13 Molecular mechanics approaches for rational drug design: forcefields and solvation models
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Boris D. Bekono
Abstract
The use of molecular mechanics (MM) in understanding the energy and target of a drug, its structures, and properties has increased recently. This is achieved by the formulation of a simple MM energy equation, which represents the sum of the different energy interactions, often referred to as “forcefields” (FFs). The concept of FFs is now widely used as one of the fundamental tools for the in silico prediction of drugtarget interactions. To generate more accurate predictions in the in silico drug discovery projects, the solvent effects are often taken into account. This review seeks to present an introductory guide for the reader on the fundamentals of MM with special emphasis on the role of FFs and the solvation models.
Abstract
The use of molecular mechanics (MM) in understanding the energy and target of a drug, its structures, and properties has increased recently. This is achieved by the formulation of a simple MM energy equation, which represents the sum of the different energy interactions, often referred to as “forcefields” (FFs). The concept of FFs is now widely used as one of the fundamental tools for the in silico prediction of drugtarget interactions. To generate more accurate predictions in the in silico drug discovery projects, the solvent effects are often taken into account. This review seeks to present an introductory guide for the reader on the fundamentals of MM with special emphasis on the role of FFs and the solvation models.
Kapitel in diesem Buch
- Frontmatter I
- Preface of the Book of Proceedings of the Virtual Conference on Computational Science (VCCS-2019) V
- Contents VII
- Corresponding authors XIII
- 1 Structural and spectroscopic properties of 3-halogenobenzaldehydes: DFT and TDDFT simulations 1
- 2 Atomistic insight into the significantly enhanced photovoltaic cells of monolayer GaTe2 via two-dimensional van der Waals heterostructures engineering 15
- 3 Fluorescent styryl chromophores with rigid (pyrazole) donor and rigid (benzothiophenedioxide) acceptor – complete density functional theory (DFT), TDDFT and nonlinear optical study 33
- 4 Comparative studies of excited state intramolecular proton transfer (ESIPT) and azohydrazone tautomerism in naphthalene-based fluorescent acid azo dyes by computational study 61
- 5 Theoretical examination of efficiency of anthocyanidins as sensitizers in dye-sensitized solar cells 83
- 6 Selection of oxypeucedanin as a potential antagonist from molecular docking analysis of HSP90 103
- 7 Mechanistic insight into the interactions between thiazolidinedione derivatives and PTP-1B combining 3D QSAR andmolecular docking in the treatment of type 2 diabetes 113
- 8 Review of research of nanocomposites based on graphene quantum dots 135
- 9 A computational study of the SNAr reaction of 2-ethoxy-3,5-dinitropyridine and 2-methoxy-3, 5-dinitropyridine with piperidine 161
- 10 Synthesis, characterization and computational studies of 1,3-bis[(E)-furan-2-yl)methylene]urea and 1,3-bis[(E)-furan-2-yl)methylene]thiourea 177
- 11 Computational studies of biologically active alkaloids of plant origin: an overview 187
- 12 Investigating the biological actions of some Schiff bases using density functional theory study 219
- 13 Molecular mechanics approaches for rational drug design: forcefields and solvation models 233
- Index 255
Kapitel in diesem Buch
- Frontmatter I
- Preface of the Book of Proceedings of the Virtual Conference on Computational Science (VCCS-2019) V
- Contents VII
- Corresponding authors XIII
- 1 Structural and spectroscopic properties of 3-halogenobenzaldehydes: DFT and TDDFT simulations 1
- 2 Atomistic insight into the significantly enhanced photovoltaic cells of monolayer GaTe2 via two-dimensional van der Waals heterostructures engineering 15
- 3 Fluorescent styryl chromophores with rigid (pyrazole) donor and rigid (benzothiophenedioxide) acceptor – complete density functional theory (DFT), TDDFT and nonlinear optical study 33
- 4 Comparative studies of excited state intramolecular proton transfer (ESIPT) and azohydrazone tautomerism in naphthalene-based fluorescent acid azo dyes by computational study 61
- 5 Theoretical examination of efficiency of anthocyanidins as sensitizers in dye-sensitized solar cells 83
- 6 Selection of oxypeucedanin as a potential antagonist from molecular docking analysis of HSP90 103
- 7 Mechanistic insight into the interactions between thiazolidinedione derivatives and PTP-1B combining 3D QSAR andmolecular docking in the treatment of type 2 diabetes 113
- 8 Review of research of nanocomposites based on graphene quantum dots 135
- 9 A computational study of the SNAr reaction of 2-ethoxy-3,5-dinitropyridine and 2-methoxy-3, 5-dinitropyridine with piperidine 161
- 10 Synthesis, characterization and computational studies of 1,3-bis[(E)-furan-2-yl)methylene]urea and 1,3-bis[(E)-furan-2-yl)methylene]thiourea 177
- 11 Computational studies of biologically active alkaloids of plant origin: an overview 187
- 12 Investigating the biological actions of some Schiff bases using density functional theory study 219
- 13 Molecular mechanics approaches for rational drug design: forcefields and solvation models 233
- Index 255
