Browsing by Subject "Molecular docking"
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Item Computational drug discovery against Hepatitis B Virus Core Protein(Department of Biotechnology, 2023) Itani, Ramesh RajHepatitis B virus infection has been a major global health concern today.The present available drugs are not able to cure the hepatitis B completely.So the scientific community in world are in search of new drugs that can fulfill the void of existing non performing drugs. The problem of the low efficacy of present drugs and development of new resistant mutant virus needs to be solved immediately for the advancement in the cure of hepatitis B infected patients. Traditional drug discovery process is time and money consuming process so computer aided drug designing can be a good alternative for drug discovery process. In this study ligand library from different databases like asinex, zinc15, selleckchem are used.Ligands from these databases are screened for ADMET properties in order to ensure the drugability characters. The selected ligands are subjected to molecular docking purpose with the target protein i.e. hepatitis B core protein under the PDB name 5T2P .The ligands that have higher binding affinity with target protein was selected for further screening .hMAT1A screening was done with selected ligands to ensure that selected lead molecules donot harm liver.The lead compounds was selected after hMAT1A screening and subjected to density function theory to study its chemical properties computationally. Benzofuranonesshows the higher binding affinity with target protein and selected as lead molecules after hMAT1A screening. Keywords: ADMET, CADD, Molecular Docking, Lead compound, FDA, hMAT1AItem Structural and Spectroscopic Studies on Cefalexin ond Methyldopa Using Quantum Mechanical Methods(Institute of Science & Technology, 2024-01) Chaudhary, TarunThe spectroscopic characteristics, conformational stability, electronic and biological activity of cefalexin and methyldopa have been investigated using quantum mechanical techniques. The density functional theory (DFT) at the B3LYP/ 6-311++G(d,p) level was utilized to optimize the molecules and explore their vibrational properties. The intramolecular and intermolecular hydrogen bonding in cephalexin has been discussed in terms of IR and Raman spectra. Additionally, the quantum theory of atoms in molecules (QTAIM) was used to predict the nature of hydrogen bonds. Similarly, determining vibrational properties, the presence of hydrogen bond interactions in methyldopa has been scrutinized more precisely, using QTAIM and the reduced density gradient (RDG) in monomer and dimer form. On the basis of electron localization function (ELF), the electron localized region and the delocalized region have been depicted. The Molecular electrostatic potential (MEP) has been used to describe the charge distribution around the molecules. From the MEP map, the electrophilic and nucleophilic sites were anticipated. The energy of the lowest unoccupied molecular orbital (ELUMO), the highest occupied molecular orbital energy, (EHOMO), and their energy gap (∆E) have been used to examine the chemical stability of the molecules. Furthermore, the nature of chemical reactivity, the energy gap, global, and local reactivity characteristics were established. Natural bond orbital (NBO) analysis was carried out to determine the stabilization energy due to charge delocalization between the bonding and antibonding. The relation of standard thermodynamic parameters like heat capacity, enthalpy and entropy with temperature has been studied. Ultimately, a molecular docking simulation has been performed to study the biological activities of the molecules. The binding activity of cefalexin with the protein matrix carbonic anhydrase II and leukotriene A-4 hydro lase was predicted from molecular docking approach. Similarly, the binding activity of ligand methyldopa with protein Lysine-specific demethylase 4D-like was performed. सेफेलेक्सिन र मेथाइलडोपाका स्पेक्ट्रोस्कोपिक स्वरुपहरु, संरचनात्मक स्थिरता, इलेक्ट्रोनिक र जैविक गतिविधि, क्वान्टम मेकानिकल विधि प्रयोग गरेर अनुसन्धान गरिएको छ। अणुहरूलाई अप्टिमाइज गर्न र तिनीहरूको भाइब्रेशनल गुणहरु अन्वेषण गर्न B3LYP/6-311++G(d,p)/Density Functional Theory (DFT) प्रयोग गरिएको थियो। सेफेलेक्सिनको IR र Raman स्पेक्ट्राका आधारमा इन्ट्रामोलिक्युलर र इन्टरमोलिक्युलर हाइड्रोजन बन्डको व्याख्या गरिएकोछ। । साथै, क्वान्टम थ्योरि अफ एटम्स इन मोलिकुल्स (QTAIM) विधि प्रयोग गरि हाइड्रोजन बन्डको प्रकृतिको बारे प्रस्तुत गरिएकोछ। त्यसै गरी, मेथाइलडोपाको मोनोमर र डाइमर संरचनाका भाइब्रेशनल गुणहरु निर्धारण गरि, हाइड्रोजन बन्डलाई QTAIM र रिडिउस्ड डेनसिटी ग्राफ (RDG) को प्रयोग गरेर थप सटीक रूपमा अध्ययन गरिएको थियो। इलेक्ट्रोन लोकलाइजेसन फंक्सन (ELF) को आधारमा, इलेक्ट्रोन लोकलाइज्ड क्षेत्र र डीलोकलाइज्ड क्षेत्रलाई चित्रण गरिएको छ। मोलिकुलर इलेक्ट्रोस्टेटिक पोटेन्सिअल (MEP) मार्फत अणुहरू वरपर रहेको चार्ज वितरणको अवस्थालाई ब्याख्या गरिएको छ । MEP को सहयोगले, इलेक्ट्रोफिलिक र न्यूक्लियोफिलिक साइटहरू पत्ता लगाइएको छ। लोयस्ट अनअकुपाइड मोलिकुलर अर्बिटल इनर्जी (ELUMO), हाइयस्ट अकुपाइड मोलिकुलर अर्बिटल इनर्जी (EHOMO) र तिनीहरूको इनर्जी ग्याप प्रयोग गरि अणुहरूको रासायनिक स्थिरता जाँच गरिएको छ। यसबाहेक, रासायनिक प्रतिक्रियाशीलताको प्रकृति, इनर्जी ग्याप (ΔE), ग्लोबल र लोकल रियाक्तिभिटीका विशेषताहरू स्थापित गरियो। बन्डिङ र एन्टिबन्डिङ बीचको चार्ज डीलोकलाइजेशनको कारणले हुने इस्ट्याविलाइजेसन इनर्जी को निर्धारण गर्न नेचुरल बन्ड अर्बिटल (NBO) को विश्लेषण गरिएको थियो। ताप क्षमता, एन्थाल्पी र एन्ट्रोपी जस्ता मानक थर्मोडायनामिक प्यारामिटरहरूको तापक्रमसँगको सम्बन्धको अध्ययन गरिएको छ । अन्ततः अणुहरूको जैविक गतिविधिहरु अध्ययन गर्न मोलिकुलर डकिङ्ग सिमुलेशनको प्रयोग गरिएको थियो। सेफेलेक्सिनको प्रोटिन म्याट्रिक्स कार्बोनिक एनहाइड्रेस-II र ल्युकोट्रिन A-4 हाइड्रोलेजसँगको बाइन्डिंग गतिविधि, मोलिकुलर डकिङ्ग विधि बाट अनुसन्धान गरिएको थियो। त्यस्तै, मेथाइलडोपाको जैविक गतिविधिहरु प्रोटीन लाइसिन-स्पेशिफिक डेमेथाइलेज 4D- लाइकसँग प्रस्तुत गरिएको छ ।