA
| | | | - Andre Guerra
- Department of Medicine, Mayo Clinic, Scottsdale, AZ, USA
| | | | - Mark Lowe
- Department of Pediatrics, Washington University School of Medicine, Saint Louis, MO, USA
| | - Vijay P Singh
- Department of Medicine, Mayo Clinic, Scottsdale, AZ, USA.
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14
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Fadaka AO, Aruleba RT, Sibuyi NRS, Klein A, Madiehe AM, Meyer M. Inhibitory potential of repurposed drugs against the SARS-CoV-2 main protease: a computational-aided approach. J Biomol Struct Dyn 2020; 40:3416-3427. [PMID: 33200673 PMCID: PMC7682381 DOI: 10.1080/07391102.2020.1847197] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The exponential increase in cases and mortality of coronavirus disease (COVID-19) has called for a need to develop drugs to treat this infection. Using in silico and molecular docking approaches, this study investigated the inhibitory effects of Pradimicin A, Lamivudine, Plerixafor and Lopinavir against SARS-CoV-2 Mpro. ADME/Tox of the ligands, pharmacophore hypothesis of the co-crystalized ligand and the receptor, and docking studies were carried out on different modules of Schrodinger (2019-4) Maestro v12.2. Among the ligands subjected to ADME/Tox by QikProp, Lamivudine demonstrated drug-like physico-chemical properties. A total of five pharmacophore binding sites (A3, A4, R9, R10, and R11) were predicted from the co-crystalized ligand and the binding cavity of the SARS-CoV-2 Mpro. The docking result showed that Lopinavir and Lamivudine bind with a higher affinity and lower free energy than the standard ligand having a glide score of -9.2 kcal/mol and -5.3 kcal/mol, respectively. Plerixafor and Pradimicin A have a glide score of -3.7 kcal/mol and -2.4 kcal/mol, respectively, which is lower than the co-crystallized ligand with a glide score of -5.3 kcal/mol. Molecular dynamics confirmed that the ligands maintained their interaction with the protein with lower RMSD fluctuations over the trajectory period of 100 nsecs and that GLU166 residue is pivotal for binding. On the whole, present study specifies the repurposing aptitude of these molecules as inhibitors of SARS-CoV-2 Mpro with higher binding scores and forms energetically stable complexes with Mpro.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Adewale Oluwaseun Fadaka
- Department of Science and Innovation/Mintek Nanotechnology Innovation Centre, Department of Biotechnology, Faculty of Natural Sciences, University of the Western Cape, Bellville, South Africa
| | - Raphael Taiwo Aruleba
- Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
| | - Nicole Remaliah Samantha Sibuyi
- Department of Science and Innovation/Mintek Nanotechnology Innovation Centre, Department of Biotechnology, Faculty of Natural Sciences, University of the Western Cape, Bellville, South Africa
| | - Ashwil Klein
- Department of Biotechnology, Faculty of Natural Sciences, University of the Western Cape, Bellville, South Africa
| | - Abram Madimabe Madiehe
- Department of Science and Innovation/Mintek Nanotechnology Innovation Centre, Department of Biotechnology, Faculty of Natural Sciences, University of the Western Cape, Bellville, South Africa.,Nanobiotechnology Research Group, Department of Biotechnology, Faculty of Natural Sciences, University of the Western Cape, Bellville, South Africa
| | - Mervin Meyer
- Department of Science and Innovation/Mintek Nanotechnology Innovation Centre, Department of Biotechnology, Faculty of Natural Sciences, University of the Western Cape, Bellville, South Africa
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15
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Discovery and characterization of pentacyclic triterpenoid acids in Styrax as potent and reversible pancreatic lipase inhibitors. J Funct Foods 2020. [DOI: 10.1016/j.jff.2020.104159] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
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16
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Choubey SK, Nachiappan M, Richard M, Chitra JP, Jeyakanthan J. Structural and functional insights of STAT2-NS5 interaction for the identification of NS5 antagonist – An approach for restoring interferon signaling. Comput Biol Chem 2020; 88:107332. [DOI: 10.1016/j.compbiolchem.2020.107332] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 07/13/2020] [Accepted: 07/16/2020] [Indexed: 11/16/2022]
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17
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Veeramachaneni GK, Thunuguntla VBSC, Bobbillapati J, Bondili JS. Structural and simulation analysis of hotspot residues interactions of SARS-CoV 2 with human ACE2 receptor. J Biomol Struct Dyn 2020; 39:4015-4025. [PMID: 32448098 PMCID: PMC7284149 DOI: 10.1080/07391102.2020.1773318] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The novel corona virus disease 2019 (SARS-CoV 2) pandemic outbreak was alarming. The binding of SARS-CoV (CoV) spike protein (S-Protein) Receptor Binding Domain (RBD) to Angiotensin converting enzyme 2 (ACE2) receptor initiates the entry of corona virus into the host cells leading to the infection. However, considering the mutations reported in the SARS-CoV 2 (nCoV), the structural changes and the binding interactions of the S-protein RBD of nCoV were not clear. The present study was designed to elucidate the structural changes, hot spot binding residues and their interactions between the nCoV S-protein RBD and ACE2 receptor through computational approaches. Based on the sequence alignment, a total of 58 residues were found mutated in nCoV S-protein RBD. These mutations led to the structural changes in the nCoV S-protein RBD 3d structure with 4 helices, 10 sheets and intermittent loops. The nCoV RBD was found binding to ACE2 receptor with 11 hydrogen bonds and 1 salt bridge. The major hot spot amino acids involved in the binding identified by interaction analysis after simulations includes Glu 35, Tyr 83, Asp 38, Lys 31, Glu 37, His 34 amino acid residues of ACE2 receptor and Gln 493, Gln 498, Asn 487, Tyr 505 and Lys 417 residues in nCoV S-protein RBD. Based on the hydrogen bonding, RMSD and RMSF, total and potential energies, the nCoV was found binding to ACE2 receptor with higher stability and rigidity. Concluding, the hotspots information will be useful in designing blockers for the nCoV spike protein RBD. Communicated by Ramaswamy H. Sarma
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18
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Peters C, Bascuñán D, Burgos CF, Bobadilla C, González-Sanmiguel J, Boopathi S, Riffo N, Fernández-Pérez EJ, Tarnok ME, Aguilar LF, Gonzalez W, Aguayo LG. Characterization of a new molecule capable of inhibiting several steps of the amyloid cascade in Alzheimer's disease. Neurobiol Dis 2020; 141:104938. [PMID: 32434047 DOI: 10.1016/j.nbd.2020.104938] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 05/04/2020] [Indexed: 11/16/2022] Open
Abstract
INTRODUCTION Alzheimer's disease (AD) is the most prevalent neurodegenerative disorder in elderly people. Existent therapies are directed at alleviating some symptoms, but are not effective in altering the course of the disease. METHODS Based on our previous study that showed that an Aβ-interacting small peptide protected against the toxic effects of amyloid-beta peptide (Aβ), we carried out an array of in silico, in vitro, and in vivo assays to identify a molecule having neuroprotective properties. RESULTS In silico studies showed that the molecule, referred to as M30 (2-Octahydroisoquinolin-2(1H)-ylethanamine), was able to interact with the Aβ peptide. Additionally, in vitro assays showed that M30 blocked Aβ aggregation, association to the plasma membrane, synaptotoxicity, intracellular calcium, and cellular toxicity, while in vivo experiments demonstrated that M30 induced a neuroprotective effect by decreasing the toxicity of Aβ in the dentate gyrus of the hippocampus and improving the alteration in spatial memory in behavior assays. DISCUSSION Therefore, we propose that this new small molecule could be a useful candidate for the additional development of a treatment against AD since it appears to block multiple steps in the amyloid cascade. Overall, since there are no drugs that effectively block the progression of AD, this approach represents an innovative strategy. SIGNIFICANCE Currently, there is no effective treatment for AD and the expectations to develop an effective therapy are low. Using in silico, in vitro, and in vivo experiments, we identified a new compound that is able to inhibit Aβ-induced neurotoxicity, specifically aggregation, association to neurons, synaptic toxicity, calcium dyshomeostasis and memory impairment induced by Aβ. Because Aβ toxicity is central to AD progression, the inhibition mediated by this new molecule might be useful as a therapeutic tool.
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Affiliation(s)
- Christian Peters
- Laboratory of Neurophysiology, Department of Physiology, Universidad de Concepción, Concepción, Chile
| | - Denisse Bascuñán
- Laboratory of Neurophysiology, Department of Physiology, Universidad de Concepción, Concepción, Chile
| | - Carlos F Burgos
- Laboratory of Neurophysiology, Department of Physiology, Universidad de Concepción, Concepción, Chile
| | - Catalina Bobadilla
- Laboratory of Neurophysiology, Department of Physiology, Universidad de Concepción, Concepción, Chile
| | | | - Subramanian Boopathi
- The Center for Bioinformatics and Molecular Simulations (CBSM), Universidad de Talca, Talca, Chile
| | - Nicolás Riffo
- Laboratory of Neurophysiology, Department of Physiology, Universidad de Concepción, Concepción, Chile
| | - Eduardo J Fernández-Pérez
- Laboratory of Neurophysiology, Department of Physiology, Universidad de Concepción, Concepción, Chile
| | - María Elena Tarnok
- Laboratory of Photophysics and Molecular Spectroscopy, Chemistry, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Luis Felipe Aguilar
- Laboratory of Photophysics and Molecular Spectroscopy, Chemistry, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Wendy Gonzalez
- The Center for Bioinformatics and Molecular Simulations (CBSM), Universidad de Talca, Talca, Chile; Millennium Nucleus of Ion Channels-Associated Diseases (MiNICAD), Universidad de Talca, Talca, Chile
| | - Luis G Aguayo
- Laboratory of Neurophysiology, Department of Physiology, Universidad de Concepción, Concepción, Chile.
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19
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Computational approaches for the discovery of natural pancreatic lipase inhibitors as antiobesity agents. Future Med Chem 2020; 12:741-757. [DOI: 10.4155/fmc-2019-0284] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Obesity is becoming one of the greatest threats to global health in the 21st century and therefore the development of novel antiobesity drugs is one of the top priorities of global drug research. An important treatment strategy includes the reduction of intestinal fat absorption through the inhibition of pancreatic lipase (PL). Natural products provide a vast pool of PL inhibitors with novel scaffolds that can possibly be developed into clinical products. Computational drug design methods have become increasingly invaluable in the drug discovery process. In recent years, the discovery of new antiobesity PL inhibitors has been facilitated by the application of computational methods. This review highlights some computer-aided drug design techniques utilized in the discovery of natural PL inhibitors.
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20
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Divyashri G, Krishna Murthy TP, Sundareshan S, Kamath P, Murahari M, Saraswathy GR, Sadanandan B. In silico approach towards the identification of potential inhibitors from Curcuma amada Roxb against H. pylori: ADMET screening and molecular docking studies. ACTA ACUST UNITED AC 2020; 11:119-127. [PMID: 33842282 PMCID: PMC8022237 DOI: 10.34172/bi.2021.19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 03/05/2020] [Accepted: 03/16/2020] [Indexed: 12/13/2022]
Abstract
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Introduction: The present study attempts to identify potential targets of H. pylori for novel inhibitors from therapeutic herb, mango ginger (Curcuma amada Roxb.). Methods: Crystal structure of all the selected drug targets obtained from Protein Data Bank (PDB) were subjected to molecular docking against a total of 130 compounds (found to have biological activity against H. pylori ) were retrieved from public databases. Compounds with good binding affinity were selected for Prime MM-GBSA rescoring and molecular dynamics (MD) simulation. Final list of compounds were taken for ADMET predictions. Results: Based on binding affinity denoted by glide score and ligand efficiency, mango ginger compounds were found selective to shikimate kinase and type II dehydroquinase through hydrogen bonding and salt bridge interactions. Stability of the interactions and free energy calculations by Prime MM-GBSA results confirmed the affinity of mango ginger compounds towards both shikimate kinase and type II dehydroquinase. From the above results, 15 compounds were calculated for ADMET parameters, Lipinski’s rule of five, and the results were found promising without any limitations. MD simulations identified gentisic acid as hit compound for shikimate kinase of H. pylori. Conclusion: Current study could identify the in silico potential of mango ginger compounds against shikimate kinase and type II dehydroquinase targets for H. pylori infections and are suitable for in vitro and in vivo evaluation.
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Affiliation(s)
- G Divyashri
- Department of Biotechnology, M S Ramaiah Institute of Technology, Bangalore, Karnataka, India
| | - T P Krishna Murthy
- Department of Biotechnology, M S Ramaiah Institute of Technology, Bangalore, Karnataka, India
| | - Subramaniam Sundareshan
- Department of Biotechnology, M S Ramaiah Institute of Technology, Bangalore, Karnataka, India
| | - Pavan Kamath
- Department of Biotechnology, M S Ramaiah Institute of Technology, Bangalore, Karnataka, India
| | - Manikanta Murahari
- Pharmacological Modelling and Simulation Centre, M.S. Ramaiah University of Applied Sciences, Bangalore, Karnataka, India.,Department of Pharmaceutical Chemistry, Faculty of Pharmacy, M.S. Ramaiah University of Applied Sciences, Bangalore, Karnataka, India
| | - G R Saraswathy
- Pharmacological Modelling and Simulation Centre, M.S. Ramaiah University of Applied Sciences, Bangalore, Karnataka, India.,Department of Pharmacy Practice, Faculty of Pharmacy, M.S. Ramaiah University of Applied Sciences, Bangalore, Karnataka, India
| | - Bindu Sadanandan
- Department of Biotechnology, M S Ramaiah Institute of Technology, Bangalore, Karnataka, India
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21
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Eda SR, Jinka R. Combined e-pharmacophore based screening and docking of PI3 kinase with potential inhibitors from a database of natural compounds. Bioinformation 2019; 15:709-715. [PMID: 31831952 PMCID: PMC6900324 DOI: 10.6026/97320630015709] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 10/15/2019] [Accepted: 10/19/2019] [Indexed: 11/23/2022] Open
Abstract
Phospho inositide 3-kinase (PI3 K) is a promising target for the design of anticancer drugs and is of significant concern in developing selective isoforms as
inhibitors for cancer treatments. The results obtained from the computational analysis were selected based on Glide score and drug binding interaction features.
Molecular docking studies and prime MM-GBSA energy calculations showed STOCK1N-77648 with optimal binding features for further consideration. The hydrogen bonding
patterns between the top three molecules STOCK1N-91335, STOCK1N-70036 and STOCK1N-77648 and the target protein based on G-scores is reported. The STOCK1N-77648
ligand molecule has protein residue interactions similar to that of interactions with the known inhibitor copanlisib. These data illustrates selectivity of the
small molecular PI3 K inhibitors through screening and molecular docking for further in vitro and in vivo consideration.
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Affiliation(s)
- Sasidhar Reddy Eda
- Department of Biochemistry, Acharya Nagarjuna University, Guntur, Andhra Pradesh, India
| | - Rajeswari Jinka
- Department of Biochemistry, Acharya Nagarjuna University, Guntur, Andhra Pradesh, India
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22
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Nain Z, Sayed SB, Karim MM, Islam MA, Adhikari UK. Energy-optimized pharmacophore coupled virtual screening in the discovery of quorum sensing inhibitors of LasR protein of Pseudomonas aeruginosa. J Biomol Struct Dyn 2019; 38:5374-5388. [DOI: 10.1080/07391102.2019.1700168] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Zulkar Nain
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Islamic University, Kushtia, Bangladesh
| | - Sifat Bin Sayed
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Islamic University, Kushtia, Bangladesh
| | - Mohammad Minnatul Karim
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Islamic University, Kushtia, Bangladesh
| | - Md Ariful Islam
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Islamic University, Kushtia, Bangladesh
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23
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Pharmacophore Directed Screening of Agonistic Natural Molecules Showing Affinity to 5HT 2C Receptor. Biomolecules 2019; 9:biom9100556. [PMID: 31581577 PMCID: PMC6843766 DOI: 10.3390/biom9100556] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 09/26/2019] [Accepted: 09/29/2019] [Indexed: 02/08/2023] Open
Abstract
Obesity prevalence continues to be a foremost health concern across the globe leading to the development of major health risk conditions like type II diabetes, hyperlipidemia, hypertension and even cancers. Because of the deprived drug-based management system, there is an urgent need for the development of new drugs aiming at satiety and appetite control targets. Among the reported satiety signaling targets, 5HT2C receptor plays a crucial role in decreasing appetite and has become a promising target for the development of anti-obesity drugs. Lorcaserin, a 5HT2C receptor agonist and the only drug available in the market, was designed based on the receptor mechanism of action. Due to limited drug options available and considering the adverse drug effects of Lorcaserin, the development of new drugs which are highly specific toward the 5HT2C target and with lesser side effects is essential. The present study is majorly focused on developing new 5HT2C agonists through computational approaches like screening, docking, and simulation using Phase, QikProp, Glide and Desmond applications of the Schrodinger suite. Screening protocols resulted in eight best hit molecules with affinity for the receptor and among them, five hits displayed binding affinity toward the conserved residue Asp 134 of the receptor. The stability of the five molecules in complex with the 5HT2C receptor was studied through molecular dynamic simulations. Three molecules, ZINC32123870, ZINC40312983 and ZINC32124535, maintained stable interactions with the Asp 134 residue throughout the 50 ns simulation run time. Further, due to the high sequence similarity seen among the receptors of 5HT2 family, the three potential hits were cross validated against other subtypes 5HT2A and 5HT2B of the 5HT2 family to determine the specificity of the molecules against the target. Among the three hits, ZINC32124535 was identified as the best potential hit based on the hydrogen bond interaction percentage with Asp residue [5HT2A (Asp 155:60%); 5HT2B (Asp155: No interaction); 5HT2C (Asp 134:86%)]. The ZINC32124535 molecule produced one salt bridge and hydrogen bond interactions with Asp 134, alike the known drug Lorcaserin. Based on the results, ZINC32124535 was identified as the best potential hit against the 5HT2C receptor.
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Peptide Mapping, In Silico and In Vivo Analysis of Allergenic Sorghum Profilin Peptides. ACTA ACUST UNITED AC 2019; 55:medicina55050178. [PMID: 31117233 PMCID: PMC6571906 DOI: 10.3390/medicina55050178] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 03/16/2019] [Accepted: 05/17/2019] [Indexed: 01/21/2023]
Abstract
Background and objectives: Nearly 20–30% of the world’s population suffers from allergic rhinitis, among them 15% are progressing to asthma conditions. Sorghum bicolor profilin (Sorb PF), one of the panallergens, was identified, but the allergen specificity is not yet characterized. Materials and Methods: To map the antigenic determinants responsible for IgE binding, the present study is focused on in silico modeling, simulation of Sorb PF and docking of the Sorb PF peptides (PF1-6) against IgG and IgE, followed by in vivo evaluation of the peptides for its allergenicity in mice. Results: Peptide PF3 and PF4 displayed high docking G-scores (−9.05) against IgE only. The mice sensitized with PF3 peptide showed increased levels of IL5, IL12, TNF-alpha, and GMCSF when compared to other peptides and controls, signifying a strong, Th2-based response. Concurrently, the Th1 pathway was inhibited by low levels of cytokine IL2, IFN-γ, and IL-10 justifying the role of PF3 in allergenic IgE response. Conclusions: Based on the results of overlapping peptides PF3 and PF4, the N-terminal part of the PF3 peptide (TGQALVI) plays a crucial role in allergenic response of Sorghum profilin.
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25
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Eda SR, Veeramachaneni GK, Bondili JS, Jinka R. Screening of caspase-3 inhibitors from natural molecule database using e-pharmacophore and docking studies. Bioinformation 2019; 15:240-245. [PMID: 31285640 PMCID: PMC6599438 DOI: 10.6026/97320630015240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 03/16/2019] [Indexed: 11/25/2022] Open
Abstract
Caspase a protease family member, have a vital role in cell death and inflammation process. Caspase-3, an effector caspase controls the regulation of apoptosis and has an anti apoptotic function. The mechanical significance of restoring apoptosis signaling to selectively target malignant cells is utilized to develop strong therapeutic strategies by the caspase family of mortality - induction molecules. Caspase-3 has currently no clear role in treatment for tumor progression and tumor sensitivity. The present study was aimed to screen caspase for potential inhibitors using computer aided docking methodologies. For this, zinc natural molecule database molecules were screened using e-pharmacophore and ADME protocols along with docking studies. Docking analysis selected two molecules, namely ZINC13341044 and ZINC13507846 with G-scores -5.27 and -6.19 respectively. These two potential hits are predicted as caspase inhibitors based on the results and can be further processed for in vitro validation.
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Affiliation(s)
- Sasidhar Reddy Eda
- Department of Biochemistry, Acharya Nagarjuna University, Guntur, Andhra Pradesh, India
| | | | | | - Rajeswari Jinka
- Department of Biochemistry, Acharya Nagarjuna University, Guntur, Andhra Pradesh, India
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26
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Nagabhishek SN, Madan Kumar A, B. S, Balakrishnan A, Katakia YT, Chatterjee S, Nagasundaram N. A marine sponge associated fungal metabolite monacolin X suppresses angiogenesis by down regulating VEGFR2 signaling. RSC Adv 2019; 9:26646-26667. [PMID: 35528587 PMCID: PMC9070443 DOI: 10.1039/c9ra05262c] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 08/08/2019] [Indexed: 12/16/2022] Open
Abstract
Cancer is one of the leading causes of global death and there is an urgent need for the development of cancer treatment; targeting VEGFR2 could be one of the promising therapies. In the present study, previously isolated marine fungal metabolite monacolin X, suppresses in vitro angiogenic characteristics such as proliferation, migration, adhesion, invasion and tube formation of HUVECs when stimulated by VEGF, at a non-toxic concentration. Monacolin X downregulated VEGFR2, PKCα and PKCη mRNA expression. Further, monacolin X inhibited in vivo angiogenesis in CAM assay, vascular sprouting in aortic ring, decreased ISV and SIV length and diameter in Tg (Kdr:EGFP)/ko1 zebrafish embryos. Monacolin X showed reduced protein expression of pVEGFR2, pAKT1, pMAPKAPK2, pFAK and pERK1 in breast cancer lines and in DMBA induced mammary carcinoma in SD rats showed tumor regression and anti-angiogenesis ability via decrease pVEGFR2 and pAKT1 protein expression. In silico studies also revealed monacolin X ability to bind to crucial amino acid Cys 919 in the active site of VEGFR2 suggesting it to be a potent VEGFR2 inhibitor. Cancer is one of the leading causes of global deaths and there is an urgent need for the development cancer treatment; targeting VEGFR2 could be one of the promising therapies.![]()
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Affiliation(s)
- Sirpu Natesh Nagabhishek
- Cancer Biology Lab
- Molecular and Nanomedicine Research Unit
- Sathyabama Institute of Science and Technology
- Chennai-600 119
- India
| | - Arumugam Madan Kumar
- Cancer Biology Lab
- Molecular and Nanomedicine Research Unit
- Sathyabama Institute of Science and Technology
- Chennai-600 119
- India
| | - Sambhavi B.
- Department of Genetics
- Dr ALM PGIBMS University of Madras Taramani
- Chennai
- India
| | | | - Yash T. Katakia
- Vascular Biology Lab
- AU-KBC Research Centre
- Department of Biotechnology
- Anna University
- Chennai
| | - Suvro Chatterjee
- Vascular Biology Lab
- AU-KBC Research Centre
- Department of Biotechnology
- Anna University
- Chennai
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27
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Bello M, Basilio-Antonio L, Fragoso-Vázquez J, Avalos-Soriano A, Correa-Basurto J. Molecular recognition between pancreatic lipase and natural and synthetic inhibitors. Int J Biol Macromol 2017; 98:855-868. [DOI: 10.1016/j.ijbiomac.2017.01.150] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Revised: 01/27/2017] [Accepted: 01/31/2017] [Indexed: 02/03/2023]
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28
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Bis-indole alkaloids from Tabernaemontana divaricata as potent pancreatic lipase inhibitors: molecular modelling studies and experimental validation. Med Chem Res 2017. [DOI: 10.1007/s00044-017-1836-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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29
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Li M, Wen F, Zhao S, Wang P, Li S, Zhang Y, Zheng N, Wang J. Exploring the Molecular Basis for Binding of Inhibitors by Threonyl-tRNA Synthetase from Brucella abortus: A Virtual Screening Study. Int J Mol Sci 2016; 17:E1078. [PMID: 27447614 PMCID: PMC4964454 DOI: 10.3390/ijms17071078] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 06/19/2016] [Accepted: 06/29/2016] [Indexed: 01/18/2023] Open
Abstract
Targeting threonyl-tRNA synthetase (ThrRS) of Brucella abortus is a promising approach to developing small-molecule drugs against bovine brucellosis. Using the BLASTp algorithm, we identified ThrRS from Escherichia coli (EThrRS, PDB ID 1QF6), which is 51% identical to ThrRS from Brucella abortus (BaThrRS) at the amino acid sequence level. EThrRS was used as the template to construct a BaThrRS homology model which was optimized using molecular dynamics simulations. To determine the residues important for substrate ATP binding, we identified the ATP-binding regions of BaThrRS, docked ATP to the protein, and identified the residues whose side chains surrounded bound ATP. We then used the binding site of ATP to virtually screen for BaThrRS inhibitors and got seven leads. We further characterized the BaThrRS-binding site of the compound with the highest predicted inhibitory activity. Our results should facilitate future experimental effects to find novel drugs for use against bovine brucellosis.
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Affiliation(s)
- Ming Li
- Ministry of Agriculture Laboratory of Quality & Safety Risk Assessment for Dairy Products (Beijing), Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
- Ministry of Agriculture-Milk and Dairy Product Inspection Center (Beijing), Beijing 100193, China.
| | - Fang Wen
- Ministry of Agriculture Laboratory of Quality & Safety Risk Assessment for Dairy Products (Beijing), Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
- Ministry of Agriculture-Milk and Dairy Product Inspection Center (Beijing), Beijing 100193, China.
| | - Shengguo Zhao
- Ministry of Agriculture Laboratory of Quality & Safety Risk Assessment for Dairy Products (Beijing), Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
- Ministry of Agriculture-Milk and Dairy Product Inspection Center (Beijing), Beijing 100193, China.
| | - Pengpeng Wang
- Ministry of Agriculture Laboratory of Quality & Safety Risk Assessment for Dairy Products (Beijing), Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
- Ministry of Agriculture-Milk and Dairy Product Inspection Center (Beijing), Beijing 100193, China.
| | - Songli Li
- Ministry of Agriculture Laboratory of Quality & Safety Risk Assessment for Dairy Products (Beijing), Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
- Ministry of Agriculture-Milk and Dairy Product Inspection Center (Beijing), Beijing 100193, China.
| | - Yangdong Zhang
- Ministry of Agriculture Laboratory of Quality & Safety Risk Assessment for Dairy Products (Beijing), Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
- Ministry of Agriculture-Milk and Dairy Product Inspection Center (Beijing), Beijing 100193, China.
| | - Nan Zheng
- Ministry of Agriculture Laboratory of Quality & Safety Risk Assessment for Dairy Products (Beijing), Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
- Ministry of Agriculture-Milk and Dairy Product Inspection Center (Beijing), Beijing 100193, China.
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Jiaqi Wang
- Ministry of Agriculture Laboratory of Quality & Safety Risk Assessment for Dairy Products (Beijing), Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
- Ministry of Agriculture-Milk and Dairy Product Inspection Center (Beijing), Beijing 100193, China.
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
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Veeramachaneni GK, Raj KK, Chalasani LM, Annamraju SK, Js B, Talluri VR. Shape based virtual screening and molecular docking towards designing novel pancreatic lipase inhibitors. Bioinformation 2015; 11:535-42. [PMID: 26770027 PMCID: PMC4702031 DOI: 10.6026/97320630011535] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 11/04/2015] [Indexed: 12/11/2022] Open
Abstract
Increase in obesity rates and obesity associated health issues became one of the greatest health concerns in the present world
population. With alarming increase in obese percentage there is a need to design new drugs related to the obesity targets. Among
the various targets linked to obesity, pancreatic lipase was one of the promising targets for obesity treatment. Using the in silico
methods like structure based virtual screening, QikProp, docking studies and binding energy calculations three molecules namely
zinc85531017, zinc95919096 and zinc33963788 from the natural database were reported as the potential inhibitors for the pancreatic
lipase. Among them zinc95919096 presented all the interactions matching to both standard and crystal ligand and hence it can be
further proceeded to drug discovery process.
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Affiliation(s)
- Ganesh Kumar Veeramachaneni
- Department of Biotechnology, K L E F University, Green Fields, Vaddeswaram, 522 502, Guntur (Dt.), A.P, India
| | - K Kranthi Raj
- Department of Biotechnology, K L E F University, Green Fields, Vaddeswaram, 522 502, Guntur (Dt.), A.P, India
| | - Leela Madhuri Chalasani
- Department of Biotechnology, K L E F University, Green Fields, Vaddeswaram, 522 502, Guntur (Dt.), A.P, India
| | - Sai Krishna Annamraju
- Department of Biotechnology, K L E F University, Green Fields, Vaddeswaram, 522 502, Guntur (Dt.), A.P, India
| | - Bondili Js
- Department of Biotechnology, K L E F University, Green Fields, Vaddeswaram, 522 502, Guntur (Dt.), A.P, India
| | - Venkateswara Rao Talluri
- Department of Biotechnology, K L E F University, Green Fields, Vaddeswaram, 522 502, Guntur (Dt.), A.P, India; Prof. TNA Innovation Center, VBTIPL, Sy no. 253/A, Jiblakpally, Pochampally, 508 284, Nalgonda (Dist), Telangana, India
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