Ivermectin as a potential drug for treatment of COVID-19: an in-sync review with clinical and computational attributes
Introduction COVID-19 cases are on surge; however, there is no efficient treatment or vaccine that can be used for its management. Numerous clinical trials are being reviewed for use of different drugs, biologics, and vaccines in COVID-19. A much empirical approach will be to repurpose existing drugs for which pharmacokinetic and safety data are available, because this will facilitate the process of drug development. The article discusses the evidence available for the use of Ivermectin, an anti-parasitic drug with antiviral properties, in COVID-19. Methods A rational review of the drugs was carried out utilizing their clinically significant attributes. A more thorough understanding was met by virtual embodiment of the drug structure and realizable viral targets using artificial intelligence (AI)-based and molecular dynamics (MD)-simulation-based study. Conclusion Certain studies have highlighted the significance of ivermectin in COVID-19; however, it requires evidences from more Randomised Controlled Trials (RCTs) and dose- response studies to support its use. In silico-based analysis of ivermectin’s molecular interaction specificity using AI and classical mechanics simulation-based methods indicates positive interaction of ivermectin with viral protein targets, which is leading for SARS-CoV 2 N-protein NTD (nucleocapsid protein N-terminal domain).
Molecular dynamics simulations-based study
Molecular dynamics simulations can be applied to analyze and conclude a framework of molecular level of microbial pathogenesis, but they are still open for improvements in algorithmic precision and methodologies that can effectively assess the bio-system of topics. In this study the molecular interactions of the ivermectin with some primary SARS-CoV-2 protein targets were simulated, namely with nucleocapsid protein N-terminal domain (6M3M), spike S1 RBD (PDB: 6M17), spike S2 fusion domain (6VXX), CL protease (6Y2F), nsp7, nsp8, nsp 12 and nsp13 (6XEZ) as distinct components of RDRP protein and lastly ORF6 protein (I-tasser model) . The proteins were optimized and simulated at physiological conditions (pH 7.4, Temp = 310 K, Press = 1.01325 Bar). All the simulations were performed on Desmond on Dell Precision tower 3630 with Quadro RTX 4000 GPU computing . The idea that can be obtained from the molecular interaction profile of ivermectin with selected viral proteins is that the ivermectin shows a distinction between the degree of interaction specificity among the various viral targets, but still exhibits comparable binding profile with some. The Cα-RMSD for the 100 ns MD simulation shows the variation in average conformation change influenced by ivermectin on the target proteins (Fig. The extremely smaller protein structures (nsp7, ORF6) encountered higher deviations in overall conformation and opposite implies for the bigger protein (S2 fusion domain). The residue interaction index and trajectory visualization add more to the information about the nature of interaction. It can be deduced that Ivermectin has efficient binding with: (1) spike S1-RBD, where it binds with Thr 500, Asn 501 and Tyr 505 residues ). These sites are critical to the SARS CoV-2 spike protein-mediated recognition from ACE-2 receptors in the host cellular system. Prominent H-bonding with Thr 500 and Asn 501 and water bridges were observed for more than 80% of simulation). (2) Spike S2-fusion domain, it binds to two specific regions of S2 fusion domain namely HR-1 sub-domain and fusion peptide domain. Major interactions were observed at the HR-1 domain, where it binds for up to 80% of simulation duration with Ser 968, Asn 969 and Gly 971 with H-bonds and water bridges. The fusion peptide region also exhibits weak affinity for ivermectin at Phe 797 and extremely weak interactions at Pro 792 residues with hydrophobic contact (Figs. c, b). The S2 fusion domain is necessary to build the fusion bridge between the viral and host membrane, where the fusion peptide is highly non-polar flexible region which facilitates the direct contact with the host membrane components. (3) N-protein, the poly-nucleotide (RNA) interacting cleft of nucleocapsid N-protein characterized by residues Arg 69, Tyr 124, Asn 127 and Glu 137 were found interacting with ivermectin with rich H-bond ratio, see Figs. and c. (4) Main protease, the main protease of the SARS-CoV 2 is another target which exhibits good affinity for ivermectin in inhibition site too at Glu 19, Thr 25, Glu 47, Leu 50 (Figs. d). The spatial localization of ivermectin molecule on the protein surface is illustrated with the active residue characterization in Fig. On the contrary, RDRP components (nsp7, nsp8, nsp12) with helicase (nsp13) and the ORF-6 fragment had weak specificity for ivermectin and could be characterized as weak targets for ivermectin as there was significantly low number of observed drug-protein collisions in simulation.
The broad specificity of the ivermectin to these proteins and other reported pharmacological targets can be attributed to its exposed hydroxyl and ester groups that can highly assist as H-bond donor.
Discussion From the evidence that is available and our artificial intelligence and molecular dynamics simulations based studies, ivermectin can be thought of as a potential drug for the treatment of COVID-19. Beneficial results have been observed with ivermectin in clinical studies. However, great diligence and regulatory review is required for testing of ivermectin in severe COVID-19 because of various reasons. As ivermectin targets the invertebrate’s glutamate gated chloride channels, it can also cross-target mammalian GABA-gated chloride channels in the CNS. In normal conditions, this is prevented by BBB; however, in individuals having hyper-inflammatory state, endothelial permeability at BBB may be enhanced, leading to drug leakage into the CNS and neurotoxicity. Furthermore, anti-retroviral drugs used against SARS-CoV-2 like lopinavir/ritonavir and darunavir/cobicstat potently inhibit cytochrome P450 3A4 (ivermectin’s main metabolic pathway) and if used concurrently with ivermectin can increase the systemic exposure to ivermectin. Ritonavir and cobicistat also inhibits P-glycoprotein efflux pump in BBB . Moreover, well-controlled dose response study needs to be considered for carrying out a clinical trial of ivermectin. Schmith et al. carried out simulations with the help of available population pharmacokinetic model for predicting total and unbound plasma concentration–time profiles of ivermectin (200 µg/kg, 60 mg, and 120 mg) after administration of single and repeat fasted dose. According to their results, the IC50 value of ivermectin as reported by Caly et al. was much higher than the maximum plasma concentration achieved after administration of the above mentioned three doses of ivermectin when administered fasted. Hence, the chances of success of a trial that use the approved ivermectin dose (200 µg/kg) are less. They further suggested evaluation of use of combined therapy in vitro and ivermectin’s inhaled treatment if feasible . Furthermore, Momekove et al. also reported that according to pharmacokinetic data that is available from clinically relevant and excessive dosing studies SARS-CoV 2 in vitro inhibitory concentrations (5 µM/L) are not probable to be achievable in humans. Next, ivermectin’s cellular uptake by endothelial cells is limited, because it is highly bound (93%) to plasma proteins. Furthermore, ivermectin’s total lung concentration reached only 100 ng/g (around 0.1 μM) in lung tissue in calves injected with 200 μg/kg, suggesting that accumulation of ivermectin would not be enough to accomplish the antiviral effect with conventional doses . Jermain et al. developed a minimal physiologically-based pharmacokinetic model to simulate ivermectin’s exposure to human lungs post oral doses (12, 30, and 120 mg). The simulated exposure of ivermectin to lungs achieved a concentration of 772 ng/mL, lower than the reported IC50 for ivermectin in vitro (1750 ng/mL) . In molecular dynamics simulation studies, the interaction of ivermectin with multiple (four) viral targets with relatable specificity and nature of interaction suggest, i.e., which majorly involves rich H-bonds, can show inhibitory actions resembling the estimated outcomes from the MD simulations prototyped in physiological conditions. The binding coordinates of ivermectin observed were at the prime regions crucial for the activity of particular SARS-CoV proteins. The least structural deviation with the nucleocapsid protein N terminal domain (1.89 Å ± 0.33) and high interaction ratio points toward the suggestion that ivermectin exhibits relatively high affinity for N protein. The nucleocapsid shuttling has been proposed to be facilitated via human Importin α/β into the nuclear matrix l]. The reported binding of ivermectin to importin α/β and notably low infection in ivermectin treated patients, might also possibly suggest that there is noticeable binding with the nucleocapsid cargo itself.
Conclusion Hence, keeping in view the available evidence from clinical studies ivermectin can be a potential drug as it reduced mortality and improved symptoms of patients with COVID-19. Moreover, ivermectin in combination with doxycycline seems effective. However, more RCTs and dose response studies are required to justify its use. The molecular specificity of ivermectin seems to be quite assorted as there can be seen good binding profiles with spike S1 and S2 domains in addition to CL protease inhibition site. The marginally efficient binding to the Nucleocapsid (N) protein might point towards the idea that nucleocapsid activity gets affected after its trans-nuclear import. Hence, ivermectin might be involved in the inhibition of N protein (has a role in nuclear import) and as the exact mechanism is not known, we are describing the best possible target estimation for ivermectin. The findings incline the possibility of ivermectin to be a multi-targeted drug (host and virus-targeted) especially in the case of COVID-19.
Future recommendations Ivermectin has been reported to show potent efficacy as an antiviral; however, its application is limited because of pharmacokinetic difficulties such as low solubility. These difficulties can be overcome by formulating liposomal ivermectin or other ivermectin formulations with improved properties. Furthermore, inhalation therapy of ivermectin can deliver high drug concentration to the lungs and airways to reduce the viral loads in such areas  or else it can be used in combination with other agents that differ in mechanism of action].
Credited to Springer link