The role of quantum mechanics in structure-based drug design

Drug Design ◽  
2010 ◽  
pp. 120-136
Author(s):  
Kenneth M. Jr. Merz
2007 ◽  
Vol 12 (17-18) ◽  
pp. 725-731 ◽  
Author(s):  
Kaushik Raha ◽  
Martin B. Peters ◽  
Bing Wang ◽  
Ning Yu ◽  
Andrew M. Wollacott ◽  
...  

2021 ◽  
Vol 2 ◽  
pp. 100026
Author(s):  
Nilesh Gajanan Bajad ◽  
Swetha Rayala ◽  
Gopichand Gutti ◽  
Anjali Sharma ◽  
Meenakshi Singh ◽  
...  

Author(s):  
Prajakta U. Kulkarni ◽  
Harshil Shah ◽  
Vivek K. Vyas

: Quantum mechanics (QM) is physics based theory which explains the physical properties of nature at the level of atoms and sub-atoms. Molecular mechanics (MM) construct molecular systems through the use of classical mechanics. So, hybrid quantum mechanics and molecular mechanics (QM/MM) when combined together can act as computer-based methods which can be used to calculate structure and property data of molecular structures. Hybrid QM/MM combines the strengths of QM with accuracy and MM with speed. QM/MM simulation can also be applied for the study of chemical process in solutions as well as in the proteins, and has a great scope in structure-based drug design (CADD) and discovery. Hybrid QM/MM also applied to HTS, to derive QSAR models and due to availability of many protein crystal structures; it has a great role in computational chemistry, especially in structure- and fragment-based drug design. Fused QM/MM simulations have been developed as a widespread method to explore chemical reactions in condensed phases. In QM/MM simulations, the quantum chemistry theory is used to treat the space in which the chemical reactions occur; however the rest is defined through molecular mechanics force field (MMFF). In this review, we have extensively reviewed recent literature pertaining to the use and applications of hybrid QM/MM simulations for ligand and structure-based computational methods for the design and discovery of therapeutic agents.


ACS Omega ◽  
2019 ◽  
Vol 4 (4) ◽  
pp. 6703-6708
Author(s):  
Scott D. Bembenek ◽  
Hariharan Venkatesan ◽  
Hillary M. Peltier ◽  
Mark D. Rosen ◽  
Terrance D. Barrett ◽  
...  

2018 ◽  
Vol 19 (7) ◽  
pp. 2105 ◽  
Author(s):  
Xiaojing Yuan ◽  
Yechun Xu

G protein-coupled receptors represent the largest family of human membrane proteins and are modulated by a variety of drugs and endogenous ligands. Molecular modeling techniques, especially enhanced sampling methods, have provided significant insight into the mechanism of GPCR–ligand recognition. Notably, the crucial role of the membrane in the ligand-receptor association process has earned much attention. Additionally, docking, together with more accurate free energy calculation methods, is playing an important role in the design of novel compounds targeting GPCRs. Here, we summarize the recent progress in the computational studies focusing on the above issues. In the future, with continuous improvement in both computational hardware and algorithms, molecular modeling would serve as an indispensable tool in a wider scope of the research concerning GPCR–ligand recognition as well as drug design targeting GPCRs.


Molecules ◽  
2021 ◽  
Vol 26 (7) ◽  
pp. 1917
Author(s):  
Babiker M. EH-Haj

Metabolic reactions that occur at alkylamino moieties may provide insight into the roles of these moieties when they are parts of drug molecules that act at different receptors. N-dealkylation of N,N-dialkylamino moieties has been associated with retaining, attenuation or loss of pharmacologic activities of metabolites compared to their parent drugs. Further, N-dealkylation has resulted in clinically used drugs, activation of prodrugs, change of receptor selectivity, and providing potential for developing fully-fledged drugs. While both secondary and tertiary alkylamino moieties (open chain aliphatic or heterocyclic) are metabolized by CYP450 isozymes oxidative N-dealkylation, only tertiary alkylamino moieties are subject to metabolic N-oxidation by Flavin-containing monooxygenase (FMO) to give N-oxide products. In this review, two aspects will be examined after surveying the metabolism of representative alkylamino-moieties-containing drugs that act at various receptors (i) the pharmacologic activities and relevant physicochemical properties (basicity and polarity) of the metabolites with respect to their parent drugs and (ii) the role of alkylamino moieties on the molecular docking of drugs in receptors. Such information is illuminative in structure-based drug design considering that fully-fledged metabolite drugs and metabolite prodrugs have been, respectively, developed from N-desalkyl and N-oxide metabolites.


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