1. Preparation and study of protein :
Methods developed to facilitate and speedup the drug designing process are Rational Drug Design (RDD). These processes are used in biopharmaceutical industry to discover and develop new drugs. RDD uses a variety of computational methods to identify novel compounds. One of those methods is docking of drug molecules with receptors. The site of drug action, which is ultimately responsible for the pharmaceutical affect, is a receptor. SARS – Protease [Fig. 1 ] In order to find novel inhibitors, we computationally screened a compound library of over 687 million compounds for binding at the recently solved crystal structure of the main protease of SARS-CoV-2. A screening of such a vast chemical space for SARS-CoV-2 protease inhibitors has not been reported before.
2. Collecting molecular structure
The collection of Ganciclovir and Salbutamol and SARS - Protease was identified via docking and their relative stabilities were evaluated using molecular dynamics and their binding affinities, using free energy simulations. There are various databases available, which offer information on small ligand molecules such as CSD (Cambridge Structural Database), ACD (Available Chemical Directory), MDDR (MDL Drug Data Report) and NCI (National Cancer Institute Database). Salbutamol is a short-acting, selective beta2-adrenergic receptor agonist used in the treatment of asthma and COPD. It is 29 times more selective for beta2 receptors than beta1 receptors giving it higher specificity for pulmonary beta receptors versus beta1-adrenergic receptors located in the heart. Salbutamol is formulated as a racemic mixture of the R- and S-isomers. The R-isomer has 150 times greater affinity for the beta2-receptor than the S-isomer and the S-isomer has been associated with toxicity. This lead to the development of levalbuterol, the single R-isomer of salbutamol. However, the high cost of levalbuterol compared to salbutamol has deterred wide-spread use of this enantiomerically pure version of the drug. Salbutamol is generally used for acute episodes of bronchospasm caused by bronchial asthma, chronic bronchitis and other chronic bronchopulmonary disorders such as chronic obstructive pulmonary disorder (COPD). It is also used prophylactically for exercise-induced asthma.
3. Selection of ligand:
In normal practice the conventional drugs like Ganciclovir , Salbutamol are used inhibit viral infection, which are specific to PROTEASE enzyme . Keeping rational drug designing approach in mind, We made an effort to design modified drugs for SARS, using conventional drugs like Ganciclovir and Salbutamol by docking against Protease receptor.
4. Selection of docking site:
The C30 Endopeptidase in various coronaviruses, often referred to as the 3C-like proteinase (3CLpro), is a family of enzymes found in the Coronavirus polyprotein. It cleaves the polyprotein at two self-cleavage sites. It is a cysteine protease under clan PA, MEROPS classification C30. In coronaviruses, it is nonstructural protein number 5 (nsp5). The Enzyme Commission refers to this family as SARS coronavirus main protease.
5. Molecular docking:
Docking is the process of fitting together of two molecules in 3-dimensional space. Docking allows the scientist to virtually screen a database of compounds and predict the strongest binders based on various scoring functions. It explores ways in which two molecules, such as drugs and an enzyme SARS - Protease fit together and dock to each other well, like pieces of a three-dimensional jigsaw puzzle. The molecules binding to a receptor, inhibit its function, and thus act as drug.
After shape screening, two docking protocols were applied followed by the determination of pharmacokinetically relevant molecular descriptors to narrow down the initial hits. Next, molecular dynamics simulations were conducted to validate the stability of docked binding modes and comprehensively quantify ligand binding energies.
6. Technical aspects:
The simplest calculations can be performed by hand, but inevitably computers are required to perform molecular modeling of any reasonably sized system. The common feature of molecular modeling methods is the atomistic level description of the molecular systems.
The interactions between neighboring atoms are described by spring-like interactions (representing chemical bonds) and Van der Waals forces. The Lennard-Jones potential is commonly used to describe the latter. The electrostatic interactions are computed based on Coulomb's law. Atoms are assigned coordinates in Cartesian space or in internal coordinates, and can also be assigned velocities in dynamical simulations. The atomic velocities are related to the temperature of the system, a macroscopic quantity.
7. TOOLS:
Tools like CHIMERA and RASMOL and DISCOVERY STUDIO are very important for drug designing and simulation for possible targets and also to see the surface temperature gradient also the RASMOL which is used to make 3D mol modeling study which are explained below in two real time figures from RASMOL both in atom form and temperature map.
PubMed:
PubMed developed by the National Center for Biotechnology Information (NCBI) at the National Library of Medicine (NLM
PDB:
The structure of Angiotensin converting enzyme 2 (ACE-2) was retrieved from Protein data bank (PDB).
RASMOL:
The retrieved structure of COVID 2 Protease was analyzed by using RasMol.
Discovery Studio:
The structures of conventional drugs like Lopinavir and Ritonavir were retrieved from PDB and the structural analogs of these drug molecules were created by using Discovery Studio.
Chimera molecular docking:
Chimera software works on preparation of ligand and protein binding structures and also analyze tensions and hydrogen bonds , hydrophobic interactions , van der waal interaction , it also have tool auto dock vina for auto docking function .