Are AM1 ligand-protein binding enthalpies good enough for use in the rational design of new drugs?

نویسندگان

  • R. Villar
  • M. J. Gil
  • J. I. García
  • V. Martínez-Merino
چکیده

We have examined the performance of semiempirical quantum mechanical methods in solving the problem of accurately predicting protein-ligand binding energies and geometries. Firstly, AM1 and PM3 geometries and binding enthalpies between small molecules that simulate typical ligand-protein interactions were compared with high level quantum mechanical techniques that include electronic correlation (e.g., MP2 or B3LYP). Species studied include alkanes, aromatic systems, molecules including groups with hypervalent sulfur or with donor or acceptor hydrogen bonding capability, as well as ammonium or carboxylate ions. B3LYP/6-311+G(2d,p) binding energies correlated very well with the BSSE corrected MP2/6-31G(d) values. AM1 binding enthalpies also showed good correlation with MP2 values, and their systematic deviation is acceptable when enthalpies are used for the comparison of interaction energies between ligands and a target. PM3 otherwise gave erratic energy differences in comparison to the B3LYP or MP2 approaches. As one would expect, the geometries of the binding complexes showed the known limitations of the semiempirical and DFT methods. AM1 calculations were subsequently applied to a test set consisting of "real" protein active site-ligand complexes. Preliminary results indicate that AM1 could be a valuable tool for the design of new drugs using proteins as templates. This approach also has a reasonable computational cost. The ligand-protein X-ray structures were reasonably reproduced by AM1 calculations and the corresponding AM1 binding enthalpies are in agreement with the results from the "small molecules" test set.

برای دانلود متن کامل این مقاله و بیش از 32 میلیون مقاله دیگر ابتدا ثبت نام کنید

ثبت نام

اگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید

منابع مشابه

Dual-Target Anticancer Drug Candidates: Rational Design and Simulation Studies

This study aims to design some dual-target anticancer candidates, capable to act as an alkylating agent as well as a thymidylate synthase (TS) inhibitor. The designed scaffold is a combination of nucleobase, amino acid and aziridine structures. The candidates are docked into TS and three DNA double strand structures and evaluated based on their binding interaction energies and ligand efficienci...

متن کامل

Biological Applications of Isothermal Titration Calorimetry

     Most of the biological phenomena are influenced by intermolecular recognition and interaction. Thus, understanding the thermodynamics of biomacromolecule ligand interaction is a very interesting area in biochemistry and biotechnology. One of the most powerful techniques to obtain precise information about the energetics of (bio) molecules binding to other biological macromolecules is isoth...

متن کامل

Design of Novel Drugs (P3TZ, H2P3TZ, M2P3TZ, H4P3TZ and M4P3TZ) Based on Zonisamide for Autism Treatment by Binding to Potassium Voltage-gated Channel Subfamily D Member 2 (Kv4.2)

The present research article relates to the discovery of the novel drugs based on Zonisamide to treatment of autism disease. In first step, the electronic properties, reactivity and stability of the said compound are discussed. To attain these properties, the said molecular structure is optimized using B3LYP/6-311++G(d,p) level of theory at room temperature. The frontier molecular orbitals (FMO...

متن کامل

Professional rational drug and biological product design methods based on chemoinformatics as a novel science

Background:                             The use of new technologies in the field of drug discovery and development plays an important role in introducing new and effective drugs, optimizing the properties of existing drugs and, in general the development of various drug-dependent industries, as well as the general health of human, animal and plant communities. These methods provide new drugs at...

متن کامل

Ligand-based pharmacophore modeling to identify plant-derived acetylcholinesterase inhibitor natural compounds in Alzheimer’s disease

Background: Alzheimer’s disease (AD) is a neurodegenerative disease characterized by decreased cognitive function in patients due to forming Aβ peptides and neurofibrillary tangles (NFT) in the brain. Therefore, the need to develop new treatments can reduce this risk. Acetylcholinesterase is one of the targets used in the design of new drugs for the treatment of AD. The researchers obtain new i...

متن کامل

ذخیره در منابع من


  با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید

برای دانلود متن کامل این مقاله و بیش از 32 میلیون مقاله دیگر ابتدا ثبت نام کنید

ثبت نام

اگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید

عنوان ژورنال:
  • Journal of computational chemistry

دوره 26 13  شماره 

صفحات  -

تاریخ انتشار 2005