Sandeep Satapathy and Rupam Ghosh
John G. Bruno
...he target antibodies, no docking simulations are possible to test this topological hypothesis, but the present work illustrates feasibility of the approach and paves the way for more sophisticated analysis that could lead to improved rickettsial serodiagnostics and aptamer-based vaccines....
Farrukh Jamil*, Samra Raheel and Haroon Rasheed
Musrrat Fatima, Muhammad Saad Khan, Hamid Rashid, Asim Mehmood, Sumaira Kanwal, Muhammad Asif Rasheed and Farrukh Jamil*
Syed Aun Muhammad1, Muhammad Soaib Said2, Shams Ur Rehman2, Muhammad Dawood2, Muneer Ahmed Qazi3 and Nighat Fatima2,*
...o the NMD-1 by molecular docking. A computational ligand-target docking approach was used to analyze structural complexes of enzyme target with diaportheins. Auto Grid model showed the most energetically favorable binding mode of natural compounds to beta-lactamase. Docked energies for diaporthein A and B were -8.02 and -8.41 kcal/mol, respectively. These outcomes revealed that these ligands could be potential drugs to treat...
Rahila Huma1,2, Tariq Mahmud1,*, Rubina Munir2, Sana Javaid Awan3,Kiran Iftikhar4 and Mufakkira-Tul-Islam5
Bibi Nazia Murtaza1,2, Azhar Qayum3, Shamaila Inayat Nadeem1, Naif Awdh Al-Maliki4, Abdulaziz Alamri4 and Abdul Rauf Shakoori2,5,*
...o analysis and molecular docking of variants with GTP. MutationTaster was used for functional analysis of genetic variants and three-dimensional structure of mutant proteins were built by Swiss-Model and were further subjected to structural alignment and stability studies by I-Mutant Suite and DUET server. Both variants were predicted as ‘disease causing’ and protein stability analysis revealed p.G138V to be more destabilizing variant than p.E31K. ...
Muhammad Shahid Nadeem*, Maryam A. Al-Ghamdi and Jalaluddin Azam Khan
... homotetramer. Molecular docking studies have revealed that Gly199, Lys300, Arg198, Arg197, Tyr201, Tyr323 are putative active site residues interacting the substrate. Anti-proliferative effect of purified enzyme was determined quantitatively using non-cancerous human fibroblast cells (FB) and hepatocellular carcinoma cells (HepG2). A dose of 5U/ml of enzyme has shown an anti-proliferative effect up to 65 percent on HepG2 cells.
...
Gul Afshan1,2,*, Soumble Zulfiqar2, Sumaira Mehboob2, Muhammad Tahir Javed Khan1 and Abdul Rauf Shakoori2,*
... was determined. Protein docking with appropriate ligand revealed that V342 and L349 residues were involved in the ligand binding. Interaction of HCV3a infected human sera with HCV3a E2 purified protein was carried out through Enzyme Linked Immunosorbant Assay (ELISA) using HCV antihuman conjugated protein. It was confirmed that the HCV3a E2 purified protein bound with the human serum almost three times more efficiently than the positive control. For raising a...
Amreen Zahra1, Mushtaq A. Saleem1*, Hasnain Javed2, Muhammad Azmat Ullah Khan3, Muhammad Naveed1 and Abdul Rauf Shakoori4
..., was used for molecular docking to reveal the drug resistance sites among the isolates under investigation. However, strikingly the binding energies resulted were -7.9 kcal/mol for Pol and -5.7 kcal/mol in Gag that predicted that SNPs in the Pol gene could be one of the reasons for drug resistance and the primary site of mutations progressing the onset of infection. These computational strategies will thus help in performing large scale studies and also in th...
Doaa Sh. Mohamed1, Nema S. Shaban2 , Mai M. Labib3, Olfat Shehata4
... elucidated by molecular docking studies. Treatment with almond oil attenuated lipid peroxidation, improved superoxide dismutase (SOD) activities that are associated with doxorubicin administration. Also almond oil considerably modulated the gene expression of toll like receptor 4 (TLR4) and lowers the serum levels of both nuclear factor κB (NF-κB) and tumor necrosis factor α (TNF-α). The elevated levels of Creatine Kinase - MB (CK-MB),...
Yaruq Jabeen1, Nida Ansari1, Haroon Rasheed1, Muhammad Asif Rasheed1,*, Muhammad Awais2, Muhammad Ibrahim1, Sumaira Kanwal1, Aqsa Khalid3, Manzoor Ahmad Zahid4 and Farrukh Jamil1,*
... past few years, several docking tools have been developed for molecular dockings such as LeDock, rDock, AutoDock Vina, AutoDock, UCSF DOCK, GOLD, Glide, Surflex-Dock, LigandFit and MOE-Dock. Among these, AutoDock Vina has been widely used by academia for molecular docking. This tool performs docking of a ligand into a protein by seven steps. For
Muhammad Idrees1, Bashir Ahmad2, Muhammad Waqas1, Syed Muhammad Mukarram Shah3 and Saad Ahmad Khan4
...Finally, on the basis of docking score and binding interactions, ten small molecules were selected for each protein as novel inhibitors. These selected novel inhibitors have significant interaction with the active site of the protein and a strong possibility to act as an additional starting opinion in the development of new and potential inhibitors. The result indicates that novel inhibitors could be a promising lead compound and be effective in treating sensi...
Muneeza Zafar1,2,3, Fazli Rabbi Awan2,*, Munazza Raza Mirza3,*, Sumaira Nishat2,4, Sajid Ali Rajput5 and Imran Riaz Malik1,*
... of APOB through protein docking. The results indicate the applicability of in silico approach to propose the most deleterious SNPs of APOB that should be prioritize for future genetic association studies in cohort of cardiovascular patients. While their structural impact on APOB may suggest these predicted nsSNPs possibly be a better drug target and contribute to the treatment and better understanding of human cardiovascular disease....
Sohail Nadeem1, Muhammad Aziz2*, Ayesha Mohy ud Din1 and Tayyaba Jamil1
...21G and 6-31G. Molecular docking is calculated using online server with Lanosterol 14α-demethylase to know antifungal properties. The theoretically computed results of heterocyclic organic molecule gives us information regarding the structural arrangement of atoms. On the basis of outcome of computational based result, it is concluded that the title molecule is a suitable future antifungal candidate....
Saba Rehman1, Faisal Salih Hayat1, Sadia Norin2, Abdul Aziz1, Siddiq Ur Rahman1* and Noor ul Haq1*
...ural inhibitors based on docking score. To design a vaccine the B-cell epitope i.e., CLIGAEYVNNSYECD was found to the highest antigenicity score. The present study identifies natural inhibitors and potential antigenic Epitopes which may be used as effective drug and vaccine candidates to suppress the novel coronavirus.
...
Muhammad Shahid Nadeem*, Jalaluddin Azam Khan and Firoz Anwar
...mer structure. Molecular docking studies with potential molecules involved in the reaction catalysed have been conducted and binding energy values were calculated for each molecule including L-alanine, pyridoxal 5 phosphate, pyruvate, alpha ketoglutarate and L-glutamate. Present study provides the first report of ALT from Pyrococcus abyssi and suggests active site residues of enzyme from archaeal origin. ...
AISHA, MUHAMMAD ASAM RAZA* AND UMME FARWA
.... Theoretical study i.e. docking of the prepared compounds was also related to experimental work. In-Silico ADMET study of both compounds exhibited various therapeutic properties, which depicted that they are quite similar to the drug-like candidates.
...
Burarah Arooj1, Zeeshan Mutahir1, Moazzam Ali1, Mohsina Akhter2, Malik Siddique Mahmood1, Arslan Hamid3 and Mahjabeen Saleem1*
...itin. The protein-ligand docking analysis and molecular dynamic simulation indicated that the interactions of amino acids Asn 204, Glu 277, Leu 278, Asp 312, Glu 314, Gln 372, Tyr 374, Trp 463, Trp 467 from GH18 catalytic domain with (NAG)2 molecule are involved in the enzyme catalytic mechanism. This is the first time a thermostable chitinase from Paenibacillus sp. Y412MC10 has been cloned, expressed heterologously, and purified....
Zhipeng Song1,2, Jialiang Xin1,3, Xiaoli Wei1,2, Abula Zulipiya1,3, Kadier Kedireya1,2 and Xinmin Mao1,3*
...helial marker. Molecular docking results showed that marein could integrate with VEGFA, PI3K and SYK, and the resulting conjugate was more potent than the positive drug metformin. Among the above factors, the combination effect of SYK and marein was the most ideal. To conclude marein can improve glucose and lipid metabolism disorders in db/db mice after a treatment period, so it has positive significance for the prevention and treatment of diabetes. Marein can...
Raed Hussein Salih Rabee1, Yahya Sabah Abdulameer1, Walla Farhan Obed1, Noor R Abady1, Adnan Mansour Jasim1*, Firas Hussein Albawi1, Mohammed Jasim Jawad2, Ahmed Samir Abukhomra3
...the thigh and liver. The docking study confirmed inhibitory activity of Cytochrome P450 3A4 (CYP3A4) and P-glycoprotein (P-gp) an enzyme responsible for the metabolism of antibiotics. Additionally, berberine demonstrated antibacterial effects against E. coli, as well as anti-inflammatory and antioxidant properties. Furthermore, histopathological examination of the intestinal broiler received BBR showed improvements and restore tissue near to normal.
Irfan Safdar Durrani*, Noreen Asim and Ammar Sohail
...structed using MEGA7 and docking of regulatory elements with the corresponding Transcription factors was performed using pyDockDNA. The OsGLP12-3 promoter region (1863bp) was PCR amplified using genomic DNA from Indica rice cultivar Dilrosh-97 and subsequently purified and sequenced. Sequence analysis using Plant Care online database revealed 32 different regulatory elements in Nipponbare while 31 different regulatory elements were found in Dilrosh-97. The cis...
Hafsa Saeed, Soumble Zulfiqar, Abeedha Tu-Allah Khan and Abdul Rauf Shakoori*
...on and protein-metal ion docking studies of the K. pneumoniae ZntR protein are being reported for the first time....
Khansa Jamil1, Muhammad Ramzan Khan1, Asad Jan2 and Ghulam Muhammad Ali1*
...e subjected to molecular docking from which all targeted compounds received scores ranging from (−3.5 to −5.9) kcal/mol with targeted protein. Hence the study revealed that bioactive compounds derived from the Caralluma tuberculata plant pose highly antibacterial activity and might be used to synthesize the antibacterial drug....
Taidong Wang1, Xiaowei Huang1, Jian Huang2, Guangfu Lv3 and Zhe Lin1*
... database, and molecular docking verification was performed on the core targets after topology analysis. Subsequently, 24 rats were randomly divided into control group, model group, wild high-dose group and wild low-dose group, 6 rats in each group. Results of in vivo experiments showed that high-dose group (P<0.01) and low-dose group (P<0.01) significantly decreased body temperature in rats; high-dose group significantly decreased TNF-α, IL-1&beta...
Roy Sukbir Singh1, Jekson Martiar Siahaan2,3*, Endy Juli Anto4, Syafruddin Ilyas5, Putri Eyanoer6, Hendrika Andriani7,8
...lysis involved molecular docking simulations to evaluate the interactions of Aloe vera compounds with inflammatory mediators such as TNF-α and COX-2. Furthermore, this study also employed a laboratory design with a post-test randomized controlled group. The study included 30 male white rats divided into six groups. Prior to the study, the rats were induced with a high-fat diet (HFD) for 14 days. The groups consisted of a normal group receiving distilled ...
Abrar ul Haq1, Shusheng Yin2, Amara Maryam1, Muhammad Khan1*, Hafiz Abdullah Shakir1, Muhammad Akhtar Ali3, Muhammad Irfan4, Muhammad Faisal Maqbool1 and Yongming Li2*
...fashion. Using Molecular docking study, we found that lathyrol exhibits strong binding interactions with STAT3 DNA binding domain through hydrogen bonding and hydrophobic interactions with various amino acid residues of STAT3. Using immunoblotting, we found that lathyrol did not inhibit STAT3 phosphorylation and dimerization. Moreover, we showed that lathyrol induces apoptosis as evident from a remarkably increased expression of cleaved caspase-3 in all four c...
Afshan Kaleem*, Iqra Noor, Roheena Abdullah and Mehwish Iqtedar
...rutin, which showed good docking results with lowest docking energy of –13.461 Kcal/mol against the caspase-3 protein. This protein is an apoptotic marker in colon cancer that prevents colon cancer cells from multiplying by triggering apoptosis, achieved by cell cycle arrest and activation of the caspase protein. While in the case of Vigna unguiculata, Beta-amyloid (APLP1 and APP) proteins were docked with various bioa...
Hend A. Hamedo, Ahmed E.M. Shokr, Omnia T. Abd-Elsalam and Naglaa Elshafey*
...noic acid. The molecular docking study displayed high potential of the extracted PHA ingredients as drugs used against liver hepatocellular carcinoma (HCC); with binding affinity ranging between -4.0 to -6.5 kcal/ mol. This is in addition to the prediction of a synergistic effect of PHAs ingredients and sorafenib drug against HCC, showing a promising binding affinity ranging from 20.2 to 23.2 kcal/ mol. Our findings indicate that Paracoccus onubensis strain E3...
Aml Ghanem1,2; Ahmed A. Al-Karmalawy3,4; Noha E. Morsy5; Mahmoud Elsabahy6; Ahmed M. Rayan2,7*
Novel Research in Microbiology Journal (2024), 8(6): 2750-2771
Hayam Albalawi1,2, Muhammad Shahid Nadeem1*, Hisham N. Altayeb1,
Saima Iftikhar3, Mariam A. Al-Ghamdi1,4,5, Jalaluddin Azam Khan1 and Ahmed Osman1
...of the enzyme. Molecular docking studies have shown that the enzyme investigated in the present study and human α-glucosidase have similar active site composition. Affinity studies with ten well established inhibitors have shown similar free energy change (ΔG) values for human and microbial enzymes indicating the evolutionary conserved structural and functional domains in the enzyme from phylogenetically different species. ...
Nusrat Jahan Lily1*, Kazi Abdus Sobur2, Minhaz Zabin Saif Mim3, Anika Thasin Bithi4, Hamja Hasanat5, Tabassum Mounita5, Foysal Ahammad6,7, Abdus Samad7,8 and Palash Bose2
...alyzed through molecular docking and extensive 200-nanosecond molecular dynamics simulations to evaluate binding affinity, stability, and interaction with the ZIKV protease structure (PDB ID: 5LC0). Among the tested ligands, PubChem CID: 56649692 showed the most favorable binding affinity at -5.321 kcal/mol, surpassing other compounds, including the control ligand. Molecular dynamics simulation confirmed that CID: 56649692 maintained stability within the accep...
