Ritu Raj | Vbu - Academia.edu (original) (raw)

Papers by Ritu Raj

Spectroscopic and computational studies on the CT complex of 1,10-phenanthroline and picric acid ... more Spectroscopic and computational studies on the CT complex of 1,10-phenanthroline and picric acid have been studied with a view to know the type and nature of interaction between them. The FTIR data revealed that the complex in the solid state is a mixture of two complexes viz. components in ionic states and non-ionic states. Quantum mechanical calculations have been carried out to investigate the nature and type of interactions between them using high level DFT-theory. The binding energy of complex involving ionic states of the components is approximately 21 times higher than that of the complex formed by components in unionized states.

In an attempt to search a new class of antibacterial drugs, for treatment of tuberculosis molecul... more In an attempt to search a new class of antibacterial drugs, for treatment
of tuberculosis molecular docking studies with proteins 1EYN was
carried out using some chromene derivatives. Some of the chromene
derivatives were found to have binding energy and docking pattern
very close to the originally docked molecule in 1EYN while some
other show higher docking scores compared to the originally docked
ligand in 1EYN protein. The quick prop results reveal that these
molecules are non-toxic. The results reveal that chromenes may exhibit
significant antibiotic activities against tuberculosis and indicate that
this class of natural product should be considered further in the
development of new and more potent antibiotics of Tuberculosis

The Human immunodeficiency virus type-1 protease is one of the most important target to highly ac... more The Human immunodeficiency virus type-1 protease is one of the most important target to highly active anti retrovirus therapy(HAART) for the treatment of all acquired immune deficiency syndrome(AIDS). Protease inhibitor “Darunavir” is most recently included as a PI in the list of HARRT(highly active anti retrovirus therapy), more effective against mutant and wild type simultaneously of Protease with increased no. of H bonding then precursors approved by FDA, So herein we have taken Darunavir as a base structure for virtually identification of more/similar efficient drug like leads then Darunavir using ten different PDB structures (3EM6, 3OXW, 3BVB, 3CYW, 3D1Y, 4DQB, 4DQH, 4DQE, 4DQF, 4DQC & 3EKT) of Protease from PDB database „RCSB‟ versus chemical compounds database „ZINC‟ using Schrodinger and Discovery Studio software. Using molecular constraint search with similarity coefficient „Tanimoto‟, 1,65,000 ligands were extracted and docking analysis were resulted some efficient in docking and in other computational medicinal parameters, we are reporting such lead molecules, and they may further undergo through high end extensive virtual investigation and beyond..

The Human immunodeficiency virus(HIV)type-1 integrase is one of the most important target of high... more The Human immunodeficiency virus(HIV)type-1 integrase is one of the most important target of highly active anti retrovirus therapy (HAART), due toits role to incorporate genetic information into the host DNA, so its prevention to its proper function results in very fine therapeutic effect for the treatment of all acquired immune deficiency syndrome(AIDS), extensive research work on integrase inhibitors(INIs) haven't carried out till present due to complexities in research with integrase and a very few drug are known to inhibit integrase. Dolutegravir is a new 2 nd generation Integrase inhibitor (INIs) in a short list of INIs, recently approved by FDA in the list of HAART, so herein we taken Dolutegravir as a reference structure for virtually identification of more/similar efficient drug like leads then Dolutegravir using three different PDB structures (4S3O, 3S3M & 3S3N) of Integrase having in different mutated state from PDB database 'RCSB' versus chemical compounds database 'ZINC' using Schrodinger and Discovery Studio software. Using molecular constraint search with similarity coefficient 'Tanimoto', 1,65,000 ligands were extracted out and further docking analysis resulted in some better efficient in docking properties and computed medicinal parameters have been reported, and, they may further undergo through high end extensive virtual investigation and beyond, in such research laboratory where adequate research facilities are available.

In order to ascertain the global and local reactivity of Picric acid theoretical calculations of ... more In order to ascertain the global and local reactivity of Picric acid theoretical calculations of the global and local parameters have been carried out. The global properties such as chemical potential, hardness, softness, and fukui functions have been calculated. In order to determine the charge build up and reactivity at various locations of the molecule Mulliken charges, Stockholder charges, electrostate potential (ESP) ,average local Ionization potential (ALIES) have been calculated.

In quest of cheap anti HIV drugs, molecular docking studies with HIV-1RT (PDB ID 1FK9) were carri... more In quest of cheap anti HIV drugs, molecular docking studies with HIV-1RT (PDB ID 1FK9) were carried out using certain succinic acid derivatives. One of the derivatives-2-(diphenylmethylene)succinic acid was found to have binding energy and docking pattern comparable to the originally docked efavirenz molecule. This molecule has been predicted theoretically to be non-toxic. Five drug molecules similar in druggability to this molecule , but used in other diseases , were identified and their molecular docking results on 1FK9 have also been reported .

Quantum mechanical calculations of different energies components of 1,3,5-trinitrobenzene (TNB) i... more Quantum mechanical calculations of different energies components of 1,3,5-trinitrobenzene (TNB) in ground state were carried out by DFT method , in isolated state and in various solvents to study the effects of solvents on various energy components. The solvation energy, chemical potential, hardness, electrophilicity of picric acid were calculated with the help of computed HOMO-LUMO gap of picric acid in different solvents in ground state .The plots of energy components and thermodynamic parameters against the dielectric constant of the corresponding solvents were found to be polynomial of higher order. The 3D plot of HOMO-LUMO of TNB and dielectric constants of various solvents in ground state reveals that LUMO of TNB is more affected than that of HOMO by change in the dielectric constant of the solvent Keyword: DFT, Ground state, TNB, energy components, HOMO, LUMO, solvation energy, dielectric constants. _____________________________________________________________________________________________

The computational study on the interactions of picric acid with some indolyl Schiff's bases havin... more The computational study on the interactions of picric acid with some indolyl Schiff's bases having four different interaction sites have been carried out by DFT method both in neutral and ionic states, The geometry of the resulting charge transfer complex, the actual site of interaction, nature of interactions and counterpoise corrected binding energies, etc. have been determined. The interaction in the ionic state was found to be much stronger than the corresponding molecules in the neutral states.

The interaction between picric acid (acceptor) and o-phenanthroline (donor) have been studied spe... more The interaction between picric acid (acceptor) and o-phenanthroline (donor) have been studied spectrophotometrically in THF solvent for the evaluation of reliable value of association constant in the formation of weakly bounded charge transfer complex. The value of association constant (K) was calculated using standard equations such as Benesi-Hildebrand, Scott, Foster Hammick Waldley, Rose Drago Ayad, El-Hati, Lang, Scatchard, Seal-Sil Mukherjee, at wavelengths358.5 378, 400 and 420 nm in THF solvent. The value of association constant of the 1:1 complex insolution, calculated by different standard equations ranges between 1561 and 4928. The wide range of variation of the calculated values of K led us to guest for the reliable value. The reliability of different calculated values was examined. The Benesi-and Hildebrand method was found to give most reliable value of K. The most reliable value of K for complex was found to be 1907. The stoichiometry of the complex was established spectrophotometrically by Jobs's method of constant variation. ABSTRACT

Quantum mechanical calculations of different energies components of Picric acid in ground and exc... more Quantum mechanical calculations of different energies components of Picric acid in ground and excited state were carried out by HatreeFock method , in isolated state and in various solvents to study the effects of solvents on various energy components. The solvation energy, chemical potential, hardness, electrophilicity of picric acid were calculated with the help of computed HOMO-LUMO gap of picric acid in different solvents in both ground and excited state. The plots of energy components and thermodynamic parameters against the dielectric constant of the corresponding solvents were found to be polynomial of higher order. The 3D plot of HOMO-LUMO of Picric acid and dielectric constants of various solvents in ground state and excited state reveals that LUMO of picric acid is more affected than that of HOMO by change in the dielectric constant of the solvent

DDQ is widely used as a -acceptor for the preparation of organic charge transfer. In this paper ... more DDQ is widely used as a -acceptor for the preparation of organic charge transfer. In this paper the effect of ten solvents on the ground state of DDQ has been reported. DFT calculations have been done on the Schrodinger software and the effect of solvents have been theoretically calculated with the help of Poisson-Boltzmann solver. The solvation energy, chemical potential, hardness, electrophilicity, HOMO-LUMO gap and the picture of the HOMO and LUMO of DDQ in the ground state in the solvents have been reported.

Druggability and toxicity of picric acid have been computed with the help of ADMET and quick prop... more Druggability and toxicity of picric acid have been computed with the help of ADMET and quick prop programs of Discovery Studio and Shrodinger software.Biological activity like anti-Fungal, antimicrobial and toxicity nature of picric acid, it was thought to predict the theoretical activity computationally using TOPKAT model and quick prop.NTP Carcinogenicity Call (Male Rat) ,NTP Carcinogenicity Call (Female Rat) NTP Carcinogenicity Call (Male Mouse), NTP Carcinogenicity Call (Female Mouse), FDA Carcinogenicity Male Rat Non vsCarc, FDA Carcinogenicity Male Rat Single vsMult, FDA Carcinogenicity Female Rat Non vsCarc for the picric acid were computed by comparing with the fragmenting of similar compounds. The

The Human immunodeficiency virus type-1 protease is one of the most important target of highly ac... more The Human immunodeficiency virus type-1 protease is one of the most important target of highly active anti retrovirus therapy (HAART) for the treatment of all acquired immune deficiency syndrome (AIDS). Protease inhibitor Darunavir is most recent included as a PI in the list of HARRT, more effective against mutant type and wild type of Protease with increased no. of H-bonding then precursors approved by FDA, So herein we taken Darunavir as a base structure for virtually identification of more/similar efficient drug like leads then Darunavir using PDB structure (3BGR) of Protease from PDB database 'RCSB' versus chemical compounds database 'ZINC' using Schrodinger and Discovery Studio software. Using molecular constraint search with similarity coefficient 'Tanimoto', 1,65,000 ligands were extracted and docking analysis resulted in some efficient in docking and in other computational medicinal parameters, we are reporting such leads, and, they may further undergo through high end extensive virtual investigation and beyond.

Quantum mechanical calculations of different energies components of 1,10-phenanthroline in ground... more Quantum mechanical calculations of different energies components of 1,10-phenanthroline in ground state were carried out by DFT method , in isolated state and in various solvents to study the effects of solvents on various energy components . The solvation energy, chemical potential, hardness, electrophilicity of 1,10-phenanthroline were calculated with the help of computed HOMO-LUMO gap of 1,10-phenanthroline in different solvents in ground state .The plots of energy components and thermodynamic parameters against the dielectric constant of the corresponding solvents were found to be polynomial of higher order. The solvation energy of 1,10phenanthroline is found to highest in

The solvation energy, chemical potential, hardness, electrophilicity of indole were calculated wi... more The solvation energy, chemical potential, hardness, electrophilicity of indole were calculated with the help of computed HOMO-LUMO gap of indole in different solvents in ground state. The plots of energy components and thermodynamic parameters against the dielectric constant of the corresponding solvents were found to be polynomial of higher order.

In search of some cheap antibiotics, molecular docking studies with proteins 1BSK and 1S17 were c... more In search of some cheap antibiotics, molecular docking studies with proteins 1BSK and 1S17 were carried out using certain succinic acid derivatives. Some of the derivatives of succinic acid were found to have binding energy and docking pattern very close to the originally docked molecule in 1BSK and 1S17. The docking result of succinic acid derivatives with the two proteins shows the more effectiveness with some well-known antibiotic such as norfloxacine, Ciprofloxacin and ofloxacin. The quick prop results reveal that these molecules are non-toxic. Some of the succinic acid derivatives shows higher docking score compared to originally docked ligand in 1S17 protein. Keyword: Molecular docking, 1BSK, 1S17, succinic derivatives, antibiotic ,quick prop, druggability. W WO OR RL LD D J JO OU UR RN NA AL L O OF F P PH HA AR RM MA AC CY Y A AN ND D P PH HA AR RM MA AC CE EU UT TI IC CA AL L S SC CI IE EN NC CE ES S V Vo ol lu um me e 3 3, , I Is ss su ue e 5 5, , 1 13 31 14 4--1 13 33 33 3. . R Re es se ea ar rc ch h A Ar rt ti ic cl le e I Srivastava et al. World Journal of Pharmacy and Pharmaceutical Sciences domain peptide analogues'. However, there is still an urgent need for the development of new and different structure of the non-peptide PDF inhibitor. Inquest of cheap and effective antibiotics, in this paper we report the results of molecular docking studies of some succinic acid derivatives on proteins designated by PDB Id's 1BSK and 1S17. The molecular docking studies have also been carried out with commonly used antibiotics such as norfloxacin, ofloxacin, ciprofloxacin and the ligands docked with the target proteins with a view to compared the docking scores with the drug candidate molecules. The druggability of these compounds having good docking scores are also being reported. MATERIAL AND METHODS The molecular docking studies were carried out on glide 5.0 platform of Schrodinger 2012 software. The druggability was also studied with the help of quick prop program of the same software. The peptide deformylase inhibitors, 1BSK and 1S17 were downloaded from the site RCSB.org. The general description of target proteins have been described below:a) 1BSK: This target protein was isolated from the pathogenic micro-organism Escherichia coli The crystal structure of 1BSK having structural weight19832.16 was determined by Hao, B., Gong et.al[ 11 ] using X-ray diffraction at a resolution of 3.0 Å. The PDB entry contains the structure of protein (peptide deformylase). This molecule has the UniProt identifier P0A6K3 (DEF_E.COLI) . The sample contained 168 residues which is 99% of the natural sequence. Out of 168 residues 166 were observed and are deposited in the PDB. It also contains one or more heterogenic compounds (e.g., ligands, co-factors, ions, modified amino acids, etc.).The molecule is most likely monomeric. b) 1S17: This target protein was isolated from the pathogenic micro-Pseudomonas aeruginosa The structure of 1S17 having structural weight 20867.0 was published by Molteni, V.etal. This crystal structure was determined using X-ray diffraction at a resolution of 1.95 Å . This PDB entry contains multiple copies of the structure of Peptide deformylase.

The computational study on the non-covalent interactions of 1,3,5-trinitrobenzene (TNB) with some... more The computational study on the non-covalent interactions of 1,3,5-trinitrobenzene (TNB) with some indolyl Schiff's bases having four different interaction sites have been carried out by DFT, The geometry of the resulting charge transfer complex, the actual site of interaction, nature of interactions and counterpoise corrected binding energies, etc. have been determined.