Frontiers in Computational Chemistry presents contemporary research on molecular modeling techniques used in drug discovery and the drug development process: computer aided molecular design, drug discovery and development, lead generation, lead optimization, database management, computer and molecular graphics, and the development of new computational methods or efficient algorithms for the simulation of chemical phenomena including analyses of biological activity.
2. The role of ensemble conformational sampling using molecular docking & dynamics in drug discovery
3. Molecular dynamics applied to discover antiviral agents
4. Pharmacophore modeling approach in drug discovery against the tropical infectious disease malaria
5. Advances in computational network pharmacology for Traditional Chinese Medicine (TCM) research
6. Progress in electronic-structure based computational methods: from small molecules to large molecular systems of biological significance
The sixth volume of this series features these six different perspectives on the application of computational chemistry in rational drug design:
1. Computer-aided molecular design in computational chemistry2. The role of ensemble conformational sampling using molecular docking & dynamics in drug discovery
3. Molecular dynamics applied to discover antiviral agents
4. Pharmacophore modeling approach in drug discovery against the tropical infectious disease malaria
5. Advances in computational network pharmacology for Traditional Chinese Medicine (TCM) research
6. Progress in electronic-structure based computational methods: from small molecules to large molecular systems of biological significance
Table of Contents
- Preface
- List of Contributors
- Munazzah Yaqoob, Mahvish Abbasi, Hira Anwar, Javed Iqbal and Muhammad Adnan Iqbal
- Introduction
- Methods
- Markovian Chemicals “In Silico” Design (March Inside)
- Methodology
- Statistical Analysis Using Match-Inside
- Iso-Contribution Zone Analysis (Iza)
- Density Functional Theory (Dft)
- Geometry Optimization
- Spectroscopical Analysis
- 2.2.1. Uv- Vis Analysis
- Ft-Ir Analysis
- Nmr Analysis
- Non-Linear Optical (Nlo) Analysis
- Cosmo-Camd: Optimization Methods Based on Computer-Aided Molecular Design
- Using Cosmo-Rs
- Framework of Cosmo-Camd
- Ab Initio Method
- Born-Oppenheimer Approximation
- Recent Developments in the Ab Initio Method
- Ab Initio Crystal Field for Lanthanides
- Hartree-Fock Method
- Ab Initio Nonreactors
- Group Contribution Method
- Continuous Molecular Targeting (Comt-Camd)
- 2Nd Step: Mapping Step for Best-Performing Components Identification
- Conclusion
- Consent for Publication
- Conflict of Interest
- Acknowlegments
- References
- Patel Dhaval, Thakor Rajkishan, Mohd Athar and Prakash Jha
- Introduction
- Drug and Drug Designing
- Computer-Aided Drug Discovery (Cadd)
- Molecular Docking
- Sampling Methods for Docking
- Rigid Docking Approach
- Semi-Flexible Docking Approach
- Flexible Docking Approach
- Limitations of Static Docking
- Molecular Dynamics (Md) Simulations
- Molecular Dynamics Simulations and Conformational Space Search
- Molecular Dynamics Simulations for Enhanced Sampling
- Collective Variables Methods (Cv)
- Collective Variables-Free Methods
- Ensemble Docking
- Applications of Ensemble Docking in Cadd
- Hybrid Docking-Md Simulations Approach for Ensemble Docking
- Construction of Ensemble/Conformations by Using Md Simulations
- Post-Processing Docked Protein-Ligand Complexes Using Md Simulations
- Conclusion
- Consent for Publication
- Conflict of Interest
- Acknowledgement
- References
- Igor José Dos Santos Nascimento, Thiago Mendonça De Aquino and Edeildo Ferreira Da
- Silva-Júnior
- Introduction
- Viral Diseases and Their Threat to Society
- Molecular Dynamics Simulations in Drug Design: Fundamentals
- And Applications
- A Brief Theoretical Rationale
- Force Fields (Ff)
- Computational Resources
- Qm/Mm Methods in Md Simulations
- Mm-Pbsa/Gbsa Calculations
- Applications of Molecular Dynamics on Drug Design
- Molecular Dynamics Methods in Machine Learning
- Drug Discovery of Antivirals
- Influenza (Infv)
- Neuraminidase (Na) Inhibitors
- Rna-Dependent Rna Polymerase (Rdrp) Inhibitors from Infv
- Hemagglutinin (Ha) Inhibitors
- Zika Virus (Zikv)
- Ns2B-Ns3 Inhibitors from Zikv
- E Protein Inhibitors from Zikv
- Ns5 (Rdrp and Mtase) Inhibitors from Zikv
- Axl Receptor Inhibitors Used Against Zikv
- Dengue Virus (Denv)
- Ns2B-Ns3 Inhibitors from Denv
- E Protein Inhibitors from Denv
- Human Hexokinase Ii (Hkii) Inhibitors Used \Against Denv
- Chikungunya Virus (Chikv)
- Nsp2 and Nsp3 Inhibitors from Chikv
- Coronaviruses (Cov)
- 3Clpro Inhibitors from Cov
- Spike (S) Glycoprotein Inhibitors from Cov
- Rna-Dependent Rna Polymerase (Rdrp) Inhibitors from Cov
- Ebola Virus (Ebov)
- Glycoproteins (Gps) Inhibitors from Ebov
- Vps Proteins Inhibitors from Ebov
- Hiv
- Protease (Pr) Inhibitors from Hiv
- Reverse Transcriptase (Rt) Inhibitors from Hiv
- Integrase (In) Inhibitors from Hiv
- Capsid (Ca) Protein Inhibitors from Hiv
- Challenges, Limitations, and Opportunities
- Conclusion and Future Outlooks
- List of Abbreviations
- Consent for Publication
- Conflict of Interest
- Acknowledgments
- References
- Anu Manhas, Siddhi Kediya and Prakash C. Jha
- Introduction
- Pharmacophore Modeling
- Malaria
- Protease Enzymes
- Electron Transport Chain Enzymes
- Folate Pathway Enzymes
- Fatty Acid Biosynthesis Enzymes
- Glycolytic Pathway Enzymes
- Isoprenoid Biosynthesis Enzyme
- Miscellaneous Targets
- Phosphocholine Cytidylyltransferase Enzyme
- Apical Membrane Antigen 1 Protein
- Orotidine-5-Monophosphate Decarboxylase Enzyme
- Stage-V Mature Gametocytes
- S-Adenosylhomocysteine Hydrolase Enzyme
- Peptide Deformylase Enzyme
- Purine Nucleoside Phosphorylase
- Bromodomain-Contain Protein 1
- Superoxide Dismutase Protein
- Calcium-Dependent Protein Kinase
- Subtilisin-Like Protease 1
- Conclusion
- Consent for Publication
- Conflict of Interest
- Acknowledgements
- References
- Yu-Xi Huang, Shi-Jun Yue, Wen-Xiao Wang and Yu-Ping Tang
- Introduction
- Computational Network Pharmacology on Tcm
- Active Compounds Mining
- Compound-Target Interactions Prediction
- Network-Based Model
- Machine Learning-Based Method
- Bipartite Graph Learning Method
- Gene Ontology Enrichment and Pathway Analysis
- Network Construction and Topology Analysis
- Network Pharmacology for Mechanism Elucidation of Tcm
- Against Covid-19
- Concluding Remarks
- Consent for Publication
- Conflict of Interest
- Acknowledgement
- Abbreviations
- References
- Biological Significance
- Laimutis Bytautas, Douglas J. Klein, Demeter Tzeli, Maxime Ferrer, José Elguero, Ibon
- Alkorta and Josep M. Oliva-Enrich
- Introduction
- Accurate Ab Initio Methods
- General Formalism of Ci Wave Functions
- Practical Implementations of Ci-Based Approaches to Achieve High-Accuracy
- Ceeis-Fci Method
- Accurate Methods Based on the Renormalization Group Approach
- Highly Accurate Ab Initio Methods Based on Quantum Monte Carlo Methodology
- Fragment-Based Approaches for Applications of Biochemical or Pharmaceutical Interest
- Dft Advances and Multi-Scaling Methodologies Qm/Mm And
- Qm/Mm/Md
- Initiating Dft
- Dft Advances
- Multi-Scaling Methodologies Qm/Mm and Qm/Mm/Md
- Perboranation of Aza-Derivatives of Aromatic Five and Sixmembered
- Rings: a Computational Review
- Introduction
- Computational Methods
- Results and Discussion
- Metadynamics
- Vertical Singlet-Triplet Energy Gaps
- Atoms-In-Molecules (Aim) Analysis
- Conclusions
- Consent for Publication
- Conflict of Interest
- Acknowledgments
- References
- Subject Index
Contributors
- Zaheer-Ul-Haq Qasmi
- Angela K. Wilson
