Pharmacophore optimization and design of competitive inhibitors of thymidine monophosphate kinase through molecular modeling studies. 2011

Trupti S Chitre, and Muthu K Kathiravan, and Kailash G Bothara, and Shashikant V Bhandari, and Rajeshwar R Jalnapurkar
Department of Pharmaceutical Chemistry (PG), AISSMS College of Pharmacy, Near RTO, Kennedy Road, Pune 411001, Maharashtra, India. drugdesign2@gmail.com

A series of N(1) -(4-substituted-benzyl)-pyrimidines were subjected to 2D and 3D quantitative structure-activity relationship analyses. Statistically significant models were generated, and the most robust model for 2D quantitative structure-activity relationship was obtained using simulated annealing-multiple linear regression. The physicochemical descriptors, viz., slogp, estate descriptors like SaaCHE index and SdsCHE index contribute significantly to the biological activity. The pharmacophore requirements for selective inhibition of Mycobacterium tuberculosis thymidine monophosphate kinase were optimized using the information derived from 2D and 3D quantitative structure-activity relationship studies. With the results from the studies, we have designed new chemical entities using the CombiLib Tool of V-Life Molecular Design Suite. In addition, using structure-based drug design, the distances between interacting groups of ligands and amino acid residues of the protein Mycobacterium tuberculosis thymidine monophosphate kinase (PDB ID:1W2H) were thoroughly analyzed. Thus, we have successfully replaced the sugar moiety with substituted aromatic ring on N1 of thymidine. Thorough studies on substitution pattern around pyrimidine ring were carried out.

UI MeSH Term Description Entries
D008958 Models, Molecular Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures. Molecular Models,Model, Molecular,Molecular Model
D009169 Mycobacterium tuberculosis A species of gram-positive, aerobic bacteria that produces TUBERCULOSIS in humans, other primates, CATTLE; DOGS; and some other animals which have contact with humans. Growth tends to be in serpentine, cordlike masses in which the bacilli show a parallel orientation. Mycobacterium tuberculosis H37Rv
D009703 Nucleoside-Phosphate Kinase An enzyme that catalyzes reversible reactions of a nucleoside triphosphate, e.g., ATP, with a nucleoside monophosphate, e.g., UMP, to form ADP and UDP. Many nucleoside monophosphates can act as acceptor while many ribo- and deoxyribonucleoside triphosphates can act as donor. EC 2.7.4.4. Nucleoside Monophosphate Kinases,Kinase, Nucleoside-Phosphate,Kinases, Nucleoside Monophosphate,Monophosphate Kinases, Nucleoside,Nucleoside Phosphate Kinase
D011743 Pyrimidines A family of 6-membered heterocyclic compounds occurring in nature in a wide variety of forms. They include several nucleic acid constituents (CYTOSINE; THYMINE; and URACIL) and form the basic structure of the barbiturates.
D003198 Computer Simulation Computer-based representation of physical systems and phenomena such as chemical processes. Computational Modeling,Computational Modelling,Computer Models,In silico Modeling,In silico Models,In silico Simulation,Models, Computer,Computerized Models,Computer Model,Computer Simulations,Computerized Model,In silico Model,Model, Computer,Model, Computerized,Model, In silico,Modeling, Computational,Modeling, In silico,Modelling, Computational,Simulation, Computer,Simulation, In silico,Simulations, Computer
D004791 Enzyme Inhibitors Compounds or agents that combine with an enzyme in such a manner as to prevent the normal substrate-enzyme combination and the catalytic reaction. Enzyme Inhibitor,Inhibitor, Enzyme,Inhibitors, Enzyme
D001665 Binding Sites The parts of a macromolecule that directly participate in its specific combination with another molecule. Combining Site,Binding Site,Combining Sites,Site, Binding,Site, Combining,Sites, Binding,Sites, Combining
D015195 Drug Design The molecular designing of drugs for specific purposes (such as DNA-binding, enzyme inhibition, anti-cancer efficacy, etc.) based on knowledge of molecular properties such as activity of functional groups, molecular geometry, and electronic structure, and also on information cataloged on analogous molecules. Drug design is generally computer-assisted molecular modeling and does not include PHARMACOKINETICS, dosage analysis, or drug administration analysis. Computer-Aided Drug Design,Computerized Drug Design,Drug Modeling,Pharmaceutical Design,Computer Aided Drug Design,Computer-Aided Drug Designs,Computerized Drug Designs,Design, Pharmaceutical,Drug Design, Computer-Aided,Drug Design, Computerized,Drug Designs,Drug Modelings,Pharmaceutical Designs
D021281 Quantitative Structure-Activity Relationship A quantitative prediction of the biological, ecotoxicological or pharmaceutical activity of a molecule. It is based upon structure and activity information gathered from a series of similar compounds. Structure Activity Relationship, Quantitative,3D-QSAR,QSAR,QSPR Modeling,Quantitative Structure Property Relationship,3D QSAR,3D-QSARs,Modeling, QSPR,Quantitative Structure Activity Relationship,Quantitative Structure-Activity Relationships,Relationship, Quantitative Structure-Activity,Relationships, Quantitative Structure-Activity,Structure-Activity Relationship, Quantitative,Structure-Activity Relationships, Quantitative

Related Publications

Trupti S Chitre, and Muthu K Kathiravan, and Kailash G Bothara, and Shashikant V Bhandari, and Rajeshwar R Jalnapurkar
January 2003, Nucleosides, nucleotides & nucleic acids,
Trupti S Chitre, and Muthu K Kathiravan, and Kailash G Bothara, and Shashikant V Bhandari, and Rajeshwar R Jalnapurkar
July 2019, Journal of biomolecular structure & dynamics,
Trupti S Chitre, and Muthu K Kathiravan, and Kailash G Bothara, and Shashikant V Bhandari, and Rajeshwar R Jalnapurkar
July 2009, Chemical & pharmaceutical bulletin,
Trupti S Chitre, and Muthu K Kathiravan, and Kailash G Bothara, and Shashikant V Bhandari, and Rajeshwar R Jalnapurkar
December 2013, Bioorganic & medicinal chemistry letters,
Trupti S Chitre, and Muthu K Kathiravan, and Kailash G Bothara, and Shashikant V Bhandari, and Rajeshwar R Jalnapurkar
January 2011, Journal of computer-aided molecular design,
Trupti S Chitre, and Muthu K Kathiravan, and Kailash G Bothara, and Shashikant V Bhandari, and Rajeshwar R Jalnapurkar
November 2010, European journal of medicinal chemistry,
Trupti S Chitre, and Muthu K Kathiravan, and Kailash G Bothara, and Shashikant V Bhandari, and Rajeshwar R Jalnapurkar
January 2005, Journal of chemical information and modeling,
Trupti S Chitre, and Muthu K Kathiravan, and Kailash G Bothara, and Shashikant V Bhandari, and Rajeshwar R Jalnapurkar
February 2009, Journal of molecular graphics & modelling,
Trupti S Chitre, and Muthu K Kathiravan, and Kailash G Bothara, and Shashikant V Bhandari, and Rajeshwar R Jalnapurkar
October 2011, Molecular informatics,
Trupti S Chitre, and Muthu K Kathiravan, and Kailash G Bothara, and Shashikant V Bhandari, and Rajeshwar R Jalnapurkar
September 2010, European journal of medicinal chemistry,
Copied contents to your clipboard!