Online Journal of Microbiological Research

Recently, we have studied drug-receptor interaction of the peptidic HIV-1 protease inhibitors based on polar and hydrophobic interactions. We have also studied pharmacokinetics of these inhibitors based on Lipinski’s rule of five and its extended form. After that there was a need to study intermolecular interactions. From literatures, drug-receptor interaction involves hydrogen bonds between acceptor and donor sites of drug... Recently, we have studied drug-receptor interaction of the peptidic HIV-1 protease inhibitors based on polar and hydrophobic interactions. We have also studied pharmacokinetics of these inhibitors based on Lipinski’s rule of five and its extended form. After that there was a need to study intermolecular interactions. From literatures, drug-receptor interaction involves hydrogen bonds between acceptor and donor sites of drug and its receptor. These donor acceptor sites must be more than four to be dominant. As single intermolecular H-bond is relatively weak and unlikely to support this type of interaction. It is also clear from literature that this interaction contribute to the alignment of reacting species in proper three-dimensional space in such a position that strong and effective polar or hydrophobic or both interaction occurs to form drug-receptor adduct or enzyme inhibitor complex as appropriate. The strength of H-bonds formed between drug and receptor was judged by bond lengths, bond angles and bond orders. As well as, its nature (strong, moderate or weak) and its number, too. Along with H-bonding, we have also studied Van der Walls i.e. non-bonding type interaction. These non-bonding interactions were studied using charge transfer from donor to acceptor and this results transfer of electron flux from donor molecule (drug/receptor) towards acceptor (receptor/ drug). Thus, lowering of energy of the system under investigation will occur. For this resulted interaction energy was also studied that very clearly explain feasibility of interactions. As we know that all above phenomena are molecular properties and do not cover involvement of orbitals. To cover this we have also studied drug-receptor interaction involving molecular orbital. It was HOMO of one reacting molecule (B) that donates electron pair, electron cloud or electron density to LUMO of another reacting molecule (A) that accepts or accommodates this electron pair, electron cloud or electron density. The quantity of the electron flux from HOMO to LUMO was judged by the value of ∆E_LH. A lower value of this will support strong and effective drug-receptor interaction. Results of orbital based study have also been found to supports the results as abstracted from interaction energy. Read more

Klopman described the chemical reaction of metal ions and base ions in term of softness, E‡n and E‡m, respectively. By simple modification of known methods, Singh et al. made it applicable for neutral Lewis acids (transition metal salts) and bases (organic molecules) and also extended its application to biological systems for site selectivity and to explain reaction mechanism (markovnikov and... Klopman described the chemical reaction of metal ions and base ions in term of softness, E^‡_n and E^‡_m, respectively. By simple modification of known methods, Singh et al. made it applicable for neutral Lewis acids (transition metal salts) and bases (organic molecules) and also extended its application to biological systems for site selectivity and to explain reaction mechanism (markovnikov and anti-markovnikov rule), ligand-receptor interaction of testosterones, estrogens and tetrahydroimidazobenzodiazepinone. In this study effective atomic softness E^‡_n(eff) and E^‡_m(eff), and their change ΔE^‡_nm have been used for site selectivity and polar interaction between 51 peptidic HIV-1 protease inhibitors and receptor amino acids. ΔE^‡_nm values derived from drug-receptor interaction show that when one moiety on receptor behaves as nucleophile (O of valine amino acid) at the same time maximum electrophilic site of the drug (C-atom of the maximum E^‡_n(eff) value) orient itself to come close the respective site and make maximum interaction, while when another moiety on receptor behaves as electrophilic site (C of isoleucine amino acid), at the same time maximum nucleophilic site of the drug (O-atom of the maximum E^‡_m(eff) value) also orient itself to come close the respective site and make maximum interaction. Read more

When a drug interacts with its receptor, the nonpolar substituent of drug and receptor proteins attract each other because they have opposite magnitude with respect to each other. X-rays structure studies reflected that the S2/S2’ pocket in HIV-1 protease enzyme are essentially hydrophobic. The residues that make up these pockets are Val-32, Ile-47, Ile-50, and Ile-84 in each monomeric polypeptidic... When a drug interacts with its receptor, the nonpolar substituent of drug and receptor proteins attract each other because they have opposite magnitude with respect to each other. X-rays structure studies reflected that the S2/S2’ pocket in HIV-1 protease enzyme are essentially hydrophobic. The residues that make up these pockets are Val-32, Ile-47, Ile-50, and Ile-84 in each monomeric polypeptidic unit of the protease enzyme. Δπ_dr and ΔSASA_dr have been used to measure the extent of hydrophobic interaction between peptidic protease inhibitors and receptor proteins (binding site: valine‒isoleucine; and catalytic site: glycine‒aspartic acid‒threonine) on the HIV-1 protease enzyme. For measurement of hydrophobic interaction, the molecular modeling and geometry optimization of all the inhibitors and the receptor amino acids have been carried out with CAChe Pro software by opting semiempirical PM3 methods. Log P was calculated using the atom-typing scheme of Ghose and Crippen, while solvent accessible surface area by conductor likes screening model. π_d, π_r, SASA_Sd and SASA_Sr well describe the hydrophobicities of the substituents and play the effective role for site selectivity for interaction of the drug with the receptor. Comparative study of values of Δπ_dr and ΔSASA_dr show the order of hydrophobic interaction with respect to amino acids: Asp > Thr > Val > Ile and Thr > Val > Asp > Ile, respectively. Further, comparative study of the values of (ΣΔπ_dr)_binding-site, (ΣΔπ_dr)_{catalytic-site}, (ΣΔSASA_dr)_binding-site, (ΣΔSASA_dr)_{catalytic-site} shows that peptidic HIV-1-PRIs interact with binding site rather than catalytic site as binding site have lower value of ΣΔπ_dr and ΣΔSASA_dr. Among the binding site, Val has maximum interaction than Ile, as it has lower vale of Δπ_dr and ΔSASA_dr. Read more

Chemical solvents are commonly used to prevent microbial growth; dangerous to human health and have limited antibacterial properties. On the other hand, Nanoparticles made of metallic elements (such as copper, silver, and gold) have several uses in the field of biotechnology. Silver nanoparticles are more efficient in their antimicrobial, antibacterial, anti-inflammatory and anti-cancer properties. The current study aimed to determine... Chemical solvents are commonly used to prevent microbial growth; dangerous to human health and have limited antibacterial properties. On the other hand, Nanoparticles made of metallic elements (such as copper, silver, and gold) have several uses in the field of biotechnology. Silver nanoparticles are more efficient in their antimicrobial, antibacterial, anti-inflammatory and anti-cancer properties. The current study aimed to determine the green synthesis of silver nanoparticles and their antibacterial activity from the aqueous extracts of leaves of Couroupita guianensis, Punica granatum, Vitex negundo, Cirtrus maxima. AgNPs of plant extracts were prepared using silver nitrate with the respective plant extract. Then they were characterized by FTIR analysis. The respective functional groups in the synthesized silver nanoparticles were confirmed with FTIR Spectra. The antibacterial activities of the synthesized nanoparticle extract were observed by zone of inhibition. From the results, the nanoparticles synthesized from the plants extract could pave a way to formulate a drug to treat microbial infection. Read more

Carboxylates and their antimony(III) complexes experimentally scanned earlier for anti-leishmanial activity (IC50) against five leishmanial strains viz., L. major, L. major (Pak), L. tropica, L. mex mex, and L. donovani. These activities have been theoretically predicted by DFT method along with quantitative structure-activity relationship (QSAR) study. Molecular modeling and geometry optimization of the all the eight compounds have been performed... Carboxylates and their antimony(III) complexes experimentally scanned earlier for anti-leishmanial activity (IC₅₀) against five leishmanial strains viz., L. major, L. major (Pak), L. tropica, L. mex mex, and L. donovani. These activities have been theoretically predicted by DFT method along with quantitative structure-activity relationship (QSAR) study. Molecular modeling and geometry optimization of the all the eight compounds have been performed on workspace program of CAChe Pro software of Fujitsu by opting B88-PW91 (Becke '88; Perdew & Wang '91) GGA (generalized-gradient approximation) energy functional with DZVP (double-zeta valence polarized ) basis set in DFT (Density Functional Theory). For QSAR, multiple linear regression (MLR) analysis has been performed on Project Leader Program associated with CAChe. The reliability of correlation between experimental activities and predicted activities are r² = 0.826, r²_CV = 0.426 (L. major); r² = 0.905, r²_CV = 0.507 (L. major (Pak)); r² = 0.980, r²_CV = 0.932 (L. tropica); r² = 0.781, r²_CV = 0.580 (L. mex mex) and r² = 0.634, r²_CV = 0.376 (L. donovani), and a comparison of the experimental values and the values obtained by theoretical calculations has been presented pictorially that shows close resemblance. Read more

The purpose of the study was to investigate the effect of computer-assisted instruction approach to the teaching and learning of photosynthesis on the performance of second year Senior High School (SHS 2) Biology students in science. The design for the study was a quasi-experimental research. This study was carried out in Sefwi Wiawso SHS and Asawinso SHS all at Sefwi... The purpose of the study was to investigate the effect of computer-assisted instruction approach to the teaching and learning of photosynthesis on the performance of second year Senior High School (SHS 2) Biology students in science. The design for the study was a quasi-experimental research. This study was carried out in Sefwi Wiawso SHS and Asawinso SHS all at Sefwi Wiawso Municipal Assembly in the Western North Region of Ghana. They are all mixed institution. The purposive sampling techniques was used to schools, classes and students for the study. One-hundred one (101) electives biology participants were purposively selected, they consist of SHS 2 Science of (55) fifty-five students from Sefwi Wiawso SHS and SHS 2 Home economics of (46) forty-six students also from Asawinso SHS. The third years were not selected because they were preparing to write their WASSCE. The main instrument for data collection was questionnaire. The study collected only quantitative data and employed quantitative method of data analysis. Data obtained from participants in both experimental and control groups on the Test 2 were analysed statistically using independent-measures t-test. The independent-measures t-Test was used to investigate whether any differences existed between experimental and control groups’ mean scores on the Test 2. The study further revealed that computer-assisted instructions gives feedback to learners to have the opportunity to master computer-assisted instructional package tool used. It is recommended that, computer-assisted instruction method should be encouraged in many Biology classes in Wiawso Municipal Assembly, since it gives students opportunity to see links between concepts, summarise and organise their works, thoughts logically and sequentially. Both genders must be encouraged to use computer-assisted instruction method to studying Biology. Read more