Iktedar Mahdi | Norwegian University of Science and Technology (original) (raw)

Papers by Iktedar Mahdi

Research paper thumbnail of Pyrrolopyrimidine based CSF1R inhibitors: Attempted departure from Flatland

European Journal of Medicinal Chemistry, Jan 31, 2024

Research paper thumbnail of Potential antiviral peptides against the nucleoprotein of SARS-CoV-2

Chemical Papers

Nucleoprotein is a conserved structural protein of SARS-CoV-2, which is involved in several funct... more Nucleoprotein is a conserved structural protein of SARS-CoV-2, which is involved in several functions, including replication, packaging, and transcription. In this research, 21 antiviral peptides that are known to have inhibitory function against nucleoprotein in several other viruses, were screened computationally against the nucleoprotein of SARS-CoV-2. The complexes of five best performing peptides (AVP1142, AVP1145, AVP1148, AVP1150, AVP1155) with nucleoprotein were selected for subsequent screening via 5 ns molecular dynamics (MD) simulation. Two peptides, namely AVP1145 and AVP1155, came out as promising candidates and hence were selected for 200 ns MD simulation for further validation, incorporating a DMPC-based membrane environment. In the long MD simulation, both AVP1155 and AVP1145 utilized multiple residuesmainly aromatic, acidic, and nonpolar residues-as interacting points to remain in contact with the nucleoprotein and formed predominantly hydrogen bonds along with hydrophobic and electrostatic interactions. However, AVP1155 proved to be superior to AVP1145 when its complex with nucleoprotein was analyzed in terms of root-mean-square deviation, root-meansquare fluctuation, radius of gyration, solvent accessible surface area and free energy landscape. In a nutshell, the findings of this research may guide future studies in the development of selective peptide inhibitors of SARS-CoV-2 nucleoprotein.

Research paper thumbnail of Identification of Plant-Based Drug-like Molecules as Potential Inhibitors against hACE2 and S-RBD of SARS-CoV-2 using Multi-step Molecular Docking and Dynamic Simulation Approach

There has been considerable interest to develop effective antiviral drugs with substantial effica... more There has been considerable interest to develop effective antiviral drugs with substantial efficacy to the varying lineage of SARS-CoV-2. The plant-based bioactive molecules (phytochemicals) have proven to exhibit promising therapeutic efficacy and immune-modulatory effect due to their inherent broad-spectrum biological properties such as antioxidant, antiviral, and anti-inflammatory with minimal or no side effects. The SARS-CoV-2 infection is initiated upon recognition and binding of the spike (S) Receptor-Binding Domain (RBD) to the host cell surface receptor, human Angiotensin-Converting Enzyme 2 (hACE2). Therefore, the underlying mechanism of interaction between host cell receptors and blocking the virus-cell interaction is considered to be a promising approach for the management and treatment of COVID-19 disease. In the present study, In-silico screening of phytochemicals against two targets of SARS-CoV-2 using a multi-step molecular docking approach was investigated. Based on ...

Research paper thumbnail of Identification of Plant-Based Drug-like Molecules as Potential Inhibitors against hACE2 and S-RBD of SARS-CoV-2 using Multi-step Molecular Docking and Dynamic Simulation Approach

There has been considerable interest to develop effective antiviral drugs with substantial effica... more There has been considerable interest to develop effective antiviral drugs with substantial efficacy to the varying lineage of SARS-CoV-2. The plant-based bioactive molecules (phytochemicals) have proven to exhibit promising therapeutic efficacy and immune-modulatory effect due to their inherent broad-spectrum biological properties such as antioxidant, antiviral, and anti-inflammatory with minimal or no side effects. The SARS-CoV-2 infection is initiated upon recognition and binding of the spike (S) Receptor-Binding Domain (RBD) to the host cell surface receptor, human Angiotensin-Converting Enzyme 2 (hACE2). Therefore, the underlying mechanism of interaction between host cell receptors and blocking the virus-cell interaction is considered to be a promising approach for the management and treatment of COVID-19 disease. In the present study, In-silico screening of phytochemicals against two targets of SARS-CoV-2 using a multi-step molecular docking approach was investigated. Based on ...

Research paper thumbnail of Pyrrolopyrimidine based CSF1R inhibitors: Attempted departure from Flatland

European Journal of Medicinal Chemistry, Jan 31, 2024

Research paper thumbnail of Potential antiviral peptides against the nucleoprotein of SARS-CoV-2

Chemical Papers

Nucleoprotein is a conserved structural protein of SARS-CoV-2, which is involved in several funct... more Nucleoprotein is a conserved structural protein of SARS-CoV-2, which is involved in several functions, including replication, packaging, and transcription. In this research, 21 antiviral peptides that are known to have inhibitory function against nucleoprotein in several other viruses, were screened computationally against the nucleoprotein of SARS-CoV-2. The complexes of five best performing peptides (AVP1142, AVP1145, AVP1148, AVP1150, AVP1155) with nucleoprotein were selected for subsequent screening via 5 ns molecular dynamics (MD) simulation. Two peptides, namely AVP1145 and AVP1155, came out as promising candidates and hence were selected for 200 ns MD simulation for further validation, incorporating a DMPC-based membrane environment. In the long MD simulation, both AVP1155 and AVP1145 utilized multiple residuesmainly aromatic, acidic, and nonpolar residues-as interacting points to remain in contact with the nucleoprotein and formed predominantly hydrogen bonds along with hydrophobic and electrostatic interactions. However, AVP1155 proved to be superior to AVP1145 when its complex with nucleoprotein was analyzed in terms of root-mean-square deviation, root-meansquare fluctuation, radius of gyration, solvent accessible surface area and free energy landscape. In a nutshell, the findings of this research may guide future studies in the development of selective peptide inhibitors of SARS-CoV-2 nucleoprotein.

Research paper thumbnail of Identification of Plant-Based Drug-like Molecules as Potential Inhibitors against hACE2 and S-RBD of SARS-CoV-2 using Multi-step Molecular Docking and Dynamic Simulation Approach

There has been considerable interest to develop effective antiviral drugs with substantial effica... more There has been considerable interest to develop effective antiviral drugs with substantial efficacy to the varying lineage of SARS-CoV-2. The plant-based bioactive molecules (phytochemicals) have proven to exhibit promising therapeutic efficacy and immune-modulatory effect due to their inherent broad-spectrum biological properties such as antioxidant, antiviral, and anti-inflammatory with minimal or no side effects. The SARS-CoV-2 infection is initiated upon recognition and binding of the spike (S) Receptor-Binding Domain (RBD) to the host cell surface receptor, human Angiotensin-Converting Enzyme 2 (hACE2). Therefore, the underlying mechanism of interaction between host cell receptors and blocking the virus-cell interaction is considered to be a promising approach for the management and treatment of COVID-19 disease. In the present study, In-silico screening of phytochemicals against two targets of SARS-CoV-2 using a multi-step molecular docking approach was investigated. Based on ...

Research paper thumbnail of Identification of Plant-Based Drug-like Molecules as Potential Inhibitors against hACE2 and S-RBD of SARS-CoV-2 using Multi-step Molecular Docking and Dynamic Simulation Approach

There has been considerable interest to develop effective antiviral drugs with substantial effica... more There has been considerable interest to develop effective antiviral drugs with substantial efficacy to the varying lineage of SARS-CoV-2. The plant-based bioactive molecules (phytochemicals) have proven to exhibit promising therapeutic efficacy and immune-modulatory effect due to their inherent broad-spectrum biological properties such as antioxidant, antiviral, and anti-inflammatory with minimal or no side effects. The SARS-CoV-2 infection is initiated upon recognition and binding of the spike (S) Receptor-Binding Domain (RBD) to the host cell surface receptor, human Angiotensin-Converting Enzyme 2 (hACE2). Therefore, the underlying mechanism of interaction between host cell receptors and blocking the virus-cell interaction is considered to be a promising approach for the management and treatment of COVID-19 disease. In the present study, In-silico screening of phytochemicals against two targets of SARS-CoV-2 using a multi-step molecular docking approach was investigated. Based on ...